3WU2

Crystal structure analysis of Photosystem II complex

• PDB DOI: https://doi.org/10.2210/pdb3WU2/pdb
• Entry: 3WU2 supersedes: 3ARC

• Classification: ELECTRON TRANSPORT, PHOTOSYNTHESIS
• Organism(s): Thermostichus vulcanus
• Mutation(s): No 
• Membrane Protein: Yes  OPMPDBTMMemProtMD


• Deposited: 2014-04-21 Released: 2014-09-03 
• Deposition Author(s): Umena, Y., Kawakami, K., Shen, J.R., Kamiya, N.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.194 (Depositor), 0.190 (DCC) 
• R-Value Work: 
  0.156 (Depositor), 0.160 (DCC) 
• R-Value Observed: 
  0.158 (Depositor) 

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

• PubMed: 21499260 
• 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 38-mer - A2B2C2D2E2F2G2H2I2J2K2L2M2N2O2P2Q2R2S2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 38-mer - A9B4C2D2E2F2G2H2I2J2K2L2M2N1O1P1 

Biological assembly 1 assigned by authors.

Macromolecule Content

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem Q(B) protein	A, T [auth a]	344	Thermostichus vulcanus	Mutation(s): 0  EC: 1.10.3.9 Membrane Entity: Yes
UniProt
Find proteins for P51765 (Thermostichus vulcanus) Explore P51765  Go to UniProtKB:  P51765

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II CP47 chlorophyll apoprotein	B, U [auth b]	504	Thermostichus vulcanus	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for D0VWR1 (Thermostichus vulcanus) Explore D0VWR1  Go to UniProtKB:  D0VWR1

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II 44 kDa reaction center protein	C, V [auth c]	455	Thermostichus vulcanus	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for D0VWR7 (Thermostichus vulcanus) Explore D0VWR7  Go to UniProtKB:  D0VWR7

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II D2 protein	D, W [auth d]	342	Thermostichus vulcanus	Mutation(s): 0  EC: 1.10.3.9 Membrane Entity: Yes
UniProt
Find proteins for D0VWR8 (Thermostichus vulcanus) Explore D0VWR8  Go to UniProtKB:  D0VWR8

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome b559 subunit alpha	E, X [auth e]	83	Thermostichus vulcanus	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for P12238 (Thermostichus vulcanus) Explore P12238  Go to UniProtKB:  P12238

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome b559 subunit beta	F, Y [auth f]	44	Thermostichus vulcanus	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for P12239 (Thermostichus vulcanus) Explore P12239  Go to UniProtKB:  P12239

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II reaction center protein H	G [auth H], Z [auth h]	63	Thermostichus vulcanus	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for P19052 (Thermostichus vulcanus) Explore P19052  Go to UniProtKB:  P19052

Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II reaction center protein I	AA [auth i], H [auth I]	38	Thermostichus vulcanus	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for P12240 (Thermostichus vulcanus) Explore P12240  Go to UniProtKB:  P12240

Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II reaction center protein J	BA [auth j], I [auth J]	40	Thermostichus vulcanus	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for Q7DGD4 (Thermostichus vulcanus) Explore Q7DGD4  Go to UniProtKB:  Q7DGD4

Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II reaction center protein K	CA [auth k], J [auth K]	37	Thermostichus vulcanus	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for P19054 (Thermostichus vulcanus) Explore P19054  Go to UniProtKB:  P19054

Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II reaction center protein L	DA [auth l], K [auth L]	37	Thermostichus vulcanus	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for P12241 (Thermostichus vulcanus) Explore P12241  Go to UniProtKB:  P12241

Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II reaction center protein M	EA [auth m], L [auth M]	36	Thermostichus vulcanus	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for P12312 (Thermostichus vulcanus) Explore P12312  Go to UniProtKB:  P12312

Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II manganese-stabilizing polypeptide	FA [auth o], M [auth O]	244	Thermostichus vulcanus	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for D0VWR2 (Thermostichus vulcanus) Explore D0VWR2  Go to UniProtKB:  D0VWR2

Entity ID: 14
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II reaction center protein T	GA [auth t], N [auth T]	32	Thermostichus vulcanus	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for P12313 (Thermostichus vulcanus) Explore P12313  Go to UniProtKB:  P12313

Entity ID: 15
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II 12 kDa extrinsic protein	HA [auth u], O [auth U]	104	Thermostichus vulcanus	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for P56152 (Thermostichus vulcanus) Explore P56152  Go to UniProtKB:  P56152

Entity ID: 16
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c-550	IA [auth v], P [auth V]	137	Thermostichus vulcanus	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for P0A387 (Thermostichus vulcanus) Explore P0A387  Go to UniProtKB:  P0A387

Entity ID: 17
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II reaction center protein Ycf12	JA [auth y], Q [auth Y]	30	Thermostichus vulcanus	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for D0VWR3 (Thermostichus vulcanus) Explore D0VWR3  Go to UniProtKB:  D0VWR3

Entity ID: 18
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II reaction center protein X	KA [auth x], R [auth X]	40	Thermostichus vulcanus	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for D0VWR4 (Thermostichus vulcanus) Explore D0VWR4  Go to UniProtKB:  D0VWR4

Entity ID: 19
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II reaction center protein Z	LA [auth z], S [auth Z]	62	Thermostichus vulcanus	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for D0VWR5 (Thermostichus vulcanus) Explore D0VWR5  Go to UniProtKB:  D0VWR5

Small Molecules

Ligands 21 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DGD	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	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	JG [auth a], KG [auth a], TA [auth A], UA [auth A]	PHEOPHYTIN A C55 H74 N4 O5 CQIKWXUXPNUNDV-RCBXBCQGSA-N
SQD	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	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	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	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	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	AK [auth h], QE [auth H]	(3R)-beta,beta-caroten-3-ol C40 H56 O DMASLKHVQRHNES-FKKUPVFPSA-N
BCR	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	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	BG [auth a], MA [auth A]	CA-MN4-O5 CLUSTER Ca Mn4 O5 SEXWDHMBWJEXOJ-UHFFFAOYSA-N
HTG	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	JF [auth O]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	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	FG [auth a], VD [auth D]	BICARBONATE ION C H O3 BVKZGUZCCUSVTD-UHFFFAOYSA-M
FE2	CG [auth a], NA [auth A]	FE (II) ION Fe CWYNVVGOOAEACU-UHFFFAOYSA-N
CA	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	DG [auth a], EG [auth a], OA [auth A], PA [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	HK [auth j], VE [auth J]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N
UNL	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
ID	Chains	Type	Formula	2D Diagram	Parent
HSK	D, W [auth d]	L-PEPTIDE LINKING	C6 H9 N3 O3		HIS
FME	AA [auth i], H [auth I]	L-PEPTIDE LINKING	C6 H11 N O3 S		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.194 (Depositor), 0.190 (DCC) 
• R-Value Work:  0.156 (Depositor), 0.160 (DCC) 
• R-Value Observed: 0.158 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 122.19	α = 90
b = 228.51	β = 90
c = 286.4	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data scaling
XDS	data reduction
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-09-03 
Deposition Author(s): Umena, Y., Kawakami, K., Shen, J.R., Kamiya, N.
• This entry supersedes: 3ARC

Revision History  

• 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