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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Ligand Structure Quality Assessment 


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 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.

Macromolecule Content 

  • Total Structure Weight: 725.27 kDa 
  • Atom Count: 54,036 
  • Modeled Residue Count: 5,243 
  • Deposited Residue Count: 5,344 
  • Unique protein chains: 19

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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Reference Sequence
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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 
UniProt
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Reference Sequence
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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 
UniProt
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Reference Sequence
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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 
UniProt
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome b559 subunit alphaE,
X [auth e]		83Thermostichus vulcanusMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Reference Sequence
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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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Reference Sequence
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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
Find proteins for P19052 (Thermostichus vulcanus)
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Reference Sequence
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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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Reference Sequence
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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 
UniProt
Find proteins for Q7DGD4 (Thermostichus vulcanus)
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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 
UniProt
Find proteins for P19054 (Thermostichus vulcanus)
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Reference Sequence
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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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Reference Sequence
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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 
UniProt
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Reference Sequence
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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 
UniProt
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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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Reference Sequence
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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 
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Find proteins for P56152 (Thermostichus vulcanus)
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Reference Sequence
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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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Reference Sequence
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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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Reference Sequence
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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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Reference Sequence
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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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Reference Sequence

Small Molecules

Ligands 21 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DGD

Query on DGD


Download:Ideal Coordinates CCD File
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


Download:Ideal Coordinates CCD File
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

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
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


Download:Ideal Coordinates CCD File
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


Download:Ideal Coordinates CCD File
JF [auth O]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL

Query on GOL


Download:Ideal Coordinates CCD File
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


Download:Ideal Coordinates CCD File
FG [auth a],
VD [auth D]		BICARBONATE ION
C H O3
BVKZGUZCCUSVTD-UHFFFAOYSA-M
FE2

Query on FE2


Download:Ideal Coordinates CCD File
CG [auth a],
NA [auth A]		FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
CA

Query on CA


Download:Ideal Coordinates CCD File
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


Download:Ideal Coordinates CCD File
DG [auth a],
EG [auth a],
OA [auth A],
PA [auth A]		CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG

Query on MG


Download:Ideal Coordinates CCD File
HK [auth j],
VE [auth J]		MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
UNL

Query on UNL


Download:Ideal Coordinates CCD File
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