6JLJ

XFEL structure of cyanobacterial photosystem II (dark state, dataset1)

• PDB DOI: https://doi.org/10.2210/pdb6JLJ/pdb

• Classification: PHOTOSYNTHESIS
• Organism(s): Thermostichus vulcanus
• Mutation(s): No 
• Membrane Protein: Yes  PDBTMmpstruc


• Deposited: 2019-03-06 Released: 2019-10-16 
• Deposition Author(s): Suga, M., Shen, J.R.
• Funding Organization(s): Japan Society for the Promotion of Science

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 
  0.198 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.152 (Depositor), 0.150 (DCC) 
• R-Value Observed: 
  0.154 (Depositor) 

Starting Model: experimental

Literature

An oxyl/oxo mechanism for oxygen-oxygen coupling in PSII revealed by an x-ray free-electron laser.

Suga, M., Akita, F., Yamashita, K., Nakajima, Y., Ueno, G., Li, H., Yamane, T., Hirata, K., Umena, Y., Yonekura, S., Yu, L.J., Murakami, H., Nomura, T., Kimura, T., Kubo, M., Baba, S., Kumasaka, T., Tono, K., Yabashi, M., Isobe, H., Yamaguchi, K., Yamamoto, M., Ago, H., Shen, J.R.

(2019) Science 366: 334-338

• PubMed: 31624207 
• DOI: https://doi.org/10.1126/science.aax6998
• Primary Citation of Related Structures:  
  6JLJ, 6JLK, 6JLL, 6JLM, 6JLN, 6JLO, 6JLP


• PubMed Abstract: 
  

  Photosynthetic water oxidation is catalyzed by the Mn ₄ CaO ₅ cluster of photosystem II (PSII) with linear progression through five S-state intermediates (S ₀ to S ₄ ). To reveal the mechanism of water oxidation, we analyzed structures of PSII in the S ₁ , S ₂ , and S ₃ states by x-ray free-electron laser serial crystallography. No insertion of water was found in S ₂ , but flipping of D1 Glu ¹⁸⁹ upon transition to S ₃ leads to the opening of a water channel and provides a space for incorporation of an additional oxygen ligand, resulting in an open cubane Mn ₄ CaO ₆ cluster with an oxyl/oxo bridge. Structural changes of PSII between the different S states reveal cooperative action of substrate water access, proton release, and dioxygen formation in photosynthetic water oxidation.

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Organizational Affiliation: 

Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University, 3-1-1 Tsushima Naka, Okayama 700-8530, Japan. [e-mail] [e-mail] [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 39-mer - A2B2C2D2E2F2G2H2I2J2K2L2M2N2O2P2Q2R2S2T1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 39-mer - A8B4C4D2E2F2G2H2I2J2K2L2M2N1O1P1 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Hetero 38-mer - A2B2C2D2E2F2G2H2I2J2K2L2M2N2O2P2Q2R2S2 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Hetero 38-mer - A2B2C2D2E2F2G2H2I2J2K2L2M2N2O2P2Q2R2S2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 729.59 kDa 
• Atom Count: 54,101 
• Modelled Residue Count: 5,293 
• Deposited Residue Count: 5,384 
• Unique protein chains: 20

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II protein D1	A, U [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, V [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, W [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, X [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, Y [auth e]	84	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, Z [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	AA [auth h], G [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	BA [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	CA [auth j], I [auth J]	39	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	DA [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	EA [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	FA [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	GA [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	HA [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	IA [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	JA [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	KA [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	LA [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	MA [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

Entity ID: 20
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II protein Y	T [auth R]	34	Thermostichus vulcanus	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for P0DM37 (Thermostichus vulcanus) Explore P0DM37  Go to UniProtKB:  P0DM37

Small Molecules

Ligands 19 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DGD	CJ [auth e], GD [auth C], GI [auth c], HD [auth C], HI [auth c], ID [auth C], II [auth c], KJ [auth h], LE [auth H], XD [auth D]	DIGALACTOSYL DIACYL GLYCEROL (DGDG) C51 H96 O15 LDQFLSUQYHBXSX-HXXRYREZSA-N
CLA	AD [auth C], AH [auth b], AI [auth c], BD [auth C], BH [auth b], BI [auth c], CD [auth C], CH [auth b], CI [auth c], DD [auth C], DH [auth b], DI [auth c], EH [auth b], EI [auth c], FH [auth b], HB [auth B], IB [auth B], JB [auth B], KB [auth B], LB [auth B], MB [auth B], NB [auth B], OB [auth B], PB [auth B], QB [auth B], QG [auth b], QI [auth d], RA [auth A], RB [auth B], RC [auth C], RG [auth b], RI [auth d], SA [auth A], SB [auth B], SC [auth C], SG [auth b], SH [auth c], SI [auth d], TA [auth A], TB [auth B], TC [auth C], TD [auth D], TG [auth b], TH [auth c], UB [auth B], UC [auth C], UD [auth D], UG [auth b], UH [auth c], VA [auth A], VB [auth B], VC [auth C], VG [auth b], VH [auth c], WB [auth B], WC [auth C], WF [auth a], WG [auth b], WH [auth c], XC [auth C], XF [auth a], XG [auth b], XH [auth c], YC [auth C], YG [auth b], YH [auth c], ZC [auth C], ZF [auth a], ZG [auth b], ZH [auth c]	CHLOROPHYLL A C55 H72 Mg N4 O5 ATNHDLDRLWWWCB-AENOIHSZSA-M
PHO	PI [auth d], SD [auth D], UA [auth A], YF [auth a]	PHEOPHYTIN A C55 H74 N4 O5 CQIKWXUXPNUNDV-RCBXBCQGSA-N
SQD	AC [auth B], BB [auth A], BG [auth a], GJ [auth f], IE [auth F], SE [auth L], SF [auth a], XA [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	CG [auth a], DK [auth z], JD [auth C], JH [auth b], JI [auth c], KD [auth C], KI [auth c], MJ [auth j], NE [auth J], NF [auth Z], QC [auth C], TE [auth M]	1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE C45 H86 O10 DCLTVZLYPPIIID-CVELTQQQSA-N
PL9	DG [auth a], EB [auth A], UI [auth d], WD [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	AE [auth D], DJ [auth e], EE [auth E], QJ [auth l], RE [auth L], VI [auth d], WI [auth d], XI [auth d], YD [auth D], ZD [auth D]	1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE C38 H75 O10 P BIABMEZBCHDPBV-MPQUPPDSSA-N
HEM	BK [auth v], EJ [auth e], FE [auth E], JF [auth V]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
BCR	AG [auth a], CF [auth T], CK [auth y], ED [auth C], FD [auth C], FI [auth c], GH [auth b], HH [auth b], IH [auth b], JJ [auth h], KE [auth H], LF [auth Y], OI [auth c], PJ [auth k], QE [auth K], TI [auth d], VD [auth D], VJ [auth t], WA [auth A], XB [auth B], YB [auth B], ZB [auth B]	BETA-CAROTENE C40 H56 OENHQHLEOONYIE-JLTXGRSLSA-N
LMT	BC [auth B], CB [auth A], DF [auth T], GG [auth a], HE [auth F], HJ [auth f], KH [auth b], LD [auth C], OC [auth B], RF [auth a], SJ [auth m], UE [auth M], WE [auth M], XE [auth M]	DODECYL-BETA-D-MALTOSIDE C24 H46 O11 NLEBIOOXCVAHBD-QKMCSOCLSA-N
OEX	DB [auth A], EG [auth a]	CA-MN4-O5 CLUSTER Ca Mn4 O5 SEXWDHMBWJEXOJ-UHFFFAOYSA-N
HTG	AJ [auth d], CC [auth B], DC [auth B], DE [auth D], EC [auth B], HG [auth b], KF [auth V], LC [auth B], LH [auth b], LI [auth c], MC [auth B], MD [auth C], MH [auth b], MI [auth c], ND [auth C], NG [auth b], OG [auth b]	heptyl 1-thio-beta-D-glucopyranoside C13 H26 O5 S HPEGNLMTTNTJSP-LBELIVKGSA-N
GOL	AB [auth A], AF [auth T], BF [auth T], FC [auth B], FF [auth V], FJ [auth f], GC [auth B], GE [auth F], GF [auth V], HC [auth B], HF [auth V], IC [auth B], IF [auth V], IG [auth b], JC [auth B], JG [auth b], KC [auth B], KG [auth b], LG [auth b], MG [auth b], OD [auth C], OF [auth a], OH [auth c], PC [auth B], PD [auth C], PF [auth a], PH [auth c], TJ [auth o], WJ [auth t], XJ [auth v], YA [auth A], YE [auth O], YJ [auth v], ZA [auth A], ZJ [auth v]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
BCT	FG [auth a], QA [auth A]	BICARBONATE ION C H O3 BVKZGUZCCUSVTD-UHFFFAOYSA-M
FE2	NA [auth A], TF [auth a]	FE (II) ION Fe CWYNVVGOOAEACU-UHFFFAOYSA-N
CA	GB [auth B], IJ [auth f], JE [auth F], PG [auth b], QD [auth C], QH [auth c], RH [auth c], UJ [auth o], ZE [auth O]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL	AK [auth v], EF [auth U], OA [auth A], PA [auth A], UF [auth a], VF [auth a]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	OJ [auth j], PE [auth J]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N
UNL	BE [auth D], BJ [auth d], CE [auth D], FB [auth A], LJ [auth i], ME [auth I], MF [auth X], NC [auth B], NH [auth b], NI [auth c], NJ [auth j], OE [auth J], QF [auth a], RD [auth C], RJ [auth m], VE [auth M], YI [auth d], ZI [auth d]	Unknown ligand JLVVSXFLKOJNIY-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
FME	BA [auth i], H [auth I]	L-PEPTIDE LINKING	C6 H11 N O3 S		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free:  0.198 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.152 (Depositor), 0.150 (DCC) 
• R-Value Observed: 0.154 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 121.97	α = 90
b = 228.72	β = 90
c = 286.98	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
CrystFEL	data reduction
CrystFEL	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-10-16 
Deposition Author(s): Suga, M., Shen, J.R.

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Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science	Japan	--

Revision History  

• Version 1.0: 2019-10-16
  Type: Initial release
  
• Version 1.1: 2019-10-30
  Changes: Data collection, Database references
• Version 1.2: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Derived calculations, Structure summary
• Version 2.0: 2023-11-22
  Changes: Advisory, Data collection, Database references, Non-polymer description, Refinement description, Structure summary
• Version 2.1: 2024-10-30
  Changes: Structure summary