5WS6

Native XFEL structure of Photosystem II (preflash two-flash dataset


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.175 
  • R-Value Work: 0.129 

wwPDB Validation 3D Report Full Report


This is version 1.0 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: 10.1038/nature21400
  • Primary Citation of Related Structures:  

  • 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). T ...

    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

    Division of Material Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan.,Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto, 606-8501, Japan.,Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, No.20 Nanxincun, Xiangshan, Beijing 100093, China.,RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan.,Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan.,Department of Picobiology, Graduate School of Life Science, University of Hyogo, 3-2-1 Kouto, Kamigori-cho, Ako-gun, Hyogo 678-1297, Japan.,Department of Chemistry, Graduate School of Science, Kobe University, 1-1 Rokkodai, Nada-ku, Kobe 657-8501, Japan.,Japan Science and Technology Agency, PRESTO, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan.,Department of Cell Biology and Anatomy, Graduate School of Medicine, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.,Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University, 3-1-1 Tsushima Naka, Okayama 700-8530, Japan.,Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo, Hyogo 679-5198, Japan.,Institute for Protein Research, Osaka University, Yamadaoka, Suita, Osaka 565-0871, Japan.,Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Photosystem II D1 protein
A, a
344Thermosynechococcus vulcanusMutation(s): 0 
Gene Names: psbA (psbA-1)
EC: 1.10.3.9
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
Photosystem II
Find proteins for P51765 (Thermosynechococcus vulcanus)
Go to UniProtKB:  P51765
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Photosystem II CP47 reaction center protein
B, b
505Thermosynechococcus vulcanusMutation(s): 0 
Gene Names: psbB
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
Photosystem II
Find proteins for D0VWR1 (Thermosynechococcus vulcanus)
Go to UniProtKB:  D0VWR1
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Photosystem II CP43 chlorophyll protein
C, c
455Thermosynechococcus vulcanusMutation(s): 0 
Gene Names: psbC
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
Photosystem II
Find proteins for D0VWR7 (Thermosynechococcus vulcanus)
Go to UniProtKB:  D0VWR7
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Photosystem II D2 protein
D, d
342Thermosynechococcus vulcanusMutation(s): 0 
Gene Names: psbD
EC: 1.10.3.9
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
Photosystem II
Find proteins for D0VWR8 (Thermosynechococcus vulcanus)
Go to UniProtKB:  D0VWR8
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Cytochrome b559 subunit alpha
E, e
84Thermosynechococcus vulcanusMutation(s): 0 
Gene Names: psbE
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
Photosystem II
Find proteins for P12238 (Thermosynechococcus vulcanus)
Go to UniProtKB:  P12238
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
Cytochrome b559 subunit beta
F, f
44Thermosynechococcus vulcanusMutation(s): 0 
Gene Names: psbF
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
Photosystem II
Find proteins for P12239 (Thermosynechococcus vulcanus)
Go to UniProtKB:  P12239
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
Photosystem II reaction center protein H
H, h
65Thermosynechococcus vulcanusMutation(s): 0 
Gene Names: psbH
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
Photosystem II
Find proteins for P19052 (Thermosynechococcus vulcanus)
Go to UniProtKB:  P19052
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
Photosystem II reaction center protein I
I, i
38Thermosynechococcus vulcanusMutation(s): 0 
Gene Names: psbI
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
Photosystem II
Find proteins for P12240 (Thermosynechococcus vulcanus)
Go to UniProtKB:  P12240
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
Photosystem II reaction center protein J
J, j
39Thermosynechococcus vulcanusMutation(s): 0 
Gene Names: psbJ
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
Photosystem II
Find proteins for Q7DGD4 (Thermosynechococcus vulcanus)
Go to UniProtKB:  Q7DGD4
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
Photosystem II reaction center protein K
K, k
37Thermosynechococcus vulcanusMutation(s): 0 
Gene Names: psbK
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
Photosystem II
Find proteins for P19054 (Thermosynechococcus vulcanus)
Go to UniProtKB:  P19054
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
Photosystem II reaction center protein L
L, l
37Thermosynechococcus vulcanusMutation(s): 0 
Gene Names: psbL
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
Photosystem II
Find proteins for P12241 (Thermosynechococcus vulcanus)
Go to UniProtKB:  P12241
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
Photosystem II reaction center protein M
M, m
36Thermosynechococcus vulcanusMutation(s): 0 
Gene Names: psbM
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
Photosystem II
Find proteins for P12312 (Thermosynechococcus vulcanus)
Go to UniProtKB:  P12312
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
Photosystem II manganese-stabilizing polypeptide
O, o
244Thermosynechococcus vulcanusMutation(s): 0 
Gene Names: psbO
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
Photosystem II
Find proteins for D0VWR2 (Thermosynechococcus vulcanus)
Go to UniProtKB:  D0VWR2
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
Photosystem II reaction center protein T
T, t
32Thermosynechococcus vulcanusMutation(s): 0 
Gene Names: psbT
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
Photosystem II
Find proteins for P12313 (Thermosynechococcus vulcanus)
Go to UniProtKB:  P12313
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
Photosystem II 12 kDa extrinsic protein
U, u
104Thermosynechococcus vulcanusMutation(s): 0 
Gene Names: psbU
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
Photosystem II
Find proteins for P56152 (Thermosynechococcus vulcanus)
Go to UniProtKB:  P56152
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
Cytochrome c-550
V, v
137Thermosynechococcus vulcanusMutation(s): 0 
Gene Names: psbV
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
Photosystem II
Find proteins for P0A387 (Thermosynechococcus vulcanus)
Go to UniProtKB:  P0A387
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
Photosystem II reaction center protein X
X, x
40Thermosynechococcus vulcanusMutation(s): 0 
Gene Names: psbX
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
Photosystem II
Find proteins for D0VWR4 (Thermosynechococcus vulcanus)
Go to UniProtKB:  D0VWR4
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
Photosystem II reaction center protein Ycf12
Y, y
30Thermosynechococcus vulcanusMutation(s): 0 
Gene Names: ycf12 (psbY)
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
Photosystem II
Find proteins for D0VWR3 (Thermosynechococcus vulcanus)
Go to UniProtKB:  D0VWR3
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
Photosystem II reaction center protein Z
Z, z
62Thermosynechococcus vulcanusMutation(s): 0 
Gene Names: psbZ
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
Photosystem II
Find proteins for D0VWR5 (Thermosynechococcus vulcanus)
Go to UniProtKB:  D0VWR5
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
Photosystem II protein Y
R
34Thermosynechococcus vulcanusMutation(s): 0 
Gene Names: psbY
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
Photosystem II
Find proteins for P0DM37 (Thermosynechococcus vulcanus)
Go to UniProtKB:  P0DM37
Small Molecules
Ligands 19 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SQD
Query on SQD

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A, a, b, B, f, F
1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL
SULFOQUINOVOSYLDIACYLGLYCEROL
C41 H78 O12 S
RVUUQPKXGDTQPG-JUDHQOGESA-N
 Ligand Interaction
CLA
Query on CLA

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A, a, B, b, c, C, d, D
CHLOROPHYLL A
C55 H72 Mg N4 O5
VIQFHHZSLDFWDU-AENOIHSZSA-M
 Ligand Interaction
PL9
Query on PL9

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a, A, D, 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
PLASTOQUINONE 9
C53 H80 O2
FKUYMLZIRPABFK-UHFFFAOYSA-N
 Ligand Interaction
OEX
Query on OEX

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a, A
CA-MN4-O5 CLUSTER
Ca Mn4 O5
SEXWDHMBWJEXOJ-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

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a, A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

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a, A, b, B, c, C, V, v
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
HTG
Query on HTG

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b, B, c, C, D, h, V
HEPTYL 1-THIOHEXOPYRANOSIDE
C13 H26 O5 S
HPEGNLMTTNTJSP-LBELIVKGSA-N
 Ligand Interaction
CA
Query on CA

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b, c, C, o, O, V, v
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
DGD
Query on DGD

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c, C, H, h
DIGALACTOSYL DIACYL GLYCEROL (DGDG)
C51 H96 O15
LDQFLSUQYHBXSX-HXXRYREZSA-N
 Ligand Interaction
LMG
Query on LMG

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A, a, b, B, c, C, j, J, Z, z
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
 Ligand Interaction
OEY
Query on OEY

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A, a
CA-MN4-O6 CLUSTER
Ca Mn4 O6
VXLJVOKMVCJEPF-UHFFFAOYSA-N
 Ligand Interaction
BCT
Query on BCT

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A, a
BICARBONATE ION
C H O3
BVKZGUZCCUSVTD-UHFFFAOYSA-M
 Ligand Interaction
MG
Query on MG

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j, J
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
HEM
Query on HEM

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e, E, v, V
PROTOPORPHYRIN IX CONTAINING FE
HEME
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
BCR
Query on BCR

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A, a, B, b, C, c, D, d, H, h, k, K, t, T, Y, y
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
 Ligand Interaction
PHO
Query on PHO

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a, A
PHEOPHYTIN A
C55 H74 N4 O5
CQIKWXUXPNUNDV-RCBXBCQGSA-N
 Ligand Interaction
FE2
Query on FE2

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a, A
FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
 Ligand Interaction
LMT
Query on LMT

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A, a, b, B, E, e, I, M, m, t
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
 Ligand Interaction
LHG
Query on LHG

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a, d, D, E, l, L
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
FME
Query on FME
I, i, M, m, t, T
L-PEPTIDE LINKINGC6 H11 N O3 SMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.175 
  • R-Value Work: 0.129 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 124.960α = 90.00
b = 230.220β = 90.00
c = 286.020γ = 90.00
Software Package:
Software NamePurpose
CrystFELdata scaling
CrystFELdata reduction
PHASERphasing
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2016-12-05 
  • Released Date: 2017-03-15 
  • Deposition Author(s): Suga, M., Shen, J.R.

Revision History 

  • Version 1.0: 2017-03-15
    Type: Initial release