5B66

Crystal structure analysis of Photosystem II complex

• PDB DOI: https://doi.org/10.2210/pdb5B66/pdb

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


• Deposited: 2016-05-25 Released: 2017-02-01 
• Deposition Author(s): Tanaka, A., Fukushima, Y., Kamiya, N.
• Funding Organization(s): Grants-in-Aid for Scientific Research

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 
  0.201 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.162 (Depositor), 0.160 (DCC) 
• R-Value Observed: 
  0.164 (Depositor) 

Starting Model: experimental

Literature

Two Different Structures of the Oxygen-Evolving Complex in the Same Polypeptide Frameworks of Photosystem II

Tanaka, A., Fukushima, Y., Kamiya, N.

(2017) J Am Chem Soc 139: 1718-1721

• PubMed: 28102667 
• DOI: https://doi.org/10.1021/jacs.6b09666
• Primary Citation of Related Structures:  
  5B5E, 5B66


• PubMed Abstract: 
  

  The oxygen-evolving complex (OEC) forms the heart of photosystem II (PSII) in photosynthesis. The crystal structure of PSII from Thermosynechococcus vulcanus has been reported at a resolution of 1.9 Å and at an averaged X-ray dose of 0.43 MGy. The OEC structure is suggested to be partially reduced to Mn(II) by EXAFS and DFT computational studies. Recently, the "radiation-damage-free" structures have been published at 1.95 Å resolution using XFEL, but reports continued to appear that the OEC is reduced to the S ₀ -state of the Kok cycle. To elucidate much more precise structure of the OEC, in this study two structures were determined at extremely low X-ray doses of 0.03 and 0.12 MGy using conventional synchrotron radiation source. The results indicated that the X-ray reduction effects on the OEC were very small in the low dose region below 0.12 MGy, that is, a threshold existed for the OEC structural changes caused by X-ray exposure. The OEC structures of the two identical monomers in the crystal were clearly different under the threshold of the radiation dose, although the surrounding polypeptide frameworks of PSII were the same. The assumption that the OECs in the crystal were in the dark-stable S ₁ -state of the Kok cycle should be re-evaluated.

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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 - A9B4C3D2E2F2G2H2I2J2K2L2M2N1O1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 744.33 kDa 
• Atom Count: 54,996 
• Modelled Residue Count: 5,234 
• Deposited Residue Count: 5,350 
• Unique protein chains: 19

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II protein D1	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 reaction center protein	B, U [auth b]	505	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 CP43 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]	65	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	AM [auth h], IF [auth H], KK [auth c], LK [auth c], MK [auth c], PE [auth D], RD [auth C], SD [auth C], TD [auth C], VL [auth d]	DIGALACTOSYL DIACYL GLYCEROL (DGDG) C51 H96 O15 LDQFLSUQYHBXSX-HXXRYREZSA-N
CLA	AK [auth c], BK [auth c], CD [auth C], CK [auth c], DD [auth C], DK [auth c], ED [auth C], EI [auth b], EK [auth c], FD [auth C], FI [auth b], FK [auth c], GD [auth C], GI [auth b], GK [auth c], HB [auth B], HD [auth C], HI [auth b], HK [auth c], HL [auth d], IB [auth B], ID [auth C], II [auth b], IK [auth c], IL [auth d], JB [auth B], JD [auth C], JI [auth b], JL [auth d], KB [auth B], KD [auth C], KE [auth D], KI [auth b], LB [auth B], LD [auth C], LE [auth D], LH [auth a], LI [auth b], MA [auth A], MB [auth B], MD [auth C], MH [auth a], MI [auth b], NA [auth A], NB [auth B], ND [auth C], NE [auth D], NI [auth b], OB [auth B], OD [auth C], OI [auth b], PA [auth A], PB [auth B], PH [auth a], PI [auth b], QB [auth B], QI [auth b], RB [auth B], RI [auth b], SB [auth B], SI [auth b], TB [auth B], TI [auth b], UB [auth B], VB [auth B], WB [auth B], WJ [auth c], XJ [auth c], YJ [auth c], ZJ [auth c]	CHLOROPHYLL A C55 H72 Mg N4 O5 ATNHDLDRLWWWCB-AENOIHSZSA-M
PHO	ME [auth D], NH [auth a], OA [auth A], OH [auth a]	PHEOPHYTIN A C55 H74 N4 O5 CQIKWXUXPNUNDV-RCBXBCQGSA-N
SQD	FF [auth F], JH [auth a], PM [auth l], RA [auth A], RH [auth a], XA [auth A], XI [auth b], YL [auth f]	1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL C41 H78 O12 S RVUUQPKXGDTQPG-JUDHQOGESA-N
LMG	AC [auth B], HM [auth j], NK [auth c], OK [auth c], SA [auth A], SF [auth J], SH [auth a], UD [auth C], YI [auth b], ZD [auth C]	1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE C45 H86 O10 DCLTVZLYPPIIID-CVELTQQQSA-N
PL9	RL [auth d], VE [auth D], WA [auth A], XH [auth a]	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	BG [auth L], DF [auth E], LL [auth d], ML [auth d], NL [auth d], QE [auth D], QM [auth l], RE [auth D], SE [auth D]	1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE C38 H75 O10 P BIABMEZBCHDPBV-MPQUPPDSSA-N
HEC	HN [auth v], XG [auth V]	HEME C C34 H34 Fe N4 O4 HXQIYSLZKNYNMH-LJNAALQVSA-N
HEM	EF [auth E], XL [auth e]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
RRX	HF [auth H], RN [auth x]	(3R)-beta,beta-caroten-3-ol C40 H56 O DMASLKHVQRHNES-FKKUPVFPSA-N
BCR	AG [auth K], BN [auth t], IM [auth j], JK [auth c], KL [auth d], NM [auth k], OE [auth D], OM [auth k], PD [auth C], QA [auth A], QD [auth C], QG [auth T], QH [auth a], UI [auth b], VI [auth b], WI [auth b], XB [auth B], YB [auth B], ZB [auth B], ZF [auth K]	BETA-CAROTENE C40 H56 OENHQHLEOONYIE-JLTXGRSLSA-N
LMT	AI [auth a], BF [auth E], CJ [auth b], DG [auth M], DJ [auth b], FC [auth B], GC [auth B], HC [auth B], HH [auth Z], MF [auth I], RG [auth T], RM [auth m], SK [auth c], SM [auth m], UF [auth J], UN [auth z], ZL [auth f]	DODECYL-BETA-D-MALTOSIDE C24 H46 O11 NLEBIOOXCVAHBD-QKMCSOCLSA-N
OEX	BI [auth a], FB [auth A]	CA-MN4-O5 CLUSTER Ca Mn4 O5 SEXWDHMBWJEXOJ-UHFFFAOYSA-N
HTG	AF [auth D], AJ [auth b], BC [auth B], CC [auth B], CI [auth b], DC [auth B], DI [auth b], DN [auth u], GG [auth O], GL [auth d], JE [auth C], LC [auth B], MC [auth B], PK [auth c], QK [auth c], QN [auth v], VD [auth C], WD [auth C], XD [auth C], YG [auth V], ZI [auth b]	heptyl 1-thio-beta-D-glucopyranoside C13 H26 O5 S HPEGNLMTTNTJSP-LBELIVKGSA-N
DMS	AB [auth A], AE [auth C], AH [auth V], AL [auth c], AN [auth o], BB [auth A], BE [auth C], BH [auth V], BL [auth c], BM [auth h], CB [auth A], CE [auth C], CH [auth V], CL [auth c], DB [auth A], DE [auth C], DH [auth V], DL [auth c], EE [auth C], EH [auth V], EL [auth c], EN [auth u], FE [auth C], FH [auth V], FL [auth c], FN [auth u], GE [auth C], GF [auth F], GJ [auth b], GM [auth i], GN [auth u], HE [auth C], HG [auth O], HJ [auth b], IE [auth C], IG [auth O], IJ [auth b], IN [auth v], JF [auth H], JG [auth O], JJ [auth b], JN [auth v], KG [auth O], KJ [auth b], KN [auth v], LG [auth O], LJ [auth b], LM [auth j], LN [auth v], MG [auth O], MJ [auth b], MN [auth v], NG [auth O], NJ [auth b], NN [auth v], OC [auth B], OG [auth O], OJ [auth b], ON [auth v], PC [auth B], PG [auth O], PJ [auth b], PN [auth v], QC [auth B], QJ [auth b], RC [auth B], SC [auth B], SL [auth d], TC [auth B], TL [auth d], UC [auth B], UG [auth U], UL [auth d], UM [auth o], VC [auth B], VG [auth U], VM [auth o], WC [auth B], WE [auth D], WG [auth U], WK [auth c], WM [auth o], XC [auth B], XE [auth D], XK [auth c], XM [auth o], YC [auth B], YE [auth D], YK [auth c], YM [auth o], ZA [auth A], ZC [auth B], ZE [auth D], ZK [auth c], ZM [auth o]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N
BCT	GB [auth A], VH [auth a]	BICARBONATE ION C H O3 BVKZGUZCCUSVTD-UHFFFAOYSA-M
FE2	EB [auth A], ZH [auth a]	FE (II) ION Fe CWYNVVGOOAEACU-UHFFFAOYSA-N
CA	BJ [auth b], EC [auth B], FG [auth O], RK [auth c], TM [auth o], ZG [auth V]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL	TA [auth A], TH [auth a], UA [auth A], UH [auth a]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	JM [auth j], TF [auth J]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N
UNL	AD [auth B], BD [auth B], CF [auth E], CG [auth L], CM [auth h], CN [auth t], DM [auth i], EG [auth M], EJ [auth b], EM [auth i], FJ [auth b], FM [auth i], GH [auth X], IC [auth B], IH [auth Z], JC [auth B], KC [auth B], KF [auth H], KH [auth a], KM [auth j], LF [auth H], MM [auth j], NC [auth B], NF [auth I], OF [auth I], OL [auth d], PF [auth I], PL [auth d], QF [auth I], QL [auth d], RF [auth I], RJ [auth b], SG [auth T], SJ [auth b], SN [auth x], TE [auth D], TG [auth U], TJ [auth b], TK [auth c], TN [auth z], UE [auth D], UJ [auth b], UK [auth c], VA [auth A], VF [auth J], VJ [auth b], VK [auth c], WF [auth J], WH [auth a], WL [auth e], XF [auth J], YA [auth A], YD [auth C], YF [auth J], YH [auth a]	Unknown ligand JLVVSXFLKOJNIY-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
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: 1.85 Å
• R-Value Free:  0.201 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.162 (Depositor), 0.160 (DCC) 
• R-Value Observed: 0.164 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 121.465	α = 90
b = 228.176	β = 90
c = 286.422	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2017-02-01 
Deposition Author(s): Tanaka, A., Fukushima, Y., Kamiya, N.

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Funding Organization	Location	Grant Number
Grants-in-Aid for Scientific Research	Japan	H24227002

Revision History  

• Version 1.0: 2017-02-01
  Type: Initial release
  
• Version 1.1: 2017-02-22
  Changes: Database references
• Version 2.0: 2019-10-09
  Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
• Version 2.1: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Derived calculations, Structure summary
• Version 3.0: 2023-11-08
  Changes: Data collection, Database references, Non-polymer description, Refinement description, Structure summary
• Version 3.1: 2024-10-23
  Changes: Structure summary