3JCU

Cryo-EM structure of spinach PSII-LHCII supercomplex at 3.2 Angstrom resolution


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Structure of spinach photosystem II-LHCII supercomplex at 3.2 A resolution

Wei, X.P.Su, X.D.Cao, P.Liu, X.Y.Chang, W.R.Li, M.Zhang, X.Z.Liu, Z.F.

(2016) Nature 534: 69-74


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II protein D1A,
Z [auth a]
344Spinacia oleraceaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II CP47 reaction center proteinAA [auth b],
B
508Spinacia oleraceaMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II CP43 reaction center proteinBA [auth c],
C
473Spinacia oleraceaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II D2 proteinCA [auth d],
D
353Spinacia oleraceaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b559 subunit alphaDA [auth e],
E
83Spinacia oleraceaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b559 subunit betaEA [auth f],
F
39Spinacia oleraceaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein, chloroplastic267Spinacia oleraceaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein HGA [auth h],
H
73Spinacia oleraceaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Protein Photosystem II reaction center protein IHA [auth i],
I
36Spinacia oleraceaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein JIA [auth j],
J
40Spinacia oleraceaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein KJA [auth k],
K
59Spinacia oleraceaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Protein Photosystem II reaction center protein LKA [auth l],
L
38Spinacia oleraceaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein MLA [auth m],
M
34Spinacia oleraceaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Oxygen-evolving enhancer protein 1, chloroplasticNA [auth o],
O
332Spinacia oleraceaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Oxygen-evolving enhancer protein 2, chloroplasticOA [auth p],
P
267Spinacia oleraceaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Oxygen-evolving enhancer protein 3, chloroplasticPA [auth q],
Q
232Spinacia oleraceaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Chlorophyll A-B Binding protein 29 kD (CP29)QA [auth r],
R
243Spinacia oleraceaMutation(s): 0 
UniProt
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
Chlorophyll A-B Binding protein 26 kD (CP26)RA [auth s],
S
295Spinacia oleraceaMutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II Reaction Center protein TcSA [auth t],
T
33Spinacia oleraceaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II Reaction Center Tn proteinTA [auth u],
U
99Spinacia oleraceaMutation(s): 0 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center W protein, chloroplasticUA [auth w],
V [auth W]
137Spinacia oleraceaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II Reaction Center X proteinVA [auth x],
W [auth X]
117Spinacia oleraceaMutation(s): 0 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein ZXA [auth z],
Y [auth Z]
62Spinacia oleraceaMutation(s): 0 
Membrane Entity: Yes 
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Small Molecules
Ligands 17 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DGD
Query on DGD

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BD [auth C]
CJ [auth c]
EJ [auth c]
FJ [auth c]
GE [auth H]
BD [auth C],
CJ [auth c],
EJ [auth c],
FJ [auth c],
GE [auth H],
LK [auth h],
YC [auth C],
ZC [auth C]
DIGALACTOSYL DIACYL GLYCEROL (DGDG)
C51 H96 O15
LDQFLSUQYHBXSX-HXXRYREZSA-N
CHL
Query on CHL

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BM [auth s]
CM [auth s]
DM [auth s]
FF [auth R]
GF [auth R]
BM [auth s],
CM [auth s],
DM [auth s],
FF [auth R],
GF [auth R],
HF [auth R],
IE [auth N],
JG [auth Y],
KL [auth r],
LL [auth r],
MD [auth G],
ME [auth N],
ML [auth r],
NE [auth N],
NG [auth Y],
NK [auth n],
OE [auth N],
OG [auth Y],
OM [auth y],
PE [auth N],
PG [auth Y],
QD [auth G],
QE [auth N],
QG [auth Y],
RD [auth G],
RG [auth Y],
RJ [auth g],
RK [auth n],
SD [auth G],
SF [auth S],
SK [auth n],
SM [auth y],
TD [auth G],
TK [auth n],
TM [auth y],
UD [auth G],
UK [auth n],
UM [auth y],
VJ [auth g],
VK [auth n],
VM [auth y],
WF [auth S],
WJ [auth g],
WM [auth y],
XF [auth S],
XJ [auth g],
XL [auth s],
YF [auth S],
YJ [auth g],
ZJ [auth g]
CHLOROPHYLL B
C55 H70 Mg N4 O6
MWVCRINOIIOUAU-UYSPMESUSA-M
CLA
Query on CLA

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AC [auth B]
AG [auth S]
AI [auth b]
AK [auth g]
AL [auth n]
AC [auth B],
AG [auth S],
AI [auth b],
AK [auth g],
AL [auth n],
AM [auth s],
AN [auth y],
BF [auth R],
BG [auth S],
BI [auth b],
BK [auth g],
BN [auth y],
CB [auth A],
CC [auth B],
CF [auth R],
CG [auth S],
CI [auth b],
CK [auth g],
DB [auth A],
DD [auth D],
DF [auth R],
DG [auth S],
DI [auth b],
DK [auth g],
EB [auth A],
ED [auth D],
EF [auth R],
EG [auth S],
EI [auth b],
EK [auth g],
EM [auth s],
FI [auth b],
FM [auth s],
GL [auth r],
GM [auth s],
HB [auth A],
HC [auth C],
HH [auth a],
HI [auth b],
HL [auth r],
HM [auth s],
IC [auth C],
IF [auth R],
IH [auth a],
IJ [auth d],
IL [auth r],
IM [auth s],
JC [auth C],
JE [auth N],
JF [auth R],
JH [auth a],
JJ [auth d],
JL [auth r],
JM [auth s],
KC [auth C],
KE [auth N],
KF [auth R],
KG [auth Y],
LC [auth C],
LE [auth N],
LF [auth R],
LG [auth Y],
MB [auth B],
MC [auth C],
MF [auth R],
MG [auth Y],
MH [auth a],
MI [auth c],
NB [auth B],
NC [auth C],
ND [auth G],
NF [auth R],
NI [auth c],
NL [auth r],
OB [auth B],
OC [auth C],
OD [auth G],
OI [auth c],
OK [auth n],
OL [auth r],
PB [auth B],
PC [auth C],
PD [auth G],
PI [auth c],
PK [auth n],
PL [auth r],
PM [auth y],
QB [auth B],
QC [auth C],
QI [auth c],
QK [auth n],
QL [auth r],
QM [auth y],
RB [auth B],
RC [auth C],
RE [auth N],
RH [auth b],
RI [auth c],
RL [auth r],
RM [auth y],
SB [auth B],
SC [auth C],
SE [auth N],
SG [auth Y],
SH [auth b],
SI [auth c],
SJ [auth g],
SL [auth r],
TB [auth B],
TC [auth C],
TE [auth N],
TF [auth S],
TG [auth Y],
TH [auth b],
TI [auth c],
TJ [auth g],
UB [auth B],
UE [auth N],
UF [auth S],
UG [auth Y],
UH [auth b],
UI [auth c],
UJ [auth g],
VB [auth B],
VD [auth G],
VE [auth N],
VF [auth S],
VG [auth Y],
VH [auth b],
VI [auth c],
WB [auth B],
WD [auth G],
WG [auth Y],
WH [auth b],
WI [auth c],
WK [auth n],
XB [auth B],
XD [auth G],
XH [auth b],
XI [auth c],
XK [auth n],
XM [auth y],
YB [auth B],
YD [auth G],
YH [auth b],
YI [auth c],
YK [auth n],
YL [auth s],
YM [auth y],
ZB [auth B],
ZD [auth G],
ZF [auth S],
ZH [auth b],
ZK [auth n],
ZL [auth s],
ZM [auth y]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
PHO
Query on PHO

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FB [auth A],
GB [auth A],
KH [auth a],
LH [auth a]
PHEOPHYTIN A
C55 H74 N4 O5
CQIKWXUXPNUNDV-RCBXBCQGSA-N
SQD
Query on SQD

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FC [auth B]
JB [auth A]
KI [auth b]
LB [auth A]
OH [auth a]
FC [auth B],
JB [auth A],
KI [auth b],
LB [auth A],
OH [auth a],
QH [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

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AD [auth C]
CH [auth Z]
GC [auth B]
GJ [auth c]
HN [auth z]
AD [auth C],
CH [auth Z],
GC [auth B],
GJ [auth c],
HN [auth z],
KB [auth A],
KD [auth D],
LI [auth b],
PH [auth a],
PJ [auth d]
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
PL9
Query on PL9

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GD [auth D],
MJ [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

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AF [auth N]
BH [auth Y]
EE [auth G]
FL [auth n]
GN [auth y]
AF [auth N],
BH [auth Y],
EE [auth G],
FL [auth n],
GN [auth y],
HD [auth D],
HE [auth L],
ID [auth D],
IG [auth S],
JD [auth D],
JK [auth g],
LJ [auth d],
MK [auth l],
NJ [auth d],
NM [auth s],
OJ [auth d],
RF [auth R],
WL [auth r]
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
HEM
Query on HEM

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LD [auth F],
QJ [auth f]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
NEX
Query on NEX

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AH [auth Y]
DE [auth G]
EL [auth n]
FN [auth y]
HG [auth S]
AH [auth Y],
DE [auth G],
EL [auth n],
FN [auth y],
HG [auth S],
IK [auth g],
MM [auth s],
QF [auth R],
VL [auth r],
ZE [auth N]
(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

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CE [auth G]
DL [auth n]
EN [auth y]
HK [auth g]
PF [auth R]
CE [auth G],
DL [auth n],
EN [auth y],
HK [auth g],
PF [auth R],
UL [auth r],
YE [auth N],
ZG [auth Y]
(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

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AE [auth G]
BE [auth G]
BL [auth n]
CL [auth n]
CN [auth y]
AE [auth G],
BE [auth G],
BL [auth n],
CL [auth n],
CN [auth y],
DN [auth y],
FG [auth S],
FK [auth g],
GG [auth S],
GK [auth g],
KM [auth s],
LM [auth s],
OF [auth R],
TL [auth r],
WE [auth N],
XE [auth N],
XG [auth Y],
YG [auth Y]
(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

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AJ [auth c]
BC [auth B]
BJ [auth c]
DC [auth B]
DJ [auth c]
AJ [auth c],
BC [auth B],
BJ [auth c],
DC [auth B],
DJ [auth c],
EC [auth B],
FD [auth D],
FE [auth H],
GI [auth b],
IB [auth A],
II [auth b],
JI [auth b],
KJ [auth d],
KK [auth h],
NH [auth a],
UC [auth C],
VC [auth C],
WC [auth C],
XC [auth C],
ZI [auth c]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
OEX
Query on OEX

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DH [auth a],
YA [auth A]
CA-MN4-O5 CLUSTER
Ca Mn4 O5
SEXWDHMBWJEXOJ-UHFFFAOYSA-N
BCT
Query on BCT

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CD [auth D],
HJ [auth d]
BICARBONATE ION
C H O3
BVKZGUZCCUSVTD-UHFFFAOYSA-M
FE2
Query on FE2

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EH [auth a],
ZA [auth A]
FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
CL
Query on CL

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AB [auth A],
BB [auth A],
FH [auth a],
GH [auth a]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONEMAN
RECONSTRUCTIONRELION

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-05-25
    Type: Initial release
  • Version 1.1: 2016-06-01
    Changes: Structure summary
  • Version 1.2: 2016-06-08
    Changes: Database references
  • Version 1.3: 2019-05-01
    Changes: Advisory, Data collection, Database references, Other
  • Version 1.4: 2019-12-18
    Changes: Data collection