5WS5

Native XFEL structure of photosystem II (preflash dark dataset)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.171 
  • R-Value Work: 0.133 
  • R-Value Observed: 0.135 

wwPDB Validation 3D Report Full Report



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
  • Structures With Same Primary Citation

  • 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

    Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, No.20 Nanxincun, Xiangshan, Beijing 100093, China.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Photosystem II D1 protein
A, a
344Thermosynechococcus vulcanusMutation(s): 0 
Gene Names: psbApsbA-1
EC: 1.10.3.9
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
Photosystem II by femtosecond X-ray pulses, preflash dark state
Find proteins for P51765 (Thermosynechococcus vulcanus)
Go to UniProtKB:  P51765

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Photosystem II CP43 protein
C, c
455Thermosynechococcus vulcanusMutation(s): 0 
Gene Names: psbC
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
Photosystem II by femtosecond X-ray pulses, preflash dark state
Find proteins for D0VWR7 (Thermosynechococcus vulcanus)
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Cytochrome b559 subunit alpha
E, e
84Thermosynechococcus vulcanusMutation(s): 0 
Gene Names: psbE
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
Photosystem II by femtosecond X-ray pulses, preflash dark state
Find proteins for P12238 (Thermosynechococcus vulcanus)
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
Cytochrome b559 subunit beta
F, f
44Thermosynechococcus vulcanusMutation(s): 0 
Gene Names: psbF
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
Photosystem II by femtosecond X-ray pulses, preflash dark state
Find proteins for P12239 (Thermosynechococcus vulcanus)
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
Photosystem II reaction center protein H
H, h
65Thermosynechococcus vulcanusMutation(s): 0 
Gene Names: psbH
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
Photosystem II by femtosecond X-ray pulses, preflash dark state
Find proteins for P19052 (Thermosynechococcus vulcanus)
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
Photosystem II reaction center protein J
J, j
39Thermosynechococcus vulcanusMutation(s): 0 
Gene Names: psbJ
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
Photosystem II by femtosecond X-ray pulses, preflash dark state
Find proteins for Q7DGD4 (Thermosynechococcus vulcanus)
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
Photosystem II reaction center protein L
L, l
37Thermosynechococcus vulcanusMutation(s): 0 
Gene Names: psbL
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
Photosystem II by femtosecond X-ray pulses, preflash dark state
Find proteins for P12241 (Thermosynechococcus vulcanus)
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
Photosystem II protein M
M, m
36Thermosynechococcus vulcanusMutation(s): 0 
Gene Names: psbM
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
Photosystem II by femtosecond X-ray pulses, preflash dark state
Find proteins for P12312 (Thermosynechococcus vulcanus)
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
Photosystem II 12 kDa extrinsic protein
U, u
104Thermosynechococcus vulcanusMutation(s): 0 
Gene Names: psbU
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
Photosystem II by femtosecond X-ray pulses, preflash dark state
Find proteins for P56152 (Thermosynechococcus vulcanus)
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
Photosystem II reaction center protein Ycf12
Y, y
30Thermosynechococcus vulcanusMutation(s): 0 
Gene Names: ycf12psbY
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
Photosystem II by femtosecond X-ray pulses, preflash dark state
Find proteins for D0VWR3 (Thermosynechococcus vulcanus)
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
Photosystem II protein Y
R
34Thermosynechococcus vulcanusMutation(s): 0 
Gene Names: psbY
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
Photosystem II by femtosecond X-ray pulses, preflash dark state
Find proteins for P0DM37 (Thermosynechococcus vulcanus)
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
Photosystem II protein K
K, k
37Thermosynechococcus vulcanusMutation(s): 0 
Gene Names: psbK
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
Photosystem II by femtosecond X-ray pulses, preflash dark state
Find proteins for P19054 (Thermosynechococcus vulcanus)
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
Photosystem II manganese-stabilizing polypeptide
O, o
244Thermosynechococcus vulcanusMutation(s): 0 
Gene Names: psbO
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
Photosystem II by femtosecond X-ray pulses, preflash dark state
Find proteins for D0VWR2 (Thermosynechococcus vulcanus)
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
Photosystem II reaction center protein T
T, t
32Thermosynechococcus vulcanusMutation(s): 0 
Gene Names: psbT
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
Photosystem II by femtosecond X-ray pulses, preflash dark state
Find proteins for P12313 (Thermosynechococcus vulcanus)
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
Cytochrome c-550
V, v
137Thermosynechococcus vulcanusMutation(s): 0 
Gene Names: psbV
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
Photosystem II by femtosecond X-ray pulses, preflash dark state
Find proteins for P0A387 (Thermosynechococcus vulcanus)
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
Photosystem II reaction center protein X
X, x
40Thermosynechococcus vulcanusMutation(s): 0 
Gene Names: psbX
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
Photosystem II by femtosecond X-ray pulses, preflash dark state
Find proteins for D0VWR4 (Thermosynechococcus vulcanus)
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
Photosystem II reaction center protein Z
Z, z
62Thermosynechococcus vulcanusMutation(s): 0 
Gene Names: psbZ
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
Photosystem II by femtosecond X-ray pulses, preflash dark state
Find proteins for D0VWR5 (Thermosynechococcus vulcanus)
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Photosystem II CP47 reaction center protein
B, b
505Thermosynechococcus vulcanusMutation(s): 0 
Gene Names: psbB
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
Photosystem II by femtosecond X-ray pulses, preflash dark state
Find proteins for D0VWR1 (Thermosynechococcus vulcanus)
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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
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
Photosystem II by femtosecond X-ray pulses, preflash dark state
Find proteins for D0VWR8 (Thermosynechococcus vulcanus)
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
Photosystem II reaction center protein I
I, i
38Thermosynechococcus vulcanusMutation(s): 0 
Gene Names: psbI
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
Photosystem II by femtosecond X-ray pulses, preflash dark state
Find proteins for P12240 (Thermosynechococcus vulcanus)
Go to UniProtKB:  P12240
Small Molecules
Ligands 20 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DGD
Query on DGD

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

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

Download CCD File 
A, a
PHEOPHYTIN A
C55 H74 N4 O5
CQIKWXUXPNUNDV-RCBXBCQGSA-N
 Ligand Interaction
SQD
Query on SQD

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

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B, C, D, Z, a, c, d, m, z
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
 Ligand Interaction
PL9
Query on PL9

Download CCD File 
A, D, a, 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
 Ligand Interaction
LHG
Query on LHG

Download CCD File 
D, E, L, d, e, l
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
 Ligand Interaction
HEC
Query on HEC

Download CCD File 
V, v
HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
 Ligand Interaction
HEM
Query on HEM

Download CCD File 
E, e
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
BCR
Query on BCR

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

Download CCD File 
A, D, E, I, M, a, b, e, m, t
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-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
HTG
Query on HTG

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

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A, B, C, V, a, b, c, v
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
BCT
Query on BCT

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A, a
BICARBONATE ION
C H O3
BVKZGUZCCUSVTD-UHFFFAOYSA-M
 Ligand Interaction
FE2
Query on FE2

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

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C, F, O, c, f, o
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

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

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

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A, B, D, I, J, K, M, X, a, b, c, d, i, j, m, x
Unknown ligand
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
FME
Query on FME
M,mL-PEPTIDE LINKINGC6 H11 N O3 SMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.171 
  • R-Value Work: 0.133 
  • R-Value Observed: 0.135 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 124.7α = 90
b = 229.89β = 90
c = 285.5γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
CrystFELdata reduction
CrystFELdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



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
  • Version 1.1: 2018-01-24
    Changes: Data collection
  • Version 2.0: 2019-10-02
    Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary