5GTH

Native XFEL structure of photosystem II (dark dataset)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.186 
  • R-Value Work: 0.139 
  • R-Value Observed: 0.142 

Starting Model: experimental
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This is version 3.0 of the entry. See complete history


Literature

Light-induced structural changes and the site of O=O bond formation in PSII caught by XFEL.

Suga, M.Akita, F.Sugahara, M.Kubo, M.Nakajima, Y.Nakane, T.Yamashita, K.Umena, Y.Nakabayashi, M.Yamane, T.Nakano, T.Suzuki, M.Masuda, T.Inoue, S.Kimura, T.Nomura, T.Yonekura, S.Yu, L.J.Sakamoto, T.Motomura, T.Chen, J.H.Kato, Y.Noguchi, T.Tono, K.Joti, Y.Kameshima, T.Hatsui, T.Nango, E.Tanaka, R.Naitow, H.Matsuura, Y.Yamashita, A.Yamamoto, M.Nureki, O.Yabashi, M.Ishikawa, T.Iwata, S.Shen, J.R.

(2017) Nature 543: 131-135

  • DOI: https://doi.org/10.1038/nature21400
  • Primary Citation of Related Structures:  
    5GTH, 5GTI, 5WS5, 5WS6

  • PubMed Abstract: 

    Photosystem II (PSII) is a huge membrane-protein complex consisting of 20 different subunits with a total molecular mass of 350 kDa for a monomer. It catalyses light-driven water oxidation at its catalytic centre, the oxygen-evolving complex (OEC). The structure of PSII has been analysed at 1.9 Å resolution by synchrotron radiation X-rays, which revealed that the OEC is a Mn 4 CaO 5 cluster organized in an asymmetric, 'distorted-chair' form. This structure was further analysed with femtosecond X-ray free electron lasers (XFEL), providing the 'radiation damage-free' structure. The mechanism of O=O bond formation, however, remains obscure owing to the lack of intermediate-state structures. Here we describe the structural changes in PSII induced by two-flash illumination at room temperature at a resolution of 2.35 Å using time-resolved serial femtosecond crystallography with an XFEL provided by the SPring-8 ångström compact free-electron laser. An isomorphous difference Fourier map between the two-flash and dark-adapted states revealed two areas of apparent changes: around the Q B /non-haem iron and the Mn 4 CaO 5 cluster. The changes around the Q B /non-haem iron region reflected the electron and proton transfers induced by the two-flash illumination. In the region around the OEC, a water molecule located 3.5 Å from the Mn 4 CaO 5 cluster disappeared from the map upon two-flash illumination. This reduced the distance between another water molecule and the oxygen atom O4, suggesting that proton transfer also occurred. Importantly, the two-flash-minus-dark isomorphous difference Fourier map showed an apparent positive peak around O5, a unique μ 4 -oxo-bridge located in the quasi-centre of Mn1 and Mn4 (refs 4,5). This suggests the insertion of a new oxygen atom (O6) close to O5, providing an O=O distance of 1.5 Å between these two oxygen atoms. This provides a mechanism for the O=O bond formation consistent with that proposed previously.


  • 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.


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 
UniProt
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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 
UniProt
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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 
UniProt
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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
Find proteins for P12238 (Thermostichus vulcanus)
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b559 subunit betaF,
Z [auth f]
44Thermostichus vulcanusMutation(s): 0 
Membrane Entity: Yes 
UniProt
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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
Find proteins for Q7DGD4 (Thermostichus vulcanus)
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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
Find proteins for P19054 (Thermostichus vulcanus)
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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 
UniProt
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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
Find proteins for P12312 (Thermostichus vulcanus)
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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 
UniProt
Find proteins for D0VWR2 (Thermostichus vulcanus)
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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
Find proteins for P12313 (Thermostichus vulcanus)
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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 XKA [auth x],
Q [auth X]
40Thermostichus vulcanusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for D0VWR4 (Thermostichus vulcanus)
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein Ycf12LA [auth y],
R [auth Y]
30Thermostichus vulcanusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for D0VWR3 (Thermostichus vulcanus)
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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
Find proteins for D0VWR5 (Thermostichus vulcanus)
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II protein YT [auth R]34Thermostichus vulcanusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P0DM37 (Thermostichus vulcanus)
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Small Molecules
Ligands 20 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DGD
Query on DGD

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AD [auth C]
BD [auth C]
CD [auth C]
EH [auth c]
EI [auth h]
AD [auth C],
BD [auth C],
CD [auth C],
EH [auth c],
EI [auth h],
FH [auth c],
GH [auth c],
ZD [auth H]
DIGALACTOSYL DIACYL GLYCEROL (DGDG)
C51 H96 O15
LDQFLSUQYHBXSX-HXXRYREZSA-N
CLA
Query on CLA

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AG [auth b]
AH [auth c]
BF [auth a]
BG [auth b]
BH [auth c]
AG [auth b],
AH [auth c],
BF [auth a],
BG [auth b],
BH [auth c],
FB [auth B],
GB [auth B],
HB [auth B],
IB [auth B],
JB [auth B],
KB [auth B],
LB [auth B],
LC [auth C],
LD [auth D],
MB [auth B],
MC [auth C],
MD [auth D],
MF [auth b],
NB [auth B],
NC [auth C],
NF [auth b],
OB [auth B],
OC [auth C],
OF [auth b],
OH [auth d],
PB [auth B],
PC [auth C],
PF [auth b],
PG [auth c],
QA [auth A],
QB [auth B],
QC [auth C],
QF [auth b],
QG [auth c],
QH [auth d],
RA [auth A],
RB [auth B],
RC [auth C],
RF [auth b],
RG [auth c],
RH [auth d],
SA [auth A],
SB [auth B],
SC [auth C],
SF [auth b],
SG [auth c],
TB [auth B],
TC [auth C],
TF [auth b],
TG [auth c],
UA [auth A],
UB [auth B],
UC [auth C],
UF [auth b],
UG [auth c],
VC [auth C],
VF [auth b],
VG [auth c],
WC [auth C],
WF [auth b],
WG [auth c],
XC [auth C],
XE [auth a],
XF [auth b],
XG [auth c],
YE [auth a],
YF [auth b],
YG [auth c],
ZF [auth b],
ZG [auth c]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
PHO
Query on PHO

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AF [auth a],
ID [auth D],
TA [auth A],
ZE [auth a]
PHEOPHYTIN A
C55 H74 N4 O5
CQIKWXUXPNUNDV-RCBXBCQGSA-N
SQD
Query on SQD

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CI [auth f]
DF [auth a]
FF [auth a]
HE [auth L]
UD [auth D]
CI [auth f],
DF [auth a],
FF [auth a],
HE [auth L],
UD [auth D],
WA [auth A],
YA [auth A],
YB [auth B]
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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CE [auth J]
DD [auth C]
FG [auth b]
GI [auth j]
HH [auth c]
CE [auth J],
DD [auth C],
FG [auth b],
GI [auth j],
HH [auth c],
IH [auth c],
JF [auth a],
KC [auth C],
SE [auth Z],
SI [auth z],
TE [auth Z],
ZB [auth B]
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
PL9
Query on PL9

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AB [auth A],
HF [auth a],
OD [auth D],
TH [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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CB [auth A]
DB [auth A]
KI [auth l]
PD [auth D]
QD [auth D]
CB [auth A],
DB [auth A],
KI [auth l],
PD [auth D],
QD [auth D],
UH [auth d],
VD [auth E],
VH [auth d],
WH [auth d],
ZH [auth e]
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
HEC
Query on HEC

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OE [auth V],
PI [auth v]
HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
HEM
Query on HEM

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BI [auth e],
XD [auth E]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
BCR
Query on BCR

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CF [auth a]
CG [auth b]
CH [auth c]
DG [auth b]
DH [auth c]
CF [auth a],
CG [auth b],
CH [auth c],
DG [auth b],
DH [auth c],
DI [auth h],
EG [auth b],
GE [auth K],
JI [auth k],
ME [auth T],
ND [auth D],
OI [auth t],
RE [auth Y],
RI [auth y],
SH [auth d],
VA [auth A],
VB [auth B],
WB [auth B],
XB [auth B],
YC [auth C],
YD [auth H],
ZC [auth C]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
LMT
Query on LMT

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AE [auth I]
AI [auth e]
GG [auth b]
HC [auth B]
IC [auth B]
AE [auth I],
AI [auth e],
GG [auth b],
HC [auth B],
IC [auth B],
IE [auth M],
JC [auth B],
JD [auth D],
KD [auth D],
KE [auth M],
KF [auth a],
MG [auth b],
MI [auth m],
WD [auth E]
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
OEX
Query on OEX

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

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AC [auth B]
BC [auth B]
CC [auth B]
ED [auth C]
FC [auth B]
AC [auth B],
BC [auth B],
CC [auth B],
ED [auth C],
FC [auth B],
FD [auth C],
HG [auth b],
IG [auth b],
JH [auth c],
KG [auth b],
KH [auth c],
NG [auth b],
PE [auth V],
TD [auth D],
YH [auth d]
heptyl 1-thio-beta-D-glucopyranoside
C13 H26 O5 S
HPEGNLMTTNTJSP-LBELIVKGSA-N
GOL
Query on GOL

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DC [auth B]
EC [auth B]
EF [auth a]
GD [auth C]
JG [auth b]
DC [auth B],
EC [auth B],
EF [auth a],
GD [auth C],
JG [auth b],
PH [auth d],
XA [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
BCT
Query on BCT

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

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

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HD [auth C]
LE [auth O]
LH [auth c]
MH [auth c]
NE [auth V]
HD [auth C],
LE [auth O],
LH [auth c],
MH [auth c],
NE [auth V],
NI [auth o]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL
Query on CL

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OA [auth A],
PA [auth A],
VE [auth a],
WE [auth a]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG
Query on MG

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

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BB [auth A]
BE [auth I]
DE [auth J]
FE [auth K]
FI [auth i]
BB [auth A],
BE [auth I],
DE [auth J],
FE [auth K],
FI [auth i],
GC [auth B],
HI [auth j],
IF [auth a],
JE [auth M],
LG [auth b],
LI [auth m],
NH [auth c],
OG [auth b],
QE [auth X],
QI [auth x],
RD [auth D],
SD [auth D],
XH [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: 2.50 Å
  • R-Value Free: 0.186 
  • R-Value Work: 0.139 
  • R-Value Observed: 0.142 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 126.52α = 90
b = 231.23β = 90
c = 287.46γ = 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--

Revision History  (Full details and data files)

  • Version 1.0: 2017-03-15
    Type: Initial release
  • Version 2.0: 2019-10-02
    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