6YP7

PSII-LHCII C2S2 supercomplex from Pisum sativum grown in high light conditions


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

High-Light versus Low-Light: Effects on Paired Photosystem II Supercomplex Structural Rearrangement in Pea Plants.

Grinzato, A.Albanese, P.Marotta, R.Swuec, P.Saracco, G.Bolognesi, M.Zanotti, G.Pagliano, C.

(2020) Int J Mol Sci 21

  • DOI: https://doi.org/10.3390/ijms21228643
  • Primary Citation of Related Structures:  
    6YP7

  • PubMed Abstract: 

    In plant grana thylakoid membranes Photosystem II (PSII) associates with a variable number of antenna proteins (LHCII) to form different types of supercomplexes (PSII-LHCII), whose organization is dynamically adjusted in response to light cues, with the C 2 S 2 more abundant in high-light and the C 2 S 2 M 2 in low-light. Paired PSII-LHCII supercomplexes interacting at their stromal surface from adjacent thylakoid membranes were previously suggested to mediate grana stacking. Here, we present the cryo-electron microscopy maps of paired C 2 S 2 and C 2 S 2 M 2 supercomplexes isolated from pea plants grown in high-light and low-light, respectively. These maps show a different rotational offset between the two supercomplexes in the pair, responsible for modifying their reciprocal interaction and energetic connectivity. This evidence reveals a different way by which paired PSII-LHCII supercomplexes can mediate grana stacking at diverse irradiances. Electrostatic stromal interactions between LHCII trimers almost completely overlapping in the paired C 2 S 2 can be the main determinant by which PSII-LHCII supercomplexes mediate grana stacking in plants grown in high-light, whereas the mutual interaction of stromal N-terminal loops of two facing Lhcb4 subunits in the paired C 2 S 2 M 2 can fulfil this task in plants grown in low-light. The high-light induced accumulation of the Lhcb4.3 protein in PSII-LHCII supercomplexes has been previously reported. Our cryo-electron microscopy map at 3.8 Å resolution of the C 2 S 2 supercomplex isolated from plants grown in high-light suggests the presence of the Lhcb4.3 protein revealing peculiar structural features of this high-light-specific antenna important for photoprotection.


  • Organizational Affiliation

    Department of Biomedical Sciences, University of Padova, Via Ugo Bassi 58 B, 35121 Padova, Italy.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein 8, chloroplastic219Pisum sativumMutation(s): 0 
Gene Names: CAB8LHCB1
Membrane Entity: Yes 
UniProt
Find proteins for P27490 (Pisum sativum)
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II protein D1G [auth a],
X [auth A]
334Pisum sativumMutation(s): 0 
Gene Names: psbApgiI
EC: 1.10.3.9
Membrane Entity: Yes 
UniProt
Find proteins for P06585 (Pisum sativum)
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II CP47 reaction center proteinH [auth b],
Y [auth B]
503Pisum sativumMutation(s): 0 
Gene Names: psbB
Membrane Entity: Yes 
UniProt
Find proteins for Q9XQR6 (Pisum sativum)
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II CP43 reaction center proteinI [auth c],
Z [auth C]
450Pisum sativumMutation(s): 0 
Gene Names: psbC
Membrane Entity: Yes 
UniProt
Find proteins for P06004 (Pisum sativum)
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II D2 proteinAA [auth D],
J [auth d]
341Pisum sativumMutation(s): 0 
Gene Names: psbD
EC: 1.10.3.9
Membrane Entity: Yes 
UniProt
Find proteins for P06006 (Pisum sativum)
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b559 subunit alphaBA [auth E],
K [auth e]
75Pisum sativumMutation(s): 0 
Gene Names: psbE
Membrane Entity: Yes 
UniProt
Find proteins for P13554 (Pisum sativum)
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b559 subunit betaCA [auth F],
L [auth f]
30Pisum sativumMutation(s): 0 
Gene Names: psbF
Membrane Entity: Yes 
UniProt
Find proteins for P62096 (Pisum sativum)
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein HDA [auth H],
M [auth h]
60Pisum sativumMutation(s): 0 
Gene Names: psbH
Membrane Entity: Yes 
UniProt
Find proteins for Q9XQR3 (Pisum sativum)
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein IEA [auth I],
N [auth i]
34Pisum sativumMutation(s): 0 
Gene Names: psbI
Membrane Entity: Yes 
UniProt
Find proteins for D5MAJ9 (Pisum sativum)
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein JFA [auth J],
O [auth j]
35Pisum sativumMutation(s): 0 
Gene Names: psbJ
Membrane Entity: Yes 
UniProt
Find proteins for P13555 (Pisum sativum)
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein KGA [auth K],
P [auth k]
37Pisum sativumMutation(s): 0 
Gene Names: psbK
Membrane Entity: Yes 
UniProt
Find proteins for D5MAJ8 (Pisum sativum)
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein LHA [auth L],
Q [auth l]
37Pisum sativumMutation(s): 0 
Gene Names: psbL
Membrane Entity: Yes 
UniProt
Find proteins for P60147 (Pisum sativum)
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein MIA [auth M],
R [auth m]
33Pisum sativumMutation(s): 0 
Gene Names: psbM
Membrane Entity: Yes 
UniProt
Find proteins for P69529 (Pisum sativum)
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Oxygen-evolving enhancer protein 1, chloroplasticJA [auth O],
S [auth o]
248Pisum sativumMutation(s): 0 
Gene Names: PSBO
Membrane Entity: Yes 
UniProt
Find proteins for P14226 (Pisum sativum)
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein TKA [auth T],
T [auth t]
32Pisum sativumMutation(s): 0 
Gene Names: psbT
Membrane Entity: Yes 
UniProt
Find proteins for Q8HS25 (Pisum sativum)
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein WLA [auth W],
U [auth w]
54Pisum sativumMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A2D0TCJ2 (Pisum sativum)
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Ultraviolet-B-repressible proteinMA [auth X],
V [auth x]
39Pisum sativumMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q8VYY1 (Pisum sativum)
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein ZNA [auth Z],
W [auth z]
62Pisum sativumMutation(s): 0 
Gene Names: psbZycf9
Membrane Entity: Yes 
UniProt
Find proteins for Q32902 (Pisum sativum)
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
Light harvesting chlorophyll a/b-binding protein Lhcb4.3OA [auth r],
RA [auth R]
222Pisum sativumMutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
Light harvesting chlorophyll a/b-binding protein Lhcb5, CP26PA [auth s],
QA [auth S]
218Pisum sativumMutation(s): 0 
UniProt
Find proteins for A0A2D0TCJ1 (Pisum sativum)
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Small Molecules
Ligands 17 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DGD
Query on DGD

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HF [auth a]
LH [auth h]
OK [auth H]
QK [auth J]
SG [auth c]
HF [auth a],
LH [auth h],
OK [auth H],
QK [auth J],
SG [auth c],
TG [auth c],
UG [auth c],
VH [auth A],
VJ [auth C],
WJ [auth C]
DIGALACTOSYL DIACYL GLYCEROL (DGDG)
C51 H96 O15
LDQFLSUQYHBXSX-HXXRYREZSA-N
CHL
Query on CHL

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AB [auth g]
AD [auth G]
BD [auth G]
BL [auth r]
CC [auth y]
AB [auth g],
AD [auth G],
BD [auth G],
BL [auth r],
CC [auth y],
CD [auth G],
EE [auth Y],
EM [auth S],
FM [auth S],
GC [auth y],
GL [auth r],
HC [auth y],
HL [auth r],
IC [auth y],
IE [auth Y],
IL [auth r],
JC [auth y],
JE [auth Y],
JM [auth S],
KC [auth y],
KE [auth Y],
KM [auth S],
LB [auth n],
LE [auth Y],
MD [auth N],
PB [auth n],
QB [auth n],
QD [auth N],
QL [auth s],
RB [auth n],
RD [auth N],
RL [auth s],
SA [auth g],
SB [auth n],
SD [auth N],
TD [auth N],
UC [auth G],
VL [auth s],
WA [auth g],
WL [auth s],
WM [auth R],
XA [auth g],
XM [auth R],
YA [auth g],
YC [auth G],
YM [auth R],
ZA [auth g],
ZC [auth G]
CHLOROPHYLL B
C55 H70 Mg N4 O6
MWVCRINOIIOUAU-UYSPMESUSA-M
CLA
Query on CLA

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AF [auth a]
AI [auth A]
AL [auth W]
AM [auth s]
AN [auth R]
AF [auth a],
AI [auth A],
AL [auth W],
AM [auth s],
AN [auth R],
BB [auth g],
BH [auth d],
BI [auth A],
BM [auth s],
BN [auth R],
CB [auth g],
CF [auth a],
CH [auth d],
CM [auth s],
CN [auth R],
DB [auth g],
DC [auth y],
DD [auth G],
DG [auth c],
DI [auth A],
DL [auth r],
EB [auth g],
EC [auth y],
ED [auth G],
EG [auth c],
EK [auth D],
EL [auth r],
FB [auth g],
FC [auth y],
FD [auth G],
FE [auth Y],
FG [auth c],
FK [auth D],
FL [auth r],
GD [auth G],
GE [auth Y],
GG [auth c],
GJ [auth C],
GM [auth S],
HD [auth G],
HE [auth Y],
HG [auth c],
HJ [auth C],
HM [auth S],
IF [auth b],
IG [auth c],
IJ [auth C],
IM [auth S],
JF [auth b],
JG [auth c],
JI [auth B],
JJ [auth C],
JL [auth r],
KF [auth b],
KG [auth c],
KI [auth B],
KJ [auth C],
KL [auth r],
LC [auth y],
LF [auth b],
LG [auth c],
LI [auth B],
LJ [auth C],
LL [auth r],
LM [auth S],
MB [auth n],
MC [auth y],
ME [auth Y],
MF [auth b],
MG [auth c],
MI [auth B],
MJ [auth C],
ML [auth r],
MM [auth S],
NB [auth n],
NC [auth y],
ND [auth N],
NE [auth Y],
NF [auth b],
NG [auth c],
NI [auth B],
NJ [auth C],
NM [auth S],
OB [auth n],
OC [auth y],
OD [auth N],
OE [auth Y],
OF [auth b],
OG [auth c],
OI [auth B],
OJ [auth C],
OM [auth S],
PD [auth N],
PE [auth Y],
PF [auth b],
PG [auth c],
PI [auth B],
PJ [auth C],
PM [auth S],
QF [auth b],
QI [auth B],
QJ [auth C],
QM [auth S],
RF [auth b],
RI [auth B],
RJ [auth C],
SF [auth b],
SH [auth w],
SI [auth B],
SJ [auth C],
SL [auth s],
TA [auth g],
TB [auth n],
TF [auth b],
TI [auth B],
TL [auth s],
TM [auth R],
UA [auth g],
UB [auth n],
UD [auth N],
UF [auth b],
UH [auth x],
UI [auth B],
UL [auth s],
UM [auth R],
VA [auth g],
VB [auth n],
VC [auth G],
VD [auth N],
VF [auth b],
VI [auth B],
VM [auth R],
WB [auth n],
WC [auth G],
WD [auth N],
WF [auth b],
WI [auth B],
XB [auth n],
XC [auth G],
XD [auth N],
XI [auth B],
XL [auth s],
YD [auth N],
YE [auth a],
YI [auth B],
YL [auth s],
ZE [auth a],
ZH [auth A],
ZL [auth s],
ZM [auth R]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
PHO
Query on PHO

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BF [auth a],
BK [auth D],
CI [auth A],
ZG [auth d]
PHEOPHYTIN A
C55 H74 N4 O5
CQIKWXUXPNUNDV-RCBXBCQGSA-N
SQD
Query on SQD

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AH [auth d]
CK [auth D]
FF [auth a]
GI [auth A]
PH [auth l]
AH [auth d],
CK [auth D],
FF [auth a],
GI [auth A],
PH [auth l],
RH [auth l],
UK [auth L],
VK [auth L]
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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AK [auth C]
BG [auth b]
DJ [auth B]
FJ [auth C]
HI [auth B]
AK [auth C],
BG [auth b],
DJ [auth B],
FJ [auth C],
HI [auth B],
IH [auth d],
LK [auth D],
OH [auth k],
PK [auth I],
TH [auth w],
TK [auth K],
XK [auth M],
YG [auth c],
YK [auth T]
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
PL9
Query on PL9

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EF [auth a],
EH [auth d],
FI [auth A],
HK [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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AG [auth b]
BC [auth n]
CJ [auth B]
CL [auth r]
DE [auth N]
AG [auth b],
BC [auth n],
CJ [auth B],
CL [auth r],
DE [auth N],
DM [auth s],
FH [auth d],
GH [auth d],
HH [auth d],
IK [auth D],
JK [auth D],
KB [auth g],
KK [auth D],
LD [auth G],
QH [auth l],
RM [auth S],
SC [auth y],
SM [auth R],
UE [auth Y],
VG [auth c],
WG [auth c],
WK [auth L],
XG [auth c],
XJ [auth C],
YJ [auth C],
ZJ [auth C]
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
HEM
Query on HEM

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

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AC [auth n]
CE [auth N]
JB [auth g]
PL [auth r]
RC [auth y]
AC [auth n],
CE [auth N],
JB [auth g],
PL [auth r],
RC [auth y],
TC [auth y],
TE [auth Y]
(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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BE [auth N]
EN [auth R]
IB [auth g]
KD [auth G]
OL [auth r]
BE [auth N],
EN [auth R],
IB [auth g],
KD [auth G],
OL [auth r],
QC [auth y],
SE [auth Y],
ZB [auth n]
(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 N]
DN [auth R]
GB [auth g]
HB [auth g]
ID [auth G]
AE [auth N],
DN [auth R],
GB [auth g],
HB [auth g],
ID [auth G],
JD [auth G],
NL [auth r],
PC [auth y],
QE [auth Y],
RE [auth Y],
YB [auth n],
ZD [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

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AJ [auth B]
BJ [auth B]
DF [auth a]
DH [auth d]
EI [auth A]
AJ [auth B],
BJ [auth B],
DF [auth a],
DH [auth d],
EI [auth A],
GK [auth D],
II [auth B],
KH [auth h],
MH [auth k],
NH [auth k],
NK [auth H],
QG [auth c],
RG [auth c],
RK [auth K],
SK [auth K],
TJ [auth C],
UJ [auth C],
XF [auth b],
YF [auth b],
ZF [auth b],
ZI [auth B],
ZK [auth T]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
OEX
Query on OEX

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

Download Ideal Coordinates CCD File 
DK [auth D],
GF [auth a]
BICARBONATE ION
C H O3
BVKZGUZCCUSVTD-UHFFFAOYSA-M
FE2
Query on FE2

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

Download Ideal Coordinates CCD File 
CG [auth c],
EJ [auth C],
XE [auth a],
YH [auth A]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-11-25
    Type: Initial release
  • Version 1.1: 2020-12-02
    Changes: Database references