5KAF

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.303 
  • R-Value Work: 0.264 
  • R-Value Observed: 0.264 

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This is version 3.0 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: https://doi.org/10.1038/nature20161
  • Primary Citation of Related Structures:  
    5KAF, 5KAI, 5TIS

  • 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 at the reaction centre with the four-electron redox chemistry of water oxidation at the Mn 4 CaO 5 cluster in the oxygen-evolving complex (OEC). Under illumination, the OEC cycles through five intermediate S-states (S 0 to S 4 ), in which S 1 is the dark-stable state and S 3 is the last semi-stable state before O-O bond formation and O 2 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 (S 1 ), two-flash illuminated (2F; S 3 -enriched), and ammonia-bound two-flash illuminated (2F-NH 3 ; S 3 -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 S 1 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 Mn 4 CaO 5 cluster in the S 2 and S 3 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.


  • Organizational Affiliation

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


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II protein D1 1A,
U [auth a]
344Thermosynechococcus vestitus BP-1Mutation(s): 0 
EC: 1.10.3.9
Membrane Entity: Yes 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II CP47 reaction center proteinB,
V [auth b]
510Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II CP43 reaction center proteinC,
W [auth c]
461Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II D2 proteinD,
X [auth d]
352Thermosynechococcus vestitus BP-1Mutation(s): 0 
EC: 1.10.3.9
Membrane Entity: Yes 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b559 subunit alphaE,
Y [auth e]
84Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b559 subunit betaF,
Z [auth f]
45Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein HAA [auth h],
G [auth H]
66Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein IBA [auth i],
H [auth I]
38Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein JCA [auth j],
I [auth J]
40Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein KDA [auth k],
J [auth K]
46Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein LEA [auth l],
K [auth L]
37Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein MFA [auth m],
L [auth M]
36Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II manganese-stabilizing polypeptideGA [auth o],
M [auth O]
272Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein THA [auth t],
N [auth T]
32Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II 12 kDa extrinsic proteinIA [auth u],
O [auth U]
134Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c-550JA [auth v],
P [auth V]
163Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein Ycf12KA [auth y],
Q [auth Y]
46Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center X proteinLA [auth x],
R [auth X]
41Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein ZMA [auth z],
S [auth Z]
62Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II protein YNA [auth r],
T [auth R]
41Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
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Small Molecules
Ligands 15 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DGD
Query on DGD

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AD [auth C]
EG [auth c]
FG [auth c]
GG [auth c]
QD [auth H]
AD [auth C],
EG [auth c],
FG [auth c],
GG [auth c],
QD [auth H],
VG [auth h],
YC [auth C],
ZC [auth C]
DIGALACTOSYL DIACYL GLYCEROL (DGDG)
C51 H96 O15
LDQFLSUQYHBXSX-HXXRYREZSA-N
CLA
Query on CLA

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AF [auth b]
AG [auth c]
BF [auth b]
BG [auth c]
CB [auth A]
AF [auth b],
AG [auth c],
BF [auth b],
BG [auth c],
CB [auth A],
CF [auth b],
DF [auth b],
EE [auth a],
EF [auth b],
FD [auth D],
FE [auth a],
FF [auth b],
GD [auth D],
GF [auth b],
HE [auth a],
IB [auth B],
JB [auth B],
JC [auth C],
KB [auth B],
KC [auth C],
KE [auth a],
LB [auth B],
LC [auth C],
LG [auth d],
MB [auth B],
MC [auth C],
MG [auth d],
NB [auth B],
NC [auth C],
OB [auth B],
OC [auth C],
PB [auth B],
PC [auth C],
PF [auth c],
QB [auth B],
QC [auth C],
QF [auth c],
RB [auth B],
RC [auth C],
RE [auth b],
RF [auth c],
SB [auth B],
SC [auth C],
SE [auth b],
SF [auth c],
TA [auth A],
TB [auth B],
TC [auth C],
TE [auth b],
TF [auth c],
UA [auth A],
UB [auth B],
UC [auth C],
UE [auth b],
UF [auth c],
VB [auth B],
VC [auth C],
VE [auth b],
VF [auth c],
WA [auth A],
WB [auth B],
WE [auth b],
WF [auth c],
XB [auth B],
XE [auth b],
XF [auth c],
YE [auth b],
YF [auth c],
ZE [auth b],
ZF [auth c]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
PHO
Query on PHO

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ED [auth D],
GE [auth a],
JG [auth d],
VA [auth A]
PHEOPHYTIN A
C55 H74 N4 O5
CQIKWXUXPNUNDV-RCBXBCQGSA-N
SQD
Query on SQD

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GB [auth A]
HC [auth B]
LD [auth D]
MD [auth D]
NF [auth c]
GB [auth A],
HC [auth B],
LD [auth D],
MD [auth D],
NF [auth c],
OE [auth b],
QA [auth A],
RD [auth I],
TG [auth f]
1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL
C41 H78 O12 S
RVUUQPKXGDTQPG-JUDHQOGESA-N
LMG
Query on LMG

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AB [auth A]
BC [auth B]
BD [auth C]
CC [auth B]
CD [auth C]
AB [auth A],
BC [auth B],
BD [auth C],
CC [auth B],
CD [auth C],
GC [auth B],
HG [auth c],
ID [auth D],
IG [auth c],
KF [auth b],
LF [auth b],
MF [auth b],
OF [auth c],
OG [auth d],
RG [auth d],
ZA [auth A]
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
PL9
Query on PL9

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JE [auth a],
KD [auth D],
QG [auth d],
YA [auth A]
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
LHG
Query on LHG

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DB [auth A]
EB [auth A]
FB [auth A]
JD [auth D]
LE [auth a]
DB [auth A],
EB [auth A],
FB [auth A],
JD [auth D],
LE [auth a],
ME [auth a],
NE [auth a],
PG [auth d],
TD [auth L],
ZG [auth l]
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
HEC
Query on HEC

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DH [auth v],
XD [auth V]
HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
HEM
Query on HEM

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ND [auth E],
SG [auth e]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
BCR
Query on BCR

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AC [auth B]
CG [auth c]
DG [auth c]
EH [auth y]
HD [auth D]
AC [auth B],
CG [auth c],
DG [auth c],
EH [auth y],
HD [auth D],
HF [auth b],
IC [auth B],
IE [auth a],
IF [auth b],
JF [auth b],
NG [auth d],
PD [auth H],
SD [auth K],
UG [auth h],
WC [auth C],
WD [auth T],
XA [auth A],
XC [auth C],
YB [auth B],
YD [auth Y],
YG [auth k],
ZB [auth B]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
OEX
Query on OEX

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OA [auth A],
ZD [auth a]
CA-MN4-O5 CLUSTER
Ca Mn4 O5
SEXWDHMBWJEXOJ-UHFFFAOYSA-N
BCT
Query on BCT

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DE [auth a],
HB [auth A]
BICARBONATE ION
C H O3
BVKZGUZCCUSVTD-UHFFFAOYSA-M
FE2
Query on FE2

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AE [auth a],
PA [auth A]
FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
CL
Query on CL

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BE [auth a],
CE [auth a],
RA [auth A],
SA [auth A]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
UNL
Query on UNL

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AH [auth m]
BB [auth A]
BH [auth m]
CH [auth t]
DC [auth B]
AH [auth m],
BB [auth A],
BH [auth m],
CH [auth t],
DC [auth B],
DD [auth C],
EC [auth B],
FC [auth B],
FH [auth z],
KG [auth d],
OD [auth H],
PE [auth b],
QE [auth b],
UD [auth M],
VD [auth M],
WG [auth i],
XG [auth j]
Unknown ligand
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
FME
Query on FME
BA [auth i],
H [auth I]
L-PEPTIDE LINKINGC6 H11 N O3 SMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.303 
  • R-Value Work: 0.264 
  • R-Value Observed: 0.264 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 117.731α = 90
b = 223.815β = 90
c = 330.818γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
cctbx.xfeldata reduction
cctbx.primedata scaling
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 


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  (Full details and data files)

  • Version 1.0: 2016-11-23
    Type: Initial release
  • Version 1.1: 2016-12-14
    Changes: Database references
  • Version 1.2: 2016-12-28
    Changes: Database references
  • Version 1.3: 2017-09-27
    Changes: Author supporting evidence, Data collection, Refinement description
  • Version 1.4: 2019-11-20
    Changes: Author supporting evidence
  • Version 2.0: 2021-03-10
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
  • Version 3.0: 2023-09-27
    Changes: Advisory, Data collection, Database references, Non-polymer description, Refinement description