6JLO

XFEL structure of cyanobacterial photosystem II (2F state, dataset2)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.151 
  • R-Value Observed: 0.154 

wwPDB Validation 3D Report Full Report


This is version 1.2 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: 10.1126/science.aax6998
  • Primary Citation of Related Structures:  
    6JLP, 6JLK, 6JLJ, 6JLM, 6JLL, 6JLO, 6JLN

  • 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 ox ...

    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
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II protein D1Aa344Thermosynechococcus vulcanusMutation(s): 0 
Gene Names: psbApsbA-1
EC: 1.10.3.9
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II CP47 reaction center proteinBb505Thermosynechococcus vulcanusMutation(s): 0 
Gene Names: psbB
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II CP43 reaction center proteinCc455Thermosynechococcus vulcanusMutation(s): 0 
Gene Names: psbC
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II D2 proteinDd342Thermosynechococcus vulcanusMutation(s): 0 
Gene Names: psbD
EC: 1.10.3.9
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome b559 subunit alphaEe84Thermosynechococcus vulcanusMutation(s): 0 
Gene Names: psbE
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome b559 subunit betaFf44Thermosynechococcus vulcanusMutation(s): 0 
Gene Names: psbF
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II reaction center protein HHh65Thermosynechococcus vulcanusMutation(s): 0 
Gene Names: psbH
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II reaction center protein IIi38Thermosynechococcus vulcanusMutation(s): 0 
Gene Names: psbI
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II reaction center protein JJj39Thermosynechococcus vulcanusMutation(s): 0 
Gene Names: psbJ
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II reaction center protein KKk37Thermosynechococcus vulcanusMutation(s): 0 
Gene Names: psbK
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II reaction center protein LLl37Thermosynechococcus vulcanusMutation(s): 0 
Gene Names: psbL
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II reaction center protein MMm36Thermosynechococcus vulcanusMutation(s): 0 
Gene Names: psbM
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II manganese-stabilizing polypeptideOo244Thermosynechococcus vulcanusMutation(s): 0 
Gene Names: psbO
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II reaction center protein TTt32Thermosynechococcus vulcanusMutation(s): 0 
Gene Names: psbT
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II 12 kDa extrinsic proteinUu104Thermosynechococcus vulcanusMutation(s): 0 
Gene Names: psbU
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome c-550Vv137Thermosynechococcus vulcanusMutation(s): 0 
Gene Names: psbV
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Entity ID: 17
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Photosystem II reaction center protein Ycf12Yy30Thermosynechococcus vulcanusMutation(s): 0 
Gene Names: ycf12psbY
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II reaction center protein XXx40Thermosynechococcus vulcanusMutation(s): 0 
Gene Names: psbX
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II reaction center protein ZZz62Thermosynechococcus vulcanusMutation(s): 0 
Gene Names: psbZ
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II protein YR34Thermosynechococcus vulcanusMutation(s): 0 
Gene Names: psbY
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  • Reference Sequence
Small Molecules
Ligands 20 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DGD
Query on DGD

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

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

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

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

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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

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A, D, L, a, b, d
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
 Ligand Interaction
HEM
Query on HEM

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F, V, e, v
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

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A, B, C, D, F, M, T, a, b, e, m
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-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
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-thio-beta-D-glucopyranoside
C13 H26 O5 S
HPEGNLMTTNTJSP-LBELIVKGSA-N
 Ligand Interaction
GOL
Query on GOL

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A, B, C, D, F, O, T, V, a, b, c, f, o, t, v
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
BCT
Query on BCT

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

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

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

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A, U, a, v
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
Unknown ligand
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
FME
Query on FME
I,iL-PEPTIDE LINKINGC6 H11 N O3 SMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.151 
  • R-Value Observed: 0.154 
  • 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

View Full Validation Report



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2019-03-06 
  • Released Date: 2019-10-16 
  • Deposition Author(s): Suga, M., Shen, J.R.

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

Revision History 

  • 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