3WU2

Crystal structure analysis of Photosystem II complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.156 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Crystal structure of oxygen-evolving photosystem II at a resolution of 1.9 A

Umena, Y.Kawakami, K.Shen, J.-R.Kamiya, N.

(2011) Nature 473: 55-60

  • DOI: 10.1038/nature09913
  • Primary Citation of Related Structures:  
  • Also Cited By: 5V2C, 4Q54

  • PubMed Abstract: 
  • Photosystem II is the site of photosynthetic water oxidation and contains 20 subunits with a total molecular mass of 350 kDa. The structure of photosystem II has been reported at resolutions from 3.8 to 2.9 Å. These resolutions have provided much inf ...

    Photosystem II is the site of photosynthetic water oxidation and contains 20 subunits with a total molecular mass of 350 kDa. The structure of photosystem II has been reported at resolutions from 3.8 to 2.9 Å. These resolutions have provided much information on the arrangement of protein subunits and cofactors but are insufficient to reveal the detailed structure of the catalytic centre of water splitting. Here we report the crystal structure of photosystem II at a resolution of 1.9 Å. From our electron density map, we located all of the metal atoms of the Mn(4)CaO(5) cluster, together with all of their ligands. We found that five oxygen atoms served as oxo bridges linking the five metal atoms, and that four water molecules were bound to the Mn(4)CaO(5) cluster; some of them may therefore serve as substrates for dioxygen formation. We identified more than 1,300 water molecules in each photosystem II monomer. Some of them formed extensive hydrogen-bonding networks that may serve as channels for protons, water or oxygen molecules. The determination of the high-resolution structure of photosystem II will allow us to analyse and understand its functions in great detail.


    Organizational Affiliation

    Department of Chemistry, Graduate School of Science, Osaka City University, 3-3-138 Sugimoto, Sumiyoshi, Osaka 558-8585, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Photosystem Q(B) protein
A, a
344Thermosynechococcus vulcanusMutation(s): 0 
Gene Names: psbA (psbA-1)
EC: 1.10.3.9
Find proteins for P51765 (Thermosynechococcus vulcanus)
Go to UniProtKB:  P51765
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Photosystem II CP47 chlorophyll apoprotein
B, b
504Thermosynechococcus vulcanusMutation(s): 0 
Gene Names: psbB
Find proteins for D0VWR1 (Thermosynechococcus vulcanus)
Go to UniProtKB:  D0VWR1
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Photosystem II 44 kDa reaction center protein
C, c
455Thermosynechococcus vulcanusMutation(s): 0 
Gene Names: psbC
Find proteins for D0VWR7 (Thermosynechococcus vulcanus)
Go to UniProtKB:  D0VWR7
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Photosystem II D2 protein
D, d
342Thermosynechococcus vulcanusMutation(s): 0 
Gene Names: psbD
EC: 1.10.3.9
Find proteins for D0VWR8 (Thermosynechococcus vulcanus)
Go to UniProtKB:  D0VWR8
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Cytochrome b559 subunit alpha
E, e
83Thermosynechococcus vulcanusMutation(s): 0 
Gene Names: psbE
Find proteins for P12238 (Thermosynechococcus vulcanus)
Go to UniProtKB:  P12238
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
Cytochrome b559 subunit beta
F, f
44Thermosynechococcus vulcanusMutation(s): 0 
Gene Names: psbF
Find proteins for P12239 (Thermosynechococcus vulcanus)
Go to UniProtKB:  P12239
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
Photosystem II reaction center protein H
H, h
63Thermosynechococcus vulcanusMutation(s): 0 
Gene Names: psbH
Find proteins for P19052 (Thermosynechococcus vulcanus)
Go to UniProtKB:  P19052
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
Photosystem II reaction center protein I
I, i
38Thermosynechococcus vulcanusMutation(s): 0 
Gene Names: psbI
Find proteins for P12240 (Thermosynechococcus vulcanus)
Go to UniProtKB:  P12240
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
Photosystem II reaction center protein J
J, j
40Thermosynechococcus vulcanusMutation(s): 0 
Gene Names: psbJ
Find proteins for Q7DGD4 (Thermosynechococcus vulcanus)
Go to UniProtKB:  Q7DGD4
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
Photosystem II reaction center protein K
K, k
37Thermosynechococcus vulcanusMutation(s): 0 
Gene Names: psbK
Find proteins for P19054 (Thermosynechococcus vulcanus)
Go to UniProtKB:  P19054
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
Photosystem II reaction center protein L
L, l
37Thermosynechococcus vulcanusMutation(s): 0 
Gene Names: psbL
Find proteins for P12241 (Thermosynechococcus vulcanus)
Go to UniProtKB:  P12241
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
Photosystem II reaction center protein M
M, m
36Thermosynechococcus vulcanusMutation(s): 0 
Gene Names: psbM
Find proteins for P12312 (Thermosynechococcus vulcanus)
Go to UniProtKB:  P12312
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
Photosystem II manganese-stabilizing polypeptide
O, o
244Thermosynechococcus vulcanusMutation(s): 0 
Gene Names: psbO
Find proteins for D0VWR2 (Thermosynechococcus vulcanus)
Go to UniProtKB:  D0VWR2
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
Photosystem II reaction center protein T
T, t
32Thermosynechococcus vulcanusMutation(s): 0 
Gene Names: psbT
Find proteins for P12313 (Thermosynechococcus vulcanus)
Go to UniProtKB:  P12313
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
Photosystem II 12 kDa extrinsic protein
U, u
104Thermosynechococcus vulcanusMutation(s): 0 
Gene Names: psbU
Find proteins for P56152 (Thermosynechococcus vulcanus)
Go to UniProtKB:  P56152
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
Cytochrome c-550
V, v
137Thermosynechococcus vulcanusMutation(s): 0 
Gene Names: psbV
Find proteins for P0A387 (Thermosynechococcus vulcanus)
Go to UniProtKB:  P0A387
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
Photosystem II reaction center protein Ycf12
Y, y
30Thermosynechococcus vulcanusMutation(s): 0 
Gene Names: ycf12 (psbY)
Find proteins for D0VWR3 (Thermosynechococcus vulcanus)
Go to UniProtKB:  D0VWR3
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
Photosystem II reaction center protein X
X, x
40Thermosynechococcus vulcanusMutation(s): 0 
Gene Names: psbX
Find proteins for D0VWR4 (Thermosynechococcus vulcanus)
Go to UniProtKB:  D0VWR4
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
Photosystem II reaction center protein Z
Z, z
62Thermosynechococcus vulcanusMutation(s): 0 
Gene Names: psbZ
Find proteins for D0VWR5 (Thermosynechococcus vulcanus)
Go to UniProtKB:  D0VWR5
Small Molecules
Ligands 20 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SQD
Query on SQD

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a, A, B, D, f, L
1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL
SULFOQUINOVOSYLDIACYLGLYCEROL
C41 H78 O12 S
RVUUQPKXGDTQPG-JUDHQOGESA-N
 Ligand Interaction
CLA
Query on CLA

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A, a, b, B, c, C, d, D
CHLOROPHYLL A
C55 H72 Mg N4 O5
VIQFHHZSLDFWDU-AENOIHSZSA-M
 Ligand Interaction
PL9
Query on PL9

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A, a, D, 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
PLASTOQUINONE 9
C53 H80 O2
FKUYMLZIRPABFK-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

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O
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
OEX
Query on OEX

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a, A
CA-MN4-O5 CLUSTER
Ca Mn4 O5
SEXWDHMBWJEXOJ-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

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A, a
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

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A, a, b, B, c, C, D, f, h, l, L, O, V, v
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
HTG
Query on HTG

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b, B, c, C, d, D, O, u, U, V
HEPTYL 1-THIOHEXOPYRANOSIDE
C13 H26 O5 S
HPEGNLMTTNTJSP-LBELIVKGSA-N
 Ligand Interaction
CA
Query on CA

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B, b, c, f, F, o, O
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
DGD
Query on DGD

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c, C, d, D, h, H
DIGALACTOSYL DIACYL GLYCEROL (DGDG)
C51 H96 O15
LDQFLSUQYHBXSX-HXXRYREZSA-N
 Ligand Interaction
LMG
Query on LMG

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A, a, B, b, c, C, D, d, Z
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
 Ligand Interaction
BCT
Query on BCT

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a, D
BICARBONATE ION
C H O3
BVKZGUZCCUSVTD-UHFFFAOYSA-M
 Ligand Interaction
MG
Query on MG

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j, J
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
HEM
Query on HEM

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F, f, v, V
PROTOPORPHYRIN IX CONTAINING FE
HEME
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
BCR
Query on BCR

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a, A, b, B, C, c, d, D, K, k, T, t
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
 Ligand Interaction
PHO
Query on PHO

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a, A
PHEOPHYTIN A
C55 H74 N4 O5
CQIKWXUXPNUNDV-RCBXBCQGSA-N
 Ligand Interaction
FE2
Query on FE2

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a, A
FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
 Ligand Interaction
LMT
Query on LMT

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A, a, B, b, c, C, F, J, M, m, t, Z, z
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
 Ligand Interaction
RRX
Query on RRX

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H, h
(3R)-beta,beta-caroten-3-ol
beta-Cryptoxanthin
C40 H56 O
DMASLKHVQRHNES-FKKUPVFPSA-N
 Ligand Interaction
LHG
Query on LHG

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a, d, D, E, l, L
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
FME
Query on FME
I, i, M, m, T, t
L-PEPTIDE LINKINGC6 H11 N O3 SMET
HSK
Query on HSK
D, d
L-PEPTIDE LINKINGC6 H9 N3 O3HIS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.156 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 122.190α = 90.00
b = 228.510β = 90.00
c = 286.400γ = 90.00
Software Package:
Software NamePurpose
XDSdata scaling
PDB_EXTRACTdata extraction
REFMACrefinement
MOLREPphasing
XDSdata reduction
XSCALEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-09-03
    Type: Initial release