6JLK

XFEL structure of cyanobacterial photosystem II (1F state, dataset1)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.149 
  • R-Value Observed: 0.151 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 2.0 of the entry. See complete history


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

  • 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.


  • 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. michisuga@okayama-u.ac.jp ago@spring8.or.jp shen@cc.okayama-u.ac.jp.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II protein D1A,
U [auth a]
344Thermostichus vulcanusMutation(s): 0 
EC: 1.10.3.9
Membrane Entity: Yes 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II CP47 reaction center proteinB,
V [auth b]
505Thermostichus vulcanusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II CP43 reaction center proteinC,
W [auth c]
455Thermostichus vulcanusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II D2 proteinD,
X [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,
Y [auth e]
84Thermostichus vulcanusMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b559 subunit betaF,
Z [auth f]
44Thermostichus vulcanusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein HAA [auth h],
G [auth H]
65Thermostichus vulcanusMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein IBA [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 JCA [auth j],
I [auth J]
39Thermostichus vulcanusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein KDA [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 LEA [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 MFA [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 polypeptideGA [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 THA [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 proteinIA [auth u],
O [auth U]
104Thermostichus vulcanusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P56152 (Thermostichus vulcanus)
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c-550JA [auth v],
P [auth V]
137Thermostichus vulcanusMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein Ycf12KA [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 XLA [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 ZMA [auth z],
S [auth Z]
62Thermostichus vulcanusMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II protein YT [auth R]34Thermostichus vulcanusMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Small Molecules
Ligands 19 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DGD
Query on DGD

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EJ [auth e]
ID [auth C]
II [auth c]
JD [auth C]
JI [auth c]
EJ [auth e],
ID [auth C],
II [auth c],
JD [auth C],
JI [auth c],
KD [auth C],
KI [auth c],
LJ [auth h],
NE [auth H],
ZD [auth D]
DIGALACTOSYL DIACYL GLYCEROL (DGDG)
C51 H96 O15
LDQFLSUQYHBXSX-HXXRYREZSA-N
CLA
Query on CLA

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AD [auth C]
AH [auth b]
AI [auth c]
BD [auth C]
BH [auth b]
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],
ED [auth C],
EH [auth b],
EI [auth c],
FD [auth C],
FH [auth b],
FI [auth c],
GI [auth c],
KB [auth B],
LB [auth B],
MB [auth B],
NB [auth B],
OB [auth B],
PB [auth B],
QB [auth B],
QG [auth b],
RA [auth A],
RB [auth B],
RG [auth b],
RI [auth d],
SA [auth A],
SB [auth B],
SG [auth b],
SI [auth d],
TA [auth A],
TB [auth B],
TC [auth C],
TG [auth b],
TI [auth d],
UB [auth B],
UC [auth C],
UG [auth b],
UH [auth c],
VB [auth B],
VC [auth C],
VD [auth D],
VF [auth a],
VG [auth b],
VH [auth c],
WA [auth A],
WB [auth B],
WC [auth C],
WD [auth D],
WF [auth a],
WG [auth b],
WH [auth c],
XB [auth B],
XC [auth C],
XG [auth b],
XH [auth c],
YB [auth B],
YC [auth C],
YF [auth a],
YG [auth b],
YH [auth c],
ZB [auth B],
ZC [auth C],
ZG [auth b],
ZH [auth c]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
PHO
Query on PHO

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EG [auth a],
UA [auth A],
VA [auth A],
XF [auth a]
PHEOPHYTIN A
C55 H74 N4 O5
CQIKWXUXPNUNDV-RCBXBCQGSA-N
SQD
Query on SQD

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AG [auth a]
CB [auth A]
DC [auth B]
HJ [auth f]
KE [auth F]
AG [auth a],
CB [auth A],
DC [auth B],
HJ [auth f],
KE [auth F],
RF [auth a],
TE [auth L],
YA [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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DJ [auth d]
DK [auth z]
EC [auth B]
GE [auth D]
HB [auth A]
DJ [auth d],
DK [auth z],
EC [auth B],
GE [auth D],
HB [auth A],
JH [auth b],
LD [auth C],
LI [auth c],
MD [auth C],
MF [auth Z],
MI [auth c],
PH [auth c]
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
PL9
Query on PL9

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BG [auth a],
FB [auth A],
VI [auth d],
YD [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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AE [auth D]
BE [auth D]
CE [auth D]
FJ [auth e]
HE [auth E]
AE [auth D],
BE [auth D],
CE [auth D],
FJ [auth e],
HE [auth E],
OH [auth b],
SE [auth L],
WI [auth d],
XI [auth d],
YI [auth d]
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
HEM
Query on HEM

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BK [auth v],
GJ [auth e],
IF [auth V],
JE [auth F]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
BCR
Query on BCR

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AC [auth B]
BC [auth B]
BF [auth T]
CC [auth B]
CK [auth y]
AC [auth B],
BC [auth B],
BF [auth T],
CC [auth B],
CK [auth y],
GD [auth C],
GH [auth b],
HD [auth C],
HH [auth b],
HI [auth c],
IH [auth b],
KF [auth Y],
KJ [auth h],
ME [auth H],
PJ [auth k],
QI [auth c],
RE [auth K],
UI [auth d],
VJ [auth t],
XA [auth A],
XD [auth D],
ZF [auth a]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
LMT
Query on LMT

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CF [auth T]
DB [auth A]
FG [auth a]
IE [auth F]
IJ [auth f]
CF [auth T],
DB [auth A],
FG [auth a],
IE [auth F],
IJ [auth f],
KH [auth b],
ND [auth C],
QF [auth a],
RC [auth B],
RJ [auth m],
SJ [auth m],
UD [auth D],
UE [auth M],
WE [auth M]
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
OEX
Query on OEX

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CG [auth a],
EB [auth A]
CA-MN4-O5 CLUSTER
Ca Mn4 O5
SEXWDHMBWJEXOJ-UHFFFAOYSA-N
HTG
Query on HTG

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BJ [auth d]
FC [auth B]
FE [auth D]
GC [auth B]
HC [auth B]
BJ [auth d],
FC [auth B],
FE [auth D],
GC [auth B],
HC [auth B],
HG [auth b],
JF [auth V],
LH [auth b],
MH [auth b],
NG [auth b],
NI [auth c],
OC [auth B],
OD [auth C],
OG [auth b],
OI [auth c],
PC [auth B],
PD [auth C]
heptyl 1-thio-beta-D-glucopyranoside
C13 H26 O5 S
HPEGNLMTTNTJSP-LBELIVKGSA-N
GOL
Query on GOL

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AB [auth A]
AF [auth T]
BB [auth A]
EF [auth V]
FF [auth V]
AB [auth A],
AF [auth T],
BB [auth A],
EF [auth V],
FF [auth V],
GF [auth V],
GG [auth a],
HF [auth V],
IB [auth A],
IC [auth B],
IG [auth b],
JC [auth B],
JG [auth b],
KC [auth B],
KG [auth b],
LC [auth B],
LG [auth b],
MC [auth B],
MG [auth b],
NC [auth B],
NF [auth a],
OF [auth a],
QD [auth C],
QH [auth c],
RD [auth C],
RH [auth c],
SC [auth B],
TJ [auth o],
WJ [auth t],
XE [auth O],
XJ [auth v],
YJ [auth v],
ZA [auth A],
ZE [auth T],
ZJ [auth v]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
BCT
Query on BCT

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DG [auth a],
QA [auth A]
BICARBONATE ION
C H O3
BVKZGUZCCUSVTD-UHFFFAOYSA-M
FE2
Query on FE2

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NA [auth A],
SF [auth a]
FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
CA
Query on CA

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JB [auth B]
JJ [auth f]
LE [auth F]
PG [auth b]
SD [auth C]
JB [auth B],
JJ [auth f],
LE [auth F],
PG [auth b],
SD [auth C],
SH [auth c],
TH [auth c],
UJ [auth o],
YE [auth O]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL
Query on CL

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AK [auth v]
DF [auth U]
OA [auth A]
PA [auth A]
TF [auth a]
AK [auth v],
DF [auth U],
OA [auth A],
PA [auth A],
TF [auth a],
UF [auth a]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG
Query on MG

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OJ [auth j],
QE [auth J]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
UNL
Query on UNL

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AJ [auth d]
CJ [auth d]
DE [auth D]
EE [auth D]
GB [auth A]
AJ [auth d],
CJ [auth d],
DE [auth D],
EE [auth D],
GB [auth A],
LF [auth X],
MJ [auth i],
NH [auth b],
NJ [auth j],
OE [auth I],
PE [auth J],
PF [auth a],
PI [auth c],
QC [auth B],
QJ [auth m],
TD [auth C],
VE [auth M],
ZI [auth d]
Unknown ligand
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
FME
Query on FME
BA [auth i],
H [auth I]
L-PEPTIDE LINKINGC6 H11 N O3 SMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.149 
  • R-Value Observed: 0.151 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 121.97α = 90
b = 228.72β = 90
c = 286.98γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
CrystFELdata reduction
CrystFELdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of ScienceJapan--

Revision History  (Full details and data files)

  • 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