6KAC

Cryo-EM structure of the C2S2-type PSII-LHCII supercomplex from Chlamydomonas reihardtii


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structural insight into light harvesting for photosystem II in green algae.

Sheng, X.Watanabe, A.Li, A.Kim, E.Song, C.Murata, K.Song, D.Minagawa, J.Liu, Z.

(2019) Nat Plants 5: 1320-1330

  • DOI: https://doi.org/10.1038/s41477-019-0543-4
  • Primary Citation of Related Structures:  
    6KAC, 6KAD

  • PubMed Abstract: 

    Green algae and plants rely on light-harvesting complex II (LHCII) to collect photon energy for oxygenic photosynthesis. In Chlamydomonas reinhardtii, LHCII molecules associate with photosystem II (PSII) to form various supercomplexes, including the C 2 S 2 M 2 L 2 type, which is the largest PSII-LHCII supercomplex in algae and plants that is presently known. Here, we report high-resolution cryo-electron microscopy (cryo-EM) maps and structural models of the C 2 S 2 M 2 L 2 and C 2 S 2 supercomplexes from C. reinhardtii. The C 2 S 2 supercomplex contains an LhcbM1-LhcbM2/7-LhcbM3 heterotrimer in the strongly associated LHCII, and the LhcbM1 subunit assembles with CP43 through two interfacial galactolipid molecules. The loosely and moderately associated LHCII trimers interact closely with the minor antenna complex CP29 to form an intricate subcomplex bound to CP47 in the C 2 S 2 M 2 L 2 supercomplex. A notable direct pathway is established for energy transfer from the loosely associated LHCII to the PSII reaction centre, as well as several indirect routes. Structure-based computational analysis on the excitation energy transfer within the two supercomplexes provides detailed mechanistic insights into the light-harvesting process in green algae.


  • Organizational Affiliation

    National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II protein D1A,
CA [auth a]
352Chlamydomonas reinhardtiiMutation(s): 0 
EC: 1.10.3.9
Membrane Entity: Yes 
UniProt
Find proteins for P07753 (Chlamydomonas reinhardtii)
Explore P07753 
Go to UniProtKB:  P07753
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP07753
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II CP47 reaction center proteinB,
DA [auth b]
508Chlamydomonas reinhardtiiMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P37255 (Chlamydomonas reinhardtii)
Explore P37255 
Go to UniProtKB:  P37255
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP37255
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein Ycf12C [auth V],
EA [auth v]
33Chlamydomonas reinhardtiiMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P50370 (Chlamydomonas reinhardtii)
Explore P50370 
Go to UniProtKB:  P50370
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP50370
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II CP43 reaction center proteinD [auth C],
FA [auth c]
461Chlamydomonas reinhardtiiMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P10898 (Chlamydomonas reinhardtii)
Explore P10898 
Go to UniProtKB:  P10898
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP10898
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II D2 proteinE [auth D],
GA [auth d]
352Chlamydomonas reinhardtiiMutation(s): 0 
EC: 1.10.3.9
Membrane Entity: Yes 
UniProt
Find proteins for P06007 (Chlamydomonas reinhardtii)
Explore P06007 
Go to UniProtKB:  P06007
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP06007
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b559 subunit alphaF [auth E],
HA [auth e]
82Chlamydomonas reinhardtiiMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P48268 (Chlamydomonas reinhardtii)
Explore P48268 
Go to UniProtKB:  P48268
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP48268
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b559 subunit betaG [auth F],
IA [auth f]
44Chlamydomonas reinhardtiiMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q08363 (Chlamydomonas reinhardtii)
Explore Q08363 
Go to UniProtKB:  Q08363
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ08363
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein HH,
JA [auth h]
88Chlamydomonas reinhardtiiMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P22666 (Chlamydomonas reinhardtii)
Explore P22666 
Go to UniProtKB:  P22666
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP22666
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein II,
KA [auth i]
37Chlamydomonas reinhardtiiMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P59763 (Chlamydomonas reinhardtii)
Explore P59763 
Go to UniProtKB:  P59763
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP59763
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein JJ,
LA [auth j]
42Chlamydomonas reinhardtiiMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for O19930 (Chlamydomonas reinhardtii)
Explore O19930 
Go to UniProtKB:  O19930
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO19930
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein KK,
MA [auth k]
46Chlamydomonas reinhardtiiMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P18263 (Chlamydomonas reinhardtii)
Explore P18263 
Go to UniProtKB:  P18263
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP18263
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein LL,
NA [auth l]
38Chlamydomonas reinhardtiiMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P32974 (Chlamydomonas reinhardtii)
Explore P32974 
Go to UniProtKB:  P32974
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP32974
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein MM,
OA [auth m]
34Chlamydomonas reinhardtiiMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P92277 (Chlamydomonas reinhardtii)
Explore P92277 
Go to UniProtKB:  P92277
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP92277
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Oxygen-evolving enhancer protein 1, chloroplasticN [auth O],
PA [auth o]
291Chlamydomonas reinhardtiiMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P12853 (Chlamydomonas reinhardtii)
Explore P12853 
Go to UniProtKB:  P12853
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP12853
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Oxygen-evolving enhancer protein 2, chloroplasticO [auth P],
QA [auth p]
245Chlamydomonas reinhardtiiMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P11471 (Chlamydomonas reinhardtii)
Explore P11471 
Go to UniProtKB:  P11471
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP11471
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Oxygen-evolving enhancer protein 3, chloroplasticP [auth Q],
RA [auth q]
199Chlamydomonas reinhardtiiMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P12852 (Chlamydomonas reinhardtii)
Explore P12852 
Go to UniProtKB:  P12852
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP12852
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein TQ [auth T],
SA [auth t]
31Chlamydomonas reinhardtiiMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P37256 (Chlamydomonas reinhardtii)
Explore P37256 
Go to UniProtKB:  P37256
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP37256
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center W protein, chloroplasticR [auth W],
TA [auth w]
115Chlamydomonas reinhardtiiMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q9SPI9 (Chlamydomonas reinhardtii)
Explore Q9SPI9 
Go to UniProtKB:  Q9SPI9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9SPI9
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
4.1 kDa photosystem II subunitS [auth X],
UA [auth x]
101Chlamydomonas reinhardtiiMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A8I846 (Chlamydomonas reinhardtii)
Explore A8I846 
Go to UniProtKB:  A8I846
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA8I846
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein ZT [auth Z],
VA [auth z]
62Chlamydomonas reinhardtiiMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P92276 (Chlamydomonas reinhardtii)
Explore P92276 
Go to UniProtKB:  P92276
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP92276
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein, chloroplasticU [auth N],
WA [auth n]
257Chlamydomonas reinhardtiiMutation(s): 0 
UniProt
Find proteins for Q93WL4 (Chlamydomonas reinhardtii)
Explore Q93WL4 
Go to UniProtKB:  Q93WL4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ93WL4
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein, chloroplasticV [auth G],
XA [auth g]
249Chlamydomonas reinhardtiiMutation(s): 0 
UniProt
Find proteins for Q93WE0 (Chlamydomonas reinhardtii)
Explore Q93WE0 
Go to UniProtKB:  Q93WE0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ93WE0
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein CP29W [auth R],
YA [auth r]
280Chlamydomonas reinhardtiiMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q93WD2 (Chlamydomonas reinhardtii)
Explore Q93WD2 
Go to UniProtKB:  Q93WD2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ93WD2
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein, chloroplasticX [auth S],
ZA [auth s]
289Chlamydomonas reinhardtiiMutation(s): 0 
UniProt
Find proteins for Q9FEK6 (Chlamydomonas reinhardtii)
Explore Q9FEK6 
Go to UniProtKB:  Q9FEK6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9FEK6
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein, chloroplasticAB [auth y],
Y
256Chlamydomonas reinhardtiiMutation(s): 0 
UniProt
Find proteins for Q93VE0 (Chlamydomonas reinhardtii)
Explore Q93VE0 
Go to UniProtKB:  Q93VE0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ93VE0
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
Predicted proteinBB [auth u],
Z [auth U]
178Chlamydomonas reinhardtiiMutation(s): 0 
UniProt
Find proteins for A8I5A0 (Chlamydomonas reinhardtii)
Explore A8I5A0 
Go to UniProtKB:  A8I5A0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA8I5A0
Sequence Annotations
Expand
  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
10 kDa photosystem II polypeptide PsbR (potential)AA [auth 1],
CB [auth 0]
25Chlamydomonas reinhardtiiMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
Unindentified Stromal Protein (USP)BA [auth 4],
DB [auth 3]
25Chlamydomonas reinhardtiiMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 18 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DGD
Query on DGD

Download Ideal Coordinates CCD File 
DD [auth C]
ED [auth C]
FD [auth C]
GJ [auth c]
HD [auth C]
DD [auth C],
ED [auth C],
FD [auth C],
GJ [auth c],
HD [auth C],
HJ [auth c],
ID [auth C],
IJ [auth c],
KJ [auth c],
LJ [auth c]
DIGALACTOSYL DIACYL GLYCEROL (DGDG)
C51 H96 O15
LDQFLSUQYHBXSX-HXXRYREZSA-N
CHL (Subject of Investigation/LOI)
Query on CHL

Download Ideal Coordinates CCD File 
AF [auth G]
AG [auth S]
AL [auth g]
BG [auth S]
BL [auth g]
AF [auth G],
AG [auth S],
AL [auth g],
BG [auth S],
BL [auth g],
CG [auth S],
CK [auth n],
CL [auth g],
DE [auth N],
DL [auth g],
DM [auth s],
EE [auth N],
EM [auth s],
FE [auth N],
FM [auth s],
GE [auth N],
GK [auth n],
HE [auth N],
HK [auth n],
IK [auth n],
JK [auth n],
KK [auth n],
NG [auth Y],
OF [auth R],
PF [auth R],
QF [auth R],
QM [auth y],
RG [auth Y],
RL [auth r],
SE [auth G],
SG [auth Y],
SL [auth r],
TG [auth Y],
TL [auth r],
UG [auth Y],
UM [auth y],
VF [auth S],
VG [auth Y],
VK [auth g],
VM [auth y],
WE [auth G],
WM [auth y],
XE [auth G],
XM [auth y],
YE [auth G],
YL [auth s],
YM [auth y],
ZD [auth N],
ZE [auth G],
ZK [auth g]
CHLOROPHYLL B
C55 H70 Mg N4 O6
MWVCRINOIIOUAU-UYSPMESUSA-M
CLA (Subject of Investigation/LOI)
Query on CLA

Download Ideal Coordinates CCD File 
AC [auth B]
AE [auth N]
AH [auth Y]
AI [auth b]
AJ [auth c]
AC [auth B],
AE [auth N],
AH [auth Y],
AI [auth b],
AJ [auth c],
AM [auth s],
AN [auth y],
BC [auth B],
BE [auth N],
BF [auth G],
BI [auth b],
BJ [auth c],
BM [auth s],
BN [auth y],
CC [auth B],
CE [auth N],
CF [auth G],
CI [auth b],
CM [auth s],
CN [auth y],
DC [auth B],
DF [auth G],
DG [auth S],
DI [auth b],
DK [auth n],
DN [auth y],
EC [auth B],
EF [auth G],
EG [auth S],
EI [auth b],
EK [auth n],
EL [auth g],
FC [auth B],
FF [auth G],
FG [auth S],
FI [auth b],
FK [auth n],
FL [auth g],
GC [auth B],
GG [auth S],
GI [auth b],
GL [auth g],
GM [auth s],
HG [auth S],
HI [auth b],
HL [auth g],
HM [auth s],
IB [auth A],
IE [auth N],
IG [auth S],
II [auth b],
IL [auth g],
IM [auth s],
JB [auth A],
JE [auth N],
JI [auth b],
JM [auth s],
KB [auth A],
KE [auth N],
KM [auth s],
LD [auth D],
LE [auth N],
LF [auth R],
LH [auth a],
LK [auth n],
LM [auth s],
MC [auth C],
MD [auth D],
ME [auth N],
MF [auth R],
MH [auth a],
MK [auth n],
NB [auth A],
NC [auth C],
NF [auth R],
NH [auth a],
NK [auth n],
OC [auth C],
OG [auth Y],
OJ [auth d],
OK [auth n],
OL [auth r],
PC [auth C],
PG [auth Y],
PI [auth c],
PJ [auth d],
PK [auth n],
PL [auth r],
QC [auth C],
QG [auth Y],
QH [auth a],
QI [auth c],
QL [auth r],
RB [auth B],
RC [auth C],
RF [auth R],
RI [auth c],
RM [auth y],
SB [auth B],
SC [auth C],
SF [auth R],
SI [auth c],
SM [auth y],
TB [auth B],
TC [auth C],
TE [auth G],
TI [auth c],
TM [auth y],
UB [auth B],
UC [auth C],
UE [auth G],
UH [auth b],
UI [auth c],
UL [auth r],
VB [auth B],
VC [auth C],
VE [auth G],
VH [auth b],
VI [auth c],
VL [auth r],
WB [auth B],
WC [auth C],
WF [auth S],
WG [auth Y],
WH [auth b],
WI [auth c],
WK [auth g],
XB [auth B],
XC [auth C],
XF [auth S],
XG [auth Y],
XH [auth b],
XI [auth c],
XK [auth g],
YB [auth B],
YC [auth C],
YF [auth S],
YG [auth Y],
YH [auth b],
YI [auth c],
YK [auth g],
ZB [auth B],
ZF [auth S],
ZG [auth Y],
ZH [auth b],
ZI [auth c],
ZL [auth s],
ZM [auth y]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
PHO
Query on PHO

Download Ideal Coordinates CCD File 
LB [auth A],
MB [auth A],
OH [auth a],
PH [auth a]
PHEOPHYTIN A
C55 H74 N4 O5
CQIKWXUXPNUNDV-RCBXBCQGSA-N
SQD
Query on SQD

Download Ideal Coordinates CCD File 
KC [auth B],
NI [auth b],
PB [auth A],
SH [auth a]
1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL
C41 H78 O12 S
RVUUQPKXGDTQPG-JUDHQOGESA-N
LMG
Query on LMG

Download Ideal Coordinates CCD File 
GD [auth C]
JJ [auth c]
LC [auth B]
OI [auth b]
QB [auth A]
GD [auth C],
JJ [auth c],
LC [auth B],
OI [auth b],
QB [auth A],
SD [auth D],
TH [auth a],
VD [auth H],
VJ [auth d],
YJ [auth h]
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
PL9
Query on PL9

Download Ideal Coordinates CCD File 
OD [auth D],
RJ [auth d]
2,3-DIMETHYL-5-(3,7,11,15,19,23,27,31,35-NONAMETHYL-2,6,10,14,18,22,26,30,34-HEXATRIACONTANONAENYL-2,5-CYCLOHEXADIENE-1,4-DIONE-2,3-DIMETHYL-5-SOLANESYL-1,4-BENZOQUINONE
C53 H80 O2
FKUYMLZIRPABFK-UHFFFAOYSA-N
LHG
Query on LHG

Download Ideal Coordinates CCD File 
FH [auth Y]
IN [auth y]
JD [auth C]
KF [auth G]
MG [auth S]
FH [auth Y],
IN [auth y],
JD [auth C],
KF [auth G],
MG [auth S],
MJ [auth c],
NL [auth g],
PD [auth D],
PM [auth s],
QD [auth D],
RD [auth D],
RE [auth N],
SJ [auth d],
TJ [auth d],
UJ [auth d],
UK [auth n],
WD [auth L],
ZJ [auth l]
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
HEM
Query on HEM

Download Ideal Coordinates CCD File 
TD [auth F],
WJ [auth f]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
NEX
Query on NEX

Download Ideal Coordinates CCD File 
EH [auth Y]
HN [auth y]
JF [auth G]
LG [auth S]
ML [auth g]
EH [auth Y],
HN [auth y],
JF [auth G],
LG [auth S],
ML [auth g],
OM [auth s],
QE [auth N],
TK [auth n],
UF [auth R],
XL [auth r]
(1R,3R)-6-{(3E,5E,7E,9E,11E,13E,15E,17E)-18-[(1S,4R,6R)-4-HYDROXY-2,2,6-TRIMETHYL-7-OXABICYCLO[4.1.0]HEPT-1-YL]-3,7,12,16-TETRAMETHYLOCTADECA-1,3,5,7,9,11,13,15,17-NONAENYLIDENE}-1,5,5-TRIMETHYLCYCLOHEXANE-1,3-DIOL
C40 H56 O4
PGYAYSRVSAJXTE-OQASCVKESA-N
XAT
Query on XAT

Download Ideal Coordinates CCD File 
DH [auth Y]
GN [auth y]
IF [auth G]
LL [auth g]
PE [auth N]
DH [auth Y],
GN [auth y],
IF [auth G],
LL [auth g],
PE [auth N],
SK [auth n],
TF [auth R],
WL [auth r]
(3S,5R,6S,3'S,5'R,6'S)-5,6,5',6'-DIEPOXY-5,6,5',6'- TETRAHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL
C40 H56 O4
SZCBXWMUOPQSOX-WVJDLNGLSA-N
LUT
Query on LUT

Download Ideal Coordinates CCD File 
BH [auth Y]
CH [auth Y]
EN [auth y]
FN [auth y]
GF [auth G]
BH [auth Y],
CH [auth Y],
EN [auth y],
FN [auth y],
GF [auth G],
HF [auth G],
JG [auth S],
JL [auth g],
KG [auth S],
KL [auth g],
MM [auth s],
NE [auth N],
NM [auth s],
OE [auth N],
QK [auth n],
RK [auth n]
(3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL
C40 H56 O2
KBPHJBAIARWVSC-NSIPBSJQSA-N
BCR
Query on BCR

Download Ideal Coordinates CCD File 
AD [auth C]
BD [auth C]
CD [auth C]
CJ [auth c]
DJ [auth c]
AD [auth C],
BD [auth C],
CD [auth C],
CJ [auth c],
DJ [auth c],
EJ [auth c],
FJ [auth c],
HC [auth B],
IC [auth B],
JC [auth B],
KI [auth b],
LI [auth b],
MI [auth b],
ND [auth D],
OB [auth A],
QJ [auth d],
RH [auth a],
UD [auth H],
XJ [auth h],
ZC [auth C]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
LMU
Query on LMU

Download Ideal Coordinates CCD File 
AK [auth z]
BK [auth z]
GH [auth Y]
JN [auth y]
XD [auth Z]
AK [auth z],
BK [auth z],
GH [auth Y],
JN [auth y],
XD [auth Z],
YD [auth Z]
DODECYL-ALPHA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-YHBSTRCHSA-N
OEX
Query on OEX

Download Ideal Coordinates CCD File 
EB [auth A],
HH [auth a]
CA-MN4-O5 CLUSTER
Ca Mn4 O5
SEXWDHMBWJEXOJ-UHFFFAOYSA-N
BCT
Query on BCT

Download Ideal Coordinates CCD File 
KD [auth D],
NJ [auth d]
BICARBONATE ION
C H O3
BVKZGUZCCUSVTD-UHFFFAOYSA-M
FE2
Query on FE2

Download Ideal Coordinates CCD File 
FB [auth A],
IH [auth a]
FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
GB [auth A],
HB [auth A],
JH [auth a],
KH [auth a]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.0
MODEL REFINEMENTPHENIX1.13

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Science and Technology (China)China2017YFA0503702
Chinese Academy of SciencesChinaXDB27020106
Chinese Academy of SciencesChinaXDB08020302
Chinese Academy of SciencesChinaQYZDB-SSW-SMC005
National Natural Science Foundation of ChinaChina31670749

Revision History  (Full details and data files)

  • Version 1.0: 2019-10-23
    Type: Initial release
  • Version 1.1: 2019-11-20
    Changes: Advisory, Derived calculations
  • Version 1.2: 2019-12-11
    Changes: Database references
  • Version 1.3: 2019-12-25
    Changes: Database references