6JLM

XFEL structure of cyanobacterial photosystem II (dark state, dataset2)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.153 
  • R-Value Observed: 0.156 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 2.1 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. [email protected] [email protected] [email protected].


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 
UniProt
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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 
UniProt
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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 
UniProt
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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 
UniProt
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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
Find proteins for P0A387 (Thermostichus vulcanus)
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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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CI [auth c]
DI [auth c]
EI [auth c]
EJ [auth e]
FD [auth C]
CI [auth c],
DI [auth c],
EI [auth c],
EJ [auth e],
FD [auth C],
GD [auth C],
HD [auth C],
JE [auth H],
KJ [auth h],
XD [auth D]
DIGALACTOSYL DIACYL GLYCEROL (DGDG)
C51 H96 O15
LDQFLSUQYHBXSX-HXXRYREZSA-N
CLA
Query on CLA

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AD [auth C]
AI [auth c]
BD [auth C]
CD [auth C]
HB [auth B]
AD [auth C],
AI [auth c],
BD [auth C],
CD [auth C],
HB [auth B],
IB [auth B],
JB [auth B],
JG [auth b],
KB [auth B],
KG [auth b],
LB [auth B],
LG [auth b],
MB [auth B],
MG [auth b],
NB [auth B],
NG [auth b],
OB [auth B],
OG [auth b],
OH [auth c],
PB [auth B],
PF [auth a],
PG [auth b],
PH [auth c],
QB [auth B],
QC [auth C],
QF [auth a],
QG [auth b],
QH [auth c],
RA [auth A],
RB [auth B],
RC [auth C],
RG [auth b],
RH [auth c],
SA [auth A],
SB [auth B],
SC [auth C],
SF [auth a],
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],
TI [auth d],
UB [auth B],
UC [auth C],
UD [auth D],
UG [auth b],
UH [auth c],
UI [auth d],
VA [auth A],
VB [auth B],
VC [auth C],
VG [auth b],
VH [auth c],
WB [auth B],
WC [auth C],
WG [auth b],
WH [auth c],
XC [auth C],
XG [auth b],
XH [auth c],
YC [auth C],
YG [auth b],
YH [auth c],
ZC [auth C],
ZH [auth c]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
PHO
Query on PHO

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QD [auth D],
RF [auth a],
RI [auth d],
UA [auth A]
PHEOPHYTIN A
C55 H74 N4 O5
CQIKWXUXPNUNDV-RCBXBCQGSA-N
SQD
Query on SQD

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AB [auth A]
AC [auth B]
GE [auth F]
HJ [auth f]
MF [auth a]
AB [auth A],
AC [auth B],
GE [auth F],
HJ [auth f],
MF [auth a],
QE [auth L],
UF [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
Query on LMG

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BC [auth B]
CH [auth b]
DJ [auth d]
DK [auth z]
FB [auth A]
BC [auth B],
CH [auth b],
DJ [auth d],
DK [auth z],
FB [auth A],
FI [auth c],
GI [auth c],
HF [auth Y],
ID [auth C],
KF [auth Z],
LE [auth J],
VF [auth a]
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
PL9
Query on PL9

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DB [auth A],
WD [auth D],
WI [auth d],
ZF [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
Query on LHG

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CG [auth a]
DE [auth E]
MH [auth b]
OC [auth B]
PE [auth L]
CG [auth a],
DE [auth E],
MH [auth b],
OC [auth B],
PE [auth L],
XI [auth d],
YD [auth D],
YI [auth d],
ZD [auth D],
ZI [auth d]
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
HEM
Query on HEM

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BF [auth V],
FE [auth F],
GJ [auth f],
XJ [auth v]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
BCR
Query on BCR

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AH [auth b]
BH [auth b]
BI [auth c]
BK [auth y]
DD [auth C]
AH [auth b],
BH [auth b],
BI [auth c],
BK [auth y],
DD [auth C],
ED [auth C],
IE [auth H],
IF [auth Y],
JJ [auth h],
NI [auth c],
OE [auth K],
OJ [auth k],
TF [auth a],
VD [auth D],
VI [auth d],
VJ [auth t],
WA [auth A],
XB [auth B],
XE [auth T],
YB [auth B],
ZB [auth B],
ZG [auth b]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
LMT
Query on LMT

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BB [auth A]
BG [auth a]
DH [auth b]
EE [auth F]
FG [auth b]
BB [auth A],
BG [auth a],
DH [auth b],
EE [auth F],
FG [auth b],
FJ [auth e],
JD [auth C],
LF [auth a],
RE [auth M],
RJ [auth m],
SD [auth D],
SJ [auth m],
TE [auth M],
UJ [auth t]
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
OEX
Query on OEX

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

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CC [auth B]
CE [auth D]
CF [auth V]
CJ [auth d]
DC [auth B]
CC [auth B],
CE [auth D],
CF [auth V],
CJ [auth d],
DC [auth B],
EC [auth B],
EG [auth b],
EH [auth b],
FH [auth b],
GG [auth b],
HG [auth b],
HI [auth c],
II [auth c],
KD [auth C],
LC [auth B],
LD [auth C],
MC [auth B]
heptyl 1-thio-beta-D-glucopyranoside
C13 H26 O5 S
HPEGNLMTTNTJSP-LBELIVKGSA-N
GOL
Query on GOL

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AF [auth V]
AK [auth v]
DF [auth V]
DG [auth a]
EF [auth V]
AF [auth V],
AK [auth v],
DF [auth V],
DG [auth a],
EF [auth V],
FC [auth B],
FF [auth V],
GC [auth B],
GF [auth V],
GH [auth b],
HC [auth B],
HH [auth b],
IC [auth B],
IH [auth b],
JC [auth B],
JH [auth b],
JI [auth c],
KC [auth B],
KH [auth b],
KI [auth c],
MD [auth C],
ND [auth C],
OI [auth c],
PC [auth B],
PJ [auth l],
RD [auth D],
VE [auth O],
WE [auth T],
WF [auth a],
XF [auth a],
YA [auth A],
YE [auth T],
YJ [auth v],
ZA [auth A],
ZJ [auth v]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
BCT
Query on BCT

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

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

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GB [auth B]
HE [auth F]
IG [auth b]
IJ [auth f]
MI [auth c]
GB [auth B],
HE [auth F],
IG [auth b],
IJ [auth f],
MI [auth c],
NH [auth c],
OD [auth C],
TJ [auth o],
UE [auth O]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL
Query on CL

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NF [auth a]
OA [auth A]
OF [auth a]
PA [auth A]
WJ [auth v]
NF [auth a],
OA [auth A],
OF [auth a],
PA [auth A],
WJ [auth v],
ZE [auth U]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG
Query on MG

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

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AE [auth D]
AJ [auth d]
BE [auth D]
BJ [auth d]
CK [auth x]
AE [auth D],
AJ [auth d],
BE [auth D],
BJ [auth d],
CK [auth x],
EB [auth A],
JF [auth X],
KE [auth I],
LH [auth b],
LI [auth c],
LJ [auth i],
ME [auth J],
MJ [auth j],
NC [auth B],
PD [auth C],
QJ [auth m],
SE [auth M],
YF [auth a]
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: 2.35 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.153 
  • R-Value Observed: 0.156 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 122.04α = 90
b = 228.84β = 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
  • Version 2.1: 2024-11-06
    Changes: Structure summary