3WU2 | pdb_00003wu2

Crystal structure analysis of Photosystem II complex

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 
    0.194 (Depositor), 0.194 (DCC) 
  • R-Value Work: 
    0.156 (Depositor), 0.157 (DCC) 
  • R-Value Observed: 
    0.158 (Depositor) 

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This is version 3.0 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: https://doi.org/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. 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
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem Q(B) proteinA,
T [auth a]		344Thermostichus vulcanusMutation(s): 0 
EC: 1.10.3.9
Membrane Entity: Yes 
UniProt
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II CP47 chlorophyll apoproteinB,
U [auth b]		504Thermostichus vulcanusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II 44 kDa reaction center proteinC,
V [auth c]		455Thermostichus vulcanusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II D2 proteinD,
W [auth d]		342Thermostichus vulcanusMutation(s): 0 
EC: 1.10.3.9
Membrane Entity: Yes 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b559 subunit alphaE,
X [auth e]		83Thermostichus vulcanusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b559 subunit betaF,
Y [auth f]		44Thermostichus vulcanusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein HG [auth H],
Z [auth h]		63Thermostichus vulcanusMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein IAA [auth i],
H [auth I]		38Thermostichus vulcanusMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein JBA [auth j],
I [auth J]		40Thermostichus vulcanusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein KCA [auth k],
J [auth K]		37Thermostichus vulcanusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein LDA [auth l],
K [auth L]		37Thermostichus vulcanusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein MEA [auth m],
L [auth M]		36Thermostichus vulcanusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II manganese-stabilizing polypeptideFA [auth o],
M [auth O]		244Thermostichus vulcanusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein TGA [auth t],
N [auth T]		32Thermostichus vulcanusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II 12 kDa extrinsic proteinHA [auth u],
O [auth U]		104Thermostichus vulcanusMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c-550IA [auth v],
P [auth V]		137Thermostichus vulcanusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein Ycf12JA [auth y],
Q [auth Y]		30Thermostichus vulcanusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein XKA [auth x],
R [auth X]		40Thermostichus vulcanusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein ZLA [auth z],
S [auth Z]		62Thermostichus vulcanusMutation(s): 0 
Membrane Entity: Yes 
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Small Molecules
Ligands 21 Unique
IDChains Name / 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]
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
CLA
Query on CLA
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AD [auth C]
AH [auth b]
BD [auth C]
BH [auth b]
CD [auth C]
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
ATNHDLDRLWWWCB-AENOIHSZSA-M
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
SQD
Query on SQD
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BE [auth D]
DB [auth A]
DC [auth B]
DF [auth L]
NG [auth a]
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
LMG
Query on LMG
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AJ [auth c]
EC [auth B]
FE [auth D]
ND [auth C]
PG [auth a]
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
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
LHG
Query on LHG
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BF [auth L]
CE [auth D]
DE [auth D]
EE [auth D]
KE [auth E]
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
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
RRX
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AK [auth h],
QE [auth H]		(3R)-beta,beta-caroten-3-ol
C40 H56 O
DMASLKHVQRHNES-FKKUPVFPSA-N
BCR
Query on BCR
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AC [auth B]
AF [auth K]
BC [auth B]
CC [auth B]
ID [auth C]
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
LMT
Query on LMT
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AL [auth z]
BJ [auth c]
EB [auth A]
FC [auth B]
FF [auth M]
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
OEX
Query on OEX
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BG [auth a],
MA [auth A]		CA-MN4-O5 CLUSTER
Ca Mn4 O5
SEXWDHMBWJEXOJ-UHFFFAOYSA-N
HTG
Query on HTG
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CJ [auth c]
DJ [auth c]
GC [auth B]
HC [auth B]
IC [auth B]
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
SO4
Query on SO4
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JF [auth O]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL
Query on GOL
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BI [auth b]
CI [auth b]
CK [auth h]
DI [auth b]
EF [auth L]
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
BCT
Query on BCT
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FG [auth a],
VD [auth D]		BICARBONATE ION
C H O3
BVKZGUZCCUSVTD-UHFFFAOYSA-M
FE2
Query on FE2
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CG [auth a],
NA [auth A]		FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
CA
Query on CA
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GI [auth c]
IF [auth O]
JB [auth B]
PE [auth F]
QK [auth o]
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
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
MG
Query on MG
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HK [auth j],
VE [auth J]		MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
UNL
Query on UNL
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AB [auth A]
AG [auth a]
AI [auth b]
BB [auth A]
BL [auth z]
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
Modified Residues  2 Unique
IDChains TypeFormula2D 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 (Depositor), 0.194 (DCC) 
  • R-Value Work:  0.156 (Depositor), 0.157 (DCC) 
  • R-Value Observed: 0.158 (Depositor) 
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

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Ligand Structure Quality Assessment 


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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
  • Version 2.0: 2025-03-26
    Changes: Data collection, Database references, Derived calculations, Non-polymer description, Structure summary
  • Version 3.0: 2025-07-30
    Changes: Advisory, Atomic model, Data collection