6DHF

RT XFEL structure of the one-flash state of Photosystem II (1F, S2-rich) at 2.08 Angstrom resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.08 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.189 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Structures of the intermediates of Kok's photosynthetic water oxidation clock.

Kern, J.Chatterjee, R.Young, I.D.Fuller, F.D.Lassalle, L.Ibrahim, M.Gul, S.Fransson, T.Brewster, A.S.Alonso-Mori, R.Hussein, R.Zhang, M.Douthit, L.de Lichtenberg, C.Cheah, M.H.Shevela, D.Wersig, J.Seuffert, I.Sokaras, D.Pastor, E.Weninger, C.Kroll, T.Sierra, R.G.Aller, P.Butryn, A.Orville, A.M.Liang, M.Batyuk, A.Koglin, J.E.Carbajo, S.Boutet, S.Moriarty, N.W.Holton, J.M.Dobbek, H.Adams, P.D.Bergmann, U.Sauter, N.K.Zouni, A.Messinger, J.Yano, J.Yachandra, V.K.

(2018) Nature 563: 421-425

  • DOI: 10.1038/s41586-018-0681-2
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Inspired by the period-four oscillation in flash-induced oxygen evolution of photosystem II discovered by Joliot in 1969, Kok performed additional experiments and proposed a five-state kinetic model for photosynthetic oxygen evolution, known as Kok's ...

    Inspired by the period-four oscillation in flash-induced oxygen evolution of photosystem II discovered by Joliot in 1969, Kok performed additional experiments and proposed a five-state kinetic model for photosynthetic oxygen evolution, known as Kok's S-state clock or cycle 1,2 . The model comprises four (meta)stable intermediates (S 0 , S 1 , S 2 and S 3 ) and one transient S 4 state, which precedes dioxygen formation occurring in a concerted reaction from two water-derived oxygens bound at an oxo-bridged tetra manganese calcium (Mn 4 CaO 5 ) cluster in the oxygen-evolving complex 3-7 . This reaction is coupled to the two-step reduction and protonation of the mobile plastoquinone Q B at the acceptor side of PSII. Here, using serial femtosecond X-ray crystallography and simultaneous X-ray emission spectroscopy with multi-flash visible laser excitation at room temperature, we visualize all (meta)stable states of Kok's cycle as high-resolution structures (2.04-2.08 Å). In addition, we report structures of two transient states at 150 and 400 µs, revealing notable structural changes including the binding of one additional 'water', Ox, during the S 2 →S 3 state transition. Our results suggest that one water ligand to calcium (W3) is directly involved in substrate delivery. The binding of the additional oxygen Ox in the S 3 state between Ca and Mn1 supports O-O bond formation mechanisms involving O5 as one substrate, where Ox is either the other substrate oxygen or is perfectly positioned to refill the O5 position during O 2 release. Thus, our results exclude peroxo-bond formation in the S 3 state, and the nucleophilic attack of W3 onto W2 is unlikely.


    Organizational Affiliation

    Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA. vkyachandra@lbl.gov.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Photosystem II protein D1 1A, a334Thermosynechococcus elongatus BP-1Mutation(s): 0 
Gene Names: psbA1psbA-1tlr1843
EC: 1.10.3.9
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Photosystem II CP47 reaction center proteinB, b505Thermosynechococcus elongatus BP-1Mutation(s): 0 
Gene Names: psbBtlr1530
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Photosystem II CP43 reaction center proteinC, c451Thermosynechococcus elongatus BP-1Mutation(s): 0 
Gene Names: psbCtlr1631
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Cytochrome b559 subunit alphaE, e82Thermosynechococcus elongatus BP-1Mutation(s): 0 
Gene Names: psbEtsr1541
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
Cytochrome b559 subunit betaF, f34Thermosynechococcus elongatus BP-1Mutation(s): 0 
Gene Names: psbFtsr1542
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
Photosystem II reaction center protein HH, h65Thermosynechococcus elongatus BP-1Mutation(s): 0 
Gene Names: psbHtsl1386
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
Photosystem II reaction center protein II, i36Thermosynechococcus elongatus BP-1Mutation(s): 0 
Gene Names: psbItsr1074
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
Photosystem II reaction center protein JJ, j36Thermosynechococcus elongatus BP-1Mutation(s): 0 
Gene Names: psbJtsr1544
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
Photosystem II reaction center protein KK, k37Thermosynechococcus elongatus BP-1Mutation(s): 0 
Gene Names: psbKtsl0176
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
Photosystem II reaction center protein LL, l37Thermosynechococcus elongatus BP-1Mutation(s): 0 
Gene Names: psbLtsr1543
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
Photosystem II reaction center protein MM, m33Thermosynechococcus elongatus BP-1Mutation(s): 0 
Gene Names: psbMtsl2052
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
Photosystem II manganese-stabilizing polypeptideO, o244Thermosynechococcus elongatus BP-1Mutation(s): 0 
Gene Names: psbOtll0444
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
Photosystem II reaction center protein TT, t30Thermosynechococcus elongatus BP-1Mutation(s): 0 
Gene Names: psbTtsr1531
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
Photosystem II 12 kDa extrinsic proteinU, u97Thermosynechococcus elongatus BP-1Mutation(s): 0 
Gene Names: psbUtll2409
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
Cytochrome c-550V, v137Thermosynechococcus elongatus BP-1Mutation(s): 0 
Gene Names: psbVtll1285
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
Photosystem II reaction center protein Ycf12Y, y30Thermosynechococcus elongatus BP-1Mutation(s): 0 
Gene Names: ycf12tsr1242
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
Photosystem II reaction center X proteinX, x38Thermosynechococcus elongatus BP-1Mutation(s): 0 
Gene Names: psbXtsr2013
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
Photosystem II protein YR, r34Thermosynechococcus elongatus BP-1Mutation(s): 0 
Gene Names: psbYtsl0836
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
Photosystem II reaction center protein ZZ, z62Thermosynechococcus elongatus BP-1Mutation(s): 0 
Gene Names: psbZtsr1967
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Photosystem II D2 proteinD, d341Thermosynechococcus elongatus BP-1Mutation(s): 0 
Gene Names: psbD1tlr0455psbD2tlr1630
EC: 1.10.3.9
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  • Reference Sequence
Small Molecules
Ligands 14 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DGD
Query on DGD

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A, C, H, a, c, 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, h
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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B, C, D, K, M, b, c, d, h
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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D, E, L, d, e, l
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, Y, a, b, c, d, h, k, t
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-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
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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A, a
FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

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

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B, C, E, H, I, J, M, T, X, a, b, c, d, j, m, t, x
Unknown ligand
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 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: 2.08 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.189 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 116.817α = 90
b = 220.888β = 90
c = 307.02γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
cctbx.xfeldata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Department of Energy (DOE, United States)United StatesDE-AC02-05CH11231
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM055302
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM110501
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM126289
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM117126
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM116423-02
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM124149
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM124169
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States5 F32 GM116423-02
Other privateUnited StatesHuman Frontier Science Program RGP0063/2013 310
Other governmentGermanyDFG Clusters of Excellence Unifying Concepts in Catalysis (UniCat)
Other governmentGermanyDeutsche forschungs Gemeinschaft Sfb1078, TP A5
Other privateSwedenUmea University, Solar Fuels Strong Research Environment
Other privateSwedenK&A Wallenberg Foundation 2011.0055
Other privateSwedenVetenskapsradet 2016-05183
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesP41GM103393
Department of Energy (DOE, United States)United StatesDE-AC02-76SF00515
Biotechnology and Biological Sciences Research Council (BBSRC)United Kingdom102593
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesP41GM111244
National Institutes of Health/Office of the DirectorUnited StatesS10OD021832
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesP30 GM124169

Revision History 

  • Version 1.0: 2018-11-21
    Type: Initial release
  • Version 1.1: 2018-11-28
    Changes: Data collection, Database references
  • Version 1.2: 2019-04-10
    Changes: Author supporting evidence, Data collection
  • Version 1.3: 2019-12-04
    Changes: Author supporting evidence
  • Version 1.4: 2020-01-01
    Changes: Author supporting evidence