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 2.0 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 
EC: 1.10.3.9
Membrane Entity: Yes 
UniProt
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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 
UniProt
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II D2 proteinCA [auth d],
D
353Spinacia oleraceaMutation(s): 0 
EC: 1.10.3.9
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 
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein, chloroplastic267Spinacia oleraceaMutation(s): 0 
Membrane Entity: Yes 
UniProt
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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 
UniProt
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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]
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]
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]
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]
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]
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]
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]
(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]
(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]
(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]
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

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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
  • Version 2.0: 2024-11-13
    Changes: Data collection, Database references, Derived calculations, Non-polymer description, Structure summary