5KAF

RT XFEL structure of Photosystem II in the dark state at 3.0 A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00001 Å
  • R-Value Free: 0.303 
  • R-Value Work: 0.264 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Structure of photosystem II and substrate binding at room temperature.

Young, I.D.Ibrahim, M.Chatterjee, R.Gul, S.Fuller, F.D.Koroidov, S.Brewster, A.S.Tran, R.Alonso-Mori, R.Kroll, T.Michels-Clark, T.Laksmono, H.Sierra, R.G.Stan, C.A.Hussein, R.Zhang, M.Douthit, L.Kubin, M.de Lichtenberg, C.Vo Pham, L.Nilsson, H.Cheah, M.H.Shevela, D.Saracini, C.Bean, M.A.Seuffert, I.Sokaras, D.Weng, T.C.Pastor, E.Weninger, C.Fransson, T.Lassalle, L.Brauer, P.Aller, P.Docker, P.T.Andi, B.Orville, A.M.Glownia, J.M.Nelson, S.Sikorski, M.Zhu, D.Hunter, M.S.Lane, T.J.Aquila, A.Koglin, J.E.Robinson, J.Liang, M.Boutet, S.Lyubimov, A.Y.Uervirojnangkoorn, M.Moriarty, N.W.Liebschner, D.Afonine, P.V.Waterman, D.G.Evans, G.Wernet, P.Dobbek, H.Weis, W.I.Brunger, A.T.Zwart, P.H.Adams, P.D.Zouni, A.Messinger, J.Bergmann, U.Sauter, N.K.Kern, J.Yachandra, V.K.Yano, J.

(2016) Nature 540: 453-457

  • DOI: 10.1038/nature20161
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Light-induced oxidation of water by photosystem II (PS II) in plants, algae and cyanobacteria has generated most of the dioxygen in the atmosphere. PS II, a membrane-bound multi-subunit pigment protein complex, couples the one-electron photochemistry ...

    Light-induced oxidation of water by photosystem II (PS II) in plants, algae and cyanobacteria has generated most of the dioxygen in the atmosphere. PS II, a membrane-bound multi-subunit pigment protein complex, couples the one-electron photochemistry at the reaction centre with the four-electron redox chemistry of water oxidation at the Mn4CaO5 cluster in the oxygen-evolving complex (OEC). Under illumination, the OEC cycles through five intermediate S-states (S0 to S4), in which S1 is the dark-stable state and S3 is the last semi-stable state before O-O bond formation and O2 evolution. A detailed understanding of the O-O bond formation mechanism remains a challenge, and will require elucidation of both the structures of the OEC in the different S-states and the binding of the two substrate waters to the catalytic site. Here we report the use of femtosecond pulses from an X-ray free electron laser (XFEL) to obtain damage-free, room temperature structures of dark-adapted (S1), two-flash illuminated (2F; S3-enriched), and ammonia-bound two-flash illuminated (2F-NH3; S3-enriched) PS II. Although the recent 1.95 Å resolution structure of PS II at cryogenic temperature using an XFEL provided a damage-free view of the S1 state, measurements at room temperature are required to study the structural landscape of proteins under functional conditions, and also for in situ advancement of the S-states. To investigate the water-binding site(s), ammonia, a water analogue, has been used as a marker, as it binds to the Mn4CaO5 cluster in the S2 and S3 states. Since the ammonia-bound OEC is active, the ammonia-binding Mn site is not a substrate water site. This approach, together with a comparison of the native dark and 2F states, is used to discriminate between proposed O-O bond formation mechanisms.


    Related Citations: 
    • Towards automated crystallographic structure refinement with phenix.refine.
      Afonine, P.V.,Grosse-Kunstleve, R.W.,Echols, N.,Headd, J.J.,Moriarty, N.W.,Mustyakimov, M.,Terwilliger, T.C.,Urzhumtsev, A.,Zwart, P.H.,Adams, P.D.
      (2012) Acta Crystallogr.,Sect.D 68: 352
    • PHENIX: a comprehensive Python-based system for macromolecular structure solution.
      Adams, P.D.,Afonine, P.V.,Bunkoczi, G.,Chen, V.B.,Davis, I.W.,Echols, N.,Headd, J.J.,Hung, L.W.,Kapral, G.J.,Grosse-Kunstleve, R.W.,McCoy, A.J.,Moriarty, N.W.,Oeffner, R.,Read, R.J.,Richardson, D.C.,Richardson, J.S.,Terwilliger, T.C.,Zwart, P.H.
      (2010) Acta Crystallogr.,Sect.D 66: 213


    Organizational Affiliation

    Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Photosystem II protein D1 1
A, a
344Thermosynechococcus elongatus (strain BP-1)Mutation(s): 0 
Gene Names: psbA1 (psbA-1)
EC: 1.10.3.9
Membrane protein
mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
Photosystem II
Find proteins for P0A444 (Thermosynechococcus elongatus (strain BP-1))
Go to UniProtKB:  P0A444
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Photosystem II CP47 reaction center protein
B, b
510Thermosynechococcus elongatus (strain BP-1)Mutation(s): 0 
Gene Names: psbB
Membrane protein
mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
Photosystem II
Find proteins for Q8DIQ1 (Thermosynechococcus elongatus (strain BP-1))
Go to UniProtKB:  Q8DIQ1
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Photosystem II CP43 reaction center protein
C, c
461Thermosynechococcus elongatus (strain BP-1)Mutation(s): 0 
Gene Names: psbC
Membrane protein
mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
Photosystem II
Find proteins for Q8DIF8 (Thermosynechococcus elongatus (strain BP-1))
Go to UniProtKB:  Q8DIF8
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Photosystem II D2 protein
D, d
352Thermosynechococcus elongatus (strain BP-1)Mutation(s): 0 
Gene Names: psbD1, psbD2
EC: 1.10.3.9
Membrane protein
mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
Photosystem II
Find proteins for Q8CM25 (Thermosynechococcus elongatus (strain BP-1))
Go to UniProtKB:  Q8CM25
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Cytochrome b559 subunit alpha
E, e
84Thermosynechococcus elongatus (strain BP-1)Mutation(s): 0 
Gene Names: psbE
Membrane protein
mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
Photosystem II
Find proteins for Q8DIP0 (Thermosynechococcus elongatus (strain BP-1))
Go to UniProtKB:  Q8DIP0
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
Cytochrome b559 subunit beta
F, f
45Thermosynechococcus elongatus (strain BP-1)Mutation(s): 0 
Gene Names: psbF
Membrane protein
mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
Photosystem II
Find proteins for Q8DIN9 (Thermosynechococcus elongatus (strain BP-1))
Go to UniProtKB:  Q8DIN9
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
Photosystem II reaction center protein H
H, h
66Thermosynechococcus elongatus (strain BP-1)Mutation(s): 0 
Gene Names: psbH
Membrane protein
mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
Photosystem II
Find proteins for Q8DJ43 (Thermosynechococcus elongatus (strain BP-1))
Go to UniProtKB:  Q8DJ43
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
Photosystem II reaction center protein I
I, i
38Thermosynechococcus elongatus (strain BP-1)Mutation(s): 0 
Gene Names: psbI
Membrane protein
mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
Photosystem II
Find proteins for Q8DJZ6 (Thermosynechococcus elongatus (strain BP-1))
Go to UniProtKB:  Q8DJZ6
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
Photosystem II reaction center protein J
J, j
40Thermosynechococcus elongatus (strain BP-1)Mutation(s): 0 
Gene Names: psbJ
Membrane protein
mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
Photosystem II
Find proteins for P59087 (Thermosynechococcus elongatus (strain BP-1))
Go to UniProtKB:  P59087
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
Photosystem II reaction center protein K
K, k
46Thermosynechococcus elongatus (strain BP-1)Mutation(s): 0 
Gene Names: psbK
Membrane protein
mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
Photosystem II
Find proteins for Q9F1K9 (Thermosynechococcus elongatus (strain BP-1))
Go to UniProtKB:  Q9F1K9
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
Photosystem II reaction center protein L
L, l
37Thermosynechococcus elongatus (strain BP-1)Mutation(s): 0 
Gene Names: psbL
Membrane protein
mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
Photosystem II
Find proteins for Q8DIN8 (Thermosynechococcus elongatus (strain BP-1))
Go to UniProtKB:  Q8DIN8
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
Photosystem II reaction center protein M
M, m
36Thermosynechococcus elongatus (strain BP-1)Mutation(s): 0 
Gene Names: psbM
Membrane protein
mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
Photosystem II
Find proteins for Q8DHA7 (Thermosynechococcus elongatus (strain BP-1))
Go to UniProtKB:  Q8DHA7
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
Photosystem II manganese-stabilizing polypeptide
O, o
272Thermosynechococcus elongatus (strain BP-1)Mutation(s): 0 
Gene Names: psbO
Membrane protein
mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
Photosystem II
Find proteins for P0A431 (Thermosynechococcus elongatus (strain BP-1))
Go to UniProtKB:  P0A431
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
Photosystem II reaction center protein T
T, t
32Thermosynechococcus elongatus (strain BP-1)Mutation(s): 0 
Gene Names: psbT
Membrane protein
mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
Photosystem II
Find proteins for Q8DIQ0 (Thermosynechococcus elongatus (strain BP-1))
Go to UniProtKB:  Q8DIQ0
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
Photosystem II 12 kDa extrinsic protein
U, u
134Thermosynechococcus elongatus (strain BP-1)Mutation(s): 0 
Gene Names: psbU
Membrane protein
mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
Photosystem II
Find proteins for Q9F1L5 (Thermosynechococcus elongatus (strain BP-1))
Go to UniProtKB:  Q9F1L5
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
Cytochrome c-550
V, v
163Thermosynechococcus elongatus (strain BP-1)Mutation(s): 0 
Gene Names: psbV
Membrane protein
mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
Photosystem II
Find proteins for P0A386 (Thermosynechococcus elongatus (strain BP-1))
Go to UniProtKB:  P0A386
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
Photosystem II reaction center protein Ycf12
Y, y
46Thermosynechococcus elongatus (strain BP-1)Mutation(s): 0 
Gene Names: ycf12
Membrane protein
mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
Photosystem II
Find proteins for Q8DJI1 (Thermosynechococcus elongatus (strain BP-1))
Go to UniProtKB:  Q8DJI1
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
Photosystem II reaction center X protein
X, x
41Thermosynechococcus elongatus (strain BP-1)Mutation(s): 0 
Gene Names: psbX
Membrane protein
mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
Photosystem II
Find proteins for Q9F1R6 (Thermosynechococcus elongatus (strain BP-1))
Go to UniProtKB:  Q9F1R6
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
Photosystem II reaction center protein Z
Z, z
62Thermosynechococcus elongatus (strain BP-1)Mutation(s): 0 
Gene Names: psbZ
Membrane protein
mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
Photosystem II
Find proteins for Q8DHJ2 (Thermosynechococcus elongatus (strain BP-1))
Go to UniProtKB:  Q8DHJ2
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
Photosystem II protein Y
R, r
41Thermosynechococcus elongatus (strain BP-1)Mutation(s): 0 
Gene Names: psbY
Membrane protein
mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
Photosystem II
Find proteins for Q8DKM3 (Thermosynechococcus elongatus (strain BP-1))
Go to UniProtKB:  Q8DKM3
Small Molecules
Ligands 13 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SQD
Query on SQD

Download SDF File 
Download CCD File 
A, b, B, c, D, f, I
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

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

Download SDF File 
Download CCD File 
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

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

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Download CCD File 
A, a
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
DGD
Query on DGD

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

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Download CCD File 
A, B, b, C, c, d, D
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
 Ligand Interaction
BCT
Query on BCT

Download SDF File 
Download CCD File 
a, A
BICARBONATE ION
C H O3
BVKZGUZCCUSVTD-UHFFFAOYSA-M
 Ligand Interaction
HEM
Query on HEM

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

Download SDF File 
Download CCD File 
A, a, d, D
PHEOPHYTIN A
C55 H74 N4 O5
CQIKWXUXPNUNDV-RCBXBCQGSA-N
 Ligand Interaction
FE2
Query on FE2

Download SDF File 
Download CCD File 
A, a
FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
 Ligand Interaction
LHG
Query on LHG

Download SDF File 
Download CCD File 
A, a, d, D, 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: 3.00001 Å
  • R-Value Free: 0.303 
  • R-Value Work: 0.264 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 117.731α = 90.00
b = 223.815β = 90.00
c = 330.818γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
PHASERphasing
cctbx.xfeldata reduction
cctbx.primedata scaling
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Department of Energy (DOE, United States)United States--
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 StatesGM095887
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM102520
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States5 F32 GM116423-02
Human Frontier Science Program (HFSP)FranceRGP0063/2013 310
Clusters of Excellence Unifying Concepts in Catalysis (UniCat)Germany--
Humboldt Universitat BerlinGermanySfb1078
Umea UniversitySwedenSolar Fuels Strong Research Environment
K&A Wallenberg FoundationSweden2011.0055
EnergimyndighetenSweden36648-1
Department of Energy (DOE, United States)United States--
Howard Hughes Medical Institute (HHMI)United StatesCollaborative Innovation Award
Collaborative Computational Project No. 4 (CCP4)United Kingdom--
National Energy Research Scientific Computing Center, Office of Science, Department of EnergyUnited StatesDE-AC02-05CH11231
Advanced Light Source, Lawrence Berkeley National Laboratory, Office of Basic Energy Science, Department of EnergyUnited States--
Stanford Synchrotron Radiation Lightsource, Office of Basic Energy Science, Department of EnergyUnited States--
SSRL Structural Molecular Biology Program, Office of Biological and Environmental Research, Department of EnergyUnited States--
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesP41GM103393
Linac Coherent Light Source (LCLS) and SSRL, SLAC National Accelerator Laboratory, Office of Basic Energy Science, Department of EnergyUnited StatesDE-AC02-76SF00515

Revision History 

  • Version 1.0: 2016-11-23
    Type: Initial release
  • Version 1.1: 2016-12-14
    Type: Database references
  • Version 1.2: 2016-12-28
    Type: Database references
  • Version 1.3: 2017-09-27
    Type: Author supporting evidence, Data collection, Refinement description
  • Version 1.4: 2019-11-20
    Type: Author supporting evidence