3WU2

Crystal structure analysis of Photosystem II complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.156 
  • R-Value Observed: 0.158 

wwPDB Validation   3D Report Full Report


This is version 1.1 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:  
    3WU2

  • 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 information on the arrangement of protein subunits and cofactors but are insufficient to reveal the detailed structure of the catalytic centre of water splitting ...

    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
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem Q(B) proteinA, T [auth a]344Thermosynechococcus vulcanusMutation(s): 0 
Gene Names: psbApsbA-1
EC: 1.10.3.9
Find proteins for P51765 (Thermosynechococcus vulcanus)
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II CP47 chlorophyll apoproteinB, U [auth b]504Thermosynechococcus vulcanusMutation(s): 0 
Gene Names: psbB
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II 44 kDa reaction center proteinC, V [auth c]455Thermosynechococcus vulcanusMutation(s): 0 
Gene Names: psbC
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II D2 proteinD, W [auth d]342Thermosynechococcus vulcanusMutation(s): 0 
Gene Names: psbD
EC: 1.10.3.9
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome b559 subunit alphaE, X [auth e]83Thermosynechococcus vulcanusMutation(s): 0 
Gene Names: psbE
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome b559 subunit betaF, Y [auth f]44Thermosynechococcus vulcanusMutation(s): 0 
Gene Names: psbF
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II reaction center protein HG [auth H], Z [auth h]63Thermosynechococcus vulcanusMutation(s): 0 
Gene Names: psbH
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II reaction center protein IH [auth I], AA [auth i]38Thermosynechococcus vulcanusMutation(s): 0 
Gene Names: psbI
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II reaction center protein JI [auth J], BA [auth j]40Thermosynechococcus vulcanusMutation(s): 0 
Gene Names: psbJ
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II reaction center protein KJ [auth K], CA [auth k]37Thermosynechococcus vulcanusMutation(s): 0 
Gene Names: psbK
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II reaction center protein LK [auth L], DA [auth l]37Thermosynechococcus vulcanusMutation(s): 0 
Gene Names: psbL
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II reaction center protein ML [auth M], EA [auth m]36Thermosynechococcus vulcanusMutation(s): 0 
Gene Names: psbM
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II manganese-stabilizing polypeptideM [auth O], FA [auth o]244Thermosynechococcus vulcanusMutation(s): 0 
Gene Names: psbO
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II reaction center protein TN [auth T], GA [auth t]32Thermosynechococcus vulcanusMutation(s): 0 
Gene Names: psbT
Find proteins for P12313 (Thermosynechococcus vulcanus)
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II 12 kDa extrinsic proteinO [auth U], HA [auth u]104Thermosynechococcus vulcanusMutation(s): 0 
Gene Names: psbU
Find proteins for P56152 (Thermosynechococcus vulcanus)
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome c-550P [auth V], IA [auth v]137Thermosynechococcus vulcanusMutation(s): 0 
Gene Names: psbV
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II reaction center protein Ycf12Q [auth Y], JA [auth y]30Thermosynechococcus vulcanusMutation(s): 0 
Gene Names: ycf12psbY
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II reaction center protein XR [auth X], KA [auth x]40Thermosynechococcus vulcanusMutation(s): 0 
Gene Names: psbX
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II reaction center protein ZS [auth Z], LA [auth z]62Thermosynechococcus vulcanusMutation(s): 0 
Gene Names: psbZ
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Small Molecules
Ligands 21 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DGD
Query on DGD

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AE [auth D] , BK [auth h] , KD [auth C] , LD [auth C] , MD [auth C] , PJ [auth d] , RE [auth H] , WI [auth c] , 
AE [auth D],  BK [auth h],  KD [auth C],  LD [auth C],  MD [auth C],  PJ [auth d],  RE [auth H],  WI [auth c],  XI [auth c],  YI [auth c]
DIGALACTOSYL DIACYL GLYCEROL (DGDG)
C51 H96 O15
LDQFLSUQYHBXSX-HXXRYREZSA-N
 Ligand Interaction
CLA
Query on CLA

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AD [auth C] , AH [auth b] , BD [auth C] , BH [auth b] , CD [auth C] , CH [auth b] , DD [auth C] , DH [auth b] , 
AD [auth C],  AH [auth b],  BD [auth C],  BH [auth b],  CD [auth C],  CH [auth b],  DD [auth C],  DH [auth b],  ED [auth C],  EH [auth b],  FD [auth C],  FH [auth b],  GD [auth C],  GG [auth a],  GH [auth b],  HD [auth C],  HG [auth a],  HH [auth b],  HI [auth c],  IG [auth a],  IH [auth b],  II [auth c],  JH [auth b],  JI [auth c],  KB [auth B],  KH [auth b],  KI [auth c],  LB [auth B],  LG [auth a],  LH [auth b],  LI [auth c],  LJ [auth d],  MB [auth B],  MH [auth b],  MI [auth c],  MJ [auth d],  NB [auth B],  NH [auth b],  NI [auth c],  OB [auth B],  OH [auth b],  OI [auth c],  PB [auth B],  PI [auth c],  QA [auth A],  QB [auth B],  QI [auth c],  RA [auth A],  RB [auth B],  RI [auth c],  SA [auth A],  SB [auth B],  SI [auth c],  TB [auth B],  TI [auth c],  UB [auth B],  VA [auth A],  VB [auth B],  VC [auth C],  WB [auth B],  WC [auth C],  WD [auth D],  XB [auth B],  XC [auth C],  XD [auth D],  YB [auth B],  YC [auth C],  ZB [auth B],  ZC [auth C],  ZG [auth b]
CHLOROPHYLL A
C55 H72 Mg N4 O5
VIQFHHZSLDFWDU-AENOIHSZSA-M
 Ligand Interaction
PHO
Query on PHO

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JG [auth a], KG [auth a], TA [auth A], UA [auth A]PHEOPHYTIN A
C55 H74 N4 O5
CQIKWXUXPNUNDV-RCBXBCQGSA-N
 Ligand Interaction
SQD
Query on SQD

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BE [auth D], DB [auth A], DC [auth B], DF [auth L], NG [auth a], XA [auth A], XJ [auth f], YF [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
 Ligand Interaction
LMG
Query on LMG

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AJ [auth c] , EC [auth B] , FE [auth D] , ND [auth C] , PG [auth a] , SH [auth b] , TJ [auth d] , VF [auth Z] , 
AJ [auth c],  EC [auth B],  FE [auth D],  ND [auth C],  PG [auth a],  SH [auth b],  TJ [auth d],  VF [auth Z],  YA [auth A],  ZI [auth c]
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
 Ligand Interaction
PL9
Query on PL9

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OJ [auth d], QG [auth a], ZA [auth A], ZD [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
 Ligand Interaction
LHG
Query on LHG

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BF [auth L] , CE [auth D] , DE [auth D] , EE [auth D] , KE [auth E] , MK [auth l] , OG [auth a] , QJ [auth d] , 
BF [auth L],  CE [auth D],  DE [auth D],  EE [auth D],  KE [auth E],  MK [auth l],  OG [auth a],  QJ [auth d],  RJ [auth d],  SJ [auth d]
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
 Ligand Interaction
HEM
Query on HEM

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NE [auth F], PF [auth V], VK [auth v], WJ [auth f]PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
RRX
Query on RRX

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AK [auth h], QE [auth H](3R)-beta,beta-caroten-3-ol
C40 H56 O
DMASLKHVQRHNES-FKKUPVFPSA-N
 Ligand Interaction
BCR
Query on BCR

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AC [auth B] , AF [auth K] , BC [auth B] , CC [auth B] , ID [auth C] , JD [auth C] , KK [auth k] , LK [auth k] , 
AC [auth B],  AF [auth K],  BC [auth B],  CC [auth B],  ID [auth C],  JD [auth C],  KK [auth k],  LK [auth k],  MF [auth T],  MG [auth a],  NJ [auth d],  PH [auth b],  QH [auth b],  RH [auth b],  RK [auth t],  UI [auth c],  VI [auth c],  WA [auth A],  YD [auth D],  ZE [auth K]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
 Ligand Interaction
LMT
Query on LMT

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AL [auth z] , BJ [auth c] , EB [auth A] , FC [auth B] , FF [auth M] , GF [auth M] , OD [auth C] , OE [auth F] , 
AL [auth z],  BJ [auth c],  EB [auth A],  FC [auth B],  FF [auth M],  GF [auth M],  OD [auth C],  OE [auth F],  OK [auth m],  PK [auth m],  SK [auth t],  TH [auth b],  UH [auth b],  WE [auth J],  WF [auth Z],  ZF [auth a]
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
 Ligand Interaction
OEX
Query on OEX

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BG [auth a], MA [auth A]CA-MN4-O5 CLUSTER
Ca Mn4 O5
SEXWDHMBWJEXOJ-UHFFFAOYSA-N
 Ligand Interaction
HTG
Query on HTG

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CJ [auth c] , DJ [auth c] , GC [auth B] , HC [auth B] , IC [auth B] , IE [auth D] , KF [auth O] , KJ [auth d] , 
CJ [auth c],  DJ [auth c],  GC [auth B],  HC [auth B],  IC [auth B],  IE [auth D],  KF [auth O],  KJ [auth d],  MC [auth B],  NC [auth B],  OF [auth U],  PD [auth C],  QD [auth C],  QF [auth V],  UK [auth u],  VH [auth b],  WG [auth b],  WH [auth b],  XG [auth b]
heptyl 1-thio-beta-D-glucopyranoside
C13 H26 O5 S
HPEGNLMTTNTJSP-LBELIVKGSA-N
 Ligand Interaction
SO4
Query on SO4

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JF [auth O]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

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BI [auth b] , CI [auth b] , CK [auth h] , DI [auth b] , EF [auth L] , EI [auth b] , FI [auth b] , GB [auth A] , 
BI [auth b],  CI [auth b],  CK [auth h],  DI [auth b],  EF [auth L],  EI [auth b],  FI [auth b],  GB [auth A],  GJ [auth c],  HB [auth A],  HJ [auth c],  IB [auth A],  IJ [auth c],  JE [auth D],  JJ [auth c],  LF [auth O],  NK [auth l],  PC [auth B],  QC [auth B],  RC [auth B],  RF [auth V],  SC [auth B],  SD [auth C],  SF [auth V],  TC [auth B],  TD [auth C],  TF [auth V],  TG [auth a],  UC [auth B],  UD [auth C],  UG [auth a],  VG [auth a],  WK [auth v],  XK [auth v],  YK [auth v],  ZJ [auth f]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
BCT
Query on BCT

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FG [auth a], VD [auth D]BICARBONATE ION
C H O3
BVKZGUZCCUSVTD-UHFFFAOYSA-M
 Ligand Interaction
FE2
Query on FE2

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CG [auth a], NA [auth A]FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

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GI [auth c], IF [auth O], JB [auth B], PE [auth F], QK [auth o], YG [auth b], YJ [auth f]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

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DG [auth a], EG [auth a], OA [auth A], PA [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
MG
Query on MG

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HK [auth j], VE [auth J]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
UNL
Query on UNL

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AB [auth A] , AG [auth a] , AI [auth b] , BB [auth A] , BL [auth z] , CB [auth A] , CF [auth L] , DK [auth i] , 
AB [auth A],  AG [auth a],  AI [auth b],  BB [auth A],  BL [auth z],  CB [auth A],  CF [auth L],  DK [auth i],  EJ [auth c],  EK [auth i],  FB [auth A],  FJ [auth c],  FK [auth i],  GE [auth D],  GK [auth i],  HE [auth D],  HF [auth M],  IK [auth j],  JC [auth B],  JK [auth j],  KC [auth B],  LC [auth B],  LE [auth E],  ME [auth E],  NF [auth T],  OC [auth B],  RD [auth C],  RG [auth a],  SE [auth H],  SG [auth a],  TE [auth I],  TK [auth t],  UE [auth I],  UF [auth X],  UJ [auth d],  VJ [auth e],  XE [auth J],  XF [auth Z],  XH [auth b],  YE [auth J],  YH [auth b],  ZH [auth b],  ZK [auth x]
Unknown ligand
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
HSK
Query on HSK
D, W [auth d]L-PEPTIDE LINKINGC6 H9 N3 O3HIS
FME
Query on FME
AA [auth i], H [auth I]L-PEPTIDE LINKINGC6 H11 N O3 SMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.156 
  • R-Value Observed: 0.158 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 122.19α = 90
b = 228.51β = 90
c = 286.4γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata scaling
XDSdata reduction
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-09-03
    Type: Initial release
  • Version 1.1: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Derived calculations, Structure summary