5TIS

Room temperature XFEL structure of the native, doubly-illuminated photosystem II complex

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.194 

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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) ...

    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.

    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 D Biol Crystallogr 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 D Biol Crystallogr 66: 213
    Organizational Affiliation: 

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



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II protein D1 1A,
U [auth a]		344Thermosynechococcus vestitus BP-1Mutation(s): 0 
Gene Names: psbA1, psbA-1, tlr1843
EC: 1.10.3.9
Membrane Entity: Yes 
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II CP47 reaction center proteinB,
V [auth b]		510Thermosynechococcus vestitus BP-1Mutation(s): 0 
Gene Names: psbB, tlr1530
Membrane Entity: Yes 
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II CP43 reaction center proteinC,
W [auth c]		461Thermosynechococcus vestitus BP-1Mutation(s): 0 
Gene Names: psbC, tlr1631
Membrane Entity: Yes 
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II D2 proteinD,
X [auth d]		352Thermosynechococcus vestitus BP-1Mutation(s): 0 
Gene Names: psbD1, tlr0455, psbD2, tlr1630
EC: 1.10.3.9
Membrane Entity: Yes 
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome b559 subunit alphaE,
Y [auth e]		84Thermosynechococcus vestitus BP-1Mutation(s): 0 
Gene Names: psbE, tsr1541
Membrane Entity: Yes 
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome b559 subunit betaF,
Z [auth f]		45Thermosynechococcus vestitus BP-1Mutation(s): 0 
Gene Names: psbF, tsr1542
Membrane Entity: Yes 
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II reaction center protein HAA [auth h],
G [auth H]		66Thermosynechococcus vestitus BP-1Mutation(s): 0 
Gene Names: psbH, tsl1386
Membrane Entity: Yes 
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II reaction center protein IBA [auth i],
H [auth I]		38Thermosynechococcus vestitus BP-1Mutation(s): 0 
Gene Names: psbI, tsr1074
Membrane Entity: Yes 
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II reaction center protein JCA [auth j],
I [auth J]		40Thermosynechococcus vestitus BP-1Mutation(s): 0 
Gene Names: psbJ, tsr1544
Membrane Entity: Yes 
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II reaction center protein KDA [auth k],
J [auth K]		46Thermosynechococcus vestitus BP-1Mutation(s): 0 
Gene Names: psbK, tsl0176
Membrane Entity: Yes 
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II reaction center protein LEA [auth l],
K [auth L]		37Thermosynechococcus vestitus BP-1Mutation(s): 0 
Gene Names: psbL, tsr1543
Membrane Entity: Yes 
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II reaction center protein MFA [auth m],
L [auth M]		36Thermosynechococcus vestitus BP-1Mutation(s): 0 
Gene Names: psbM, tsl2052
Membrane Entity: Yes 
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II manganese-stabilizing polypeptideGA [auth o],
M [auth O]		272Thermosynechococcus vestitus BP-1Mutation(s): 0 
Gene Names: psbO, tll0444
Membrane Entity: Yes 
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II reaction center protein THA [auth t],
N [auth T]		32Thermosynechococcus vestitus BP-1Mutation(s): 0 
Gene Names: psbT, tsr1531
Membrane Entity: Yes 
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II 12 kDa extrinsic proteinIA [auth u],
O [auth U]		134Thermosynechococcus vestitus BP-1Mutation(s): 0 
Gene Names: psbU, tll2409
Membrane Entity: Yes 
UniProt
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome c-550JA [auth v],
P [auth V]		163Thermosynechococcus vestitus BP-1Mutation(s): 0 
Gene Names: psbV, tll1285
Membrane Entity: Yes 
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II reaction center protein Ycf12KA [auth y],
Q [auth Y]		46Thermosynechococcus vestitus BP-1Mutation(s): 0 
Gene Names: ycf12, tsr1242
Membrane Entity: Yes 
UniProt
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II reaction center X proteinLA [auth x],
R [auth X]		41Thermosynechococcus vestitus BP-1Mutation(s): 0 
Gene Names: psbX, tsr2013
Membrane Entity: Yes 
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II reaction center protein ZMA [auth z],
S [auth Z]		62Thermosynechococcus vestitus BP-1Mutation(s): 0 
Gene Names: psbZ, tsr1967
Membrane Entity: Yes 
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II protein YNA [auth r],
T [auth R]		41Thermosynechococcus vestitus BP-1Mutation(s): 0 
Gene Names: psbY, tsl0836
Membrane Entity: Yes 
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Small Molecules
Ligands 15 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DGD
Query on DGD
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JH [auth h]
NG [auth c]
OG [auth c]
PG [auth c]
SD [auth H]
JH [auth h],
NG [auth c],
OG [auth c],
PG [auth c],
SD [auth H],
XC [auth C],
YC [auth C],
ZC [auth C]
DIGALACTOSYL DIACYL GLYCEROL (DGDG)
C51 H96 O15
LDQFLSUQYHBXSX-HXXRYREZSA-N		 Ligand Interaction
CLA
Query on CLA
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AB [auth A]
AG [auth c]
BF [auth b]
BG [auth c]
CF [auth b]
AB [auth A],
AG [auth c],
BF [auth b],
BG [auth c],
CF [auth b],
CG [auth c],
DF [auth b],
DG [auth c],
EF [auth b],
EG [auth c],
FD [auth D],
FF [auth b],
FG [auth c],
GB [auth B],
GD [auth D],
GF [auth b],
GG [auth c],
HB [auth B],
HF [auth b],
HG [auth c],
IB [auth B],
IC [auth C],
IF [auth b],
IG [auth c],
JB [auth B],
JC [auth C],
JF [auth b],
JG [auth c],
KB [auth B],
KC [auth C],
KF [auth b],
KG [auth c],
LB [auth B],
LC [auth C],
LF [auth b],
MB [auth B],
MC [auth C],
MF [auth b],
NB [auth B],
NC [auth C],
NE [auth a],
NF [auth b],
OB [auth B],
OC [auth C],
OE [auth a],
OF [auth b],
PB [auth B],
PC [auth C],
PF [auth b],
QB [auth B],
QC [auth C],
QF [auth b],
RB [auth B],
RC [auth C],
RE [auth a],
SB [auth B],
SC [auth C],
TA [auth A],
TB [auth B],
TC [auth C],
UA [auth A],
UB [auth B],
UC [auth C],
VB [auth B],
WA [auth A],
WE [auth a],
XG [auth d],
YF [auth c],
YG [auth d],
ZF [auth c]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M		 Ligand Interaction
PHO
Query on PHO
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ED [auth D],
PE [auth a],
QE [auth a],
VA [auth A]		PHEOPHYTIN A
C55 H74 N4 O5
CQIKWXUXPNUNDV-RCBXBCQGSA-N		 Ligand Interaction
SQD
Query on SQD
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DB [auth A]
DC [auth B]
EC [auth B]
HH [auth f]
LD [auth D]
DB [auth A],
DC [auth B],
EC [auth B],
HH [auth f],
LD [auth D],
MD [auth D],
UE [auth a],
VF [auth b],
ZA [auth A],
ZD [auth L]
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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AC [auth B]
AD [auth C]
BD [auth C]
DH [auth d]
EH [auth d]
AC [auth B],
AD [auth C],
BD [auth C],
DH [auth d],
EH [auth d],
FC [auth B],
HC [auth C],
KD [auth D],
PH [auth m],
QG [auth c],
RG [auth c],
UF [auth b],
VE [auth a],
ZB [auth B]
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N		 Ligand Interaction
PL9
Query on PL9
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AH [auth d],
ID [auth D],
TE [auth a],
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		 Ligand Interaction
LHG
Query on LHG
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AE [auth L]
BB [auth A]
BH [auth d]
CC [auth B]
CH [auth d]
AE [auth L],
BB [auth A],
BH [auth d],
CC [auth B],
CH [auth d],
FB [auth A],
JD [auth D],
NH [auth l],
XE [auth a],
YE [auth a]
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N		 Ligand Interaction
HEC
Query on HEC
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GE [auth V],
TH [auth v]		HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N		 Ligand Interaction
HEM
Query on HEM
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GH [auth e],
PD [auth E]		PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L		 Ligand Interaction
BCR
Query on BCR
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DE [auth T]
HD [auth D]
HE [auth Y]
IH [auth h]
LG [auth c]
DE [auth T],
HD [auth D],
HE [auth Y],
IH [auth h],
LG [auth c],
MG [auth c],
RD [auth H],
RF [auth b],
RH [auth t],
SE [auth a],
SF [auth b],
SG [auth c],
TF [auth b],
TG [auth c],
VC [auth C],
WB [auth B],
WC [auth C],
XA [auth A],
XB [auth B],
YB [auth B],
YD [auth K],
ZG [auth d]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N		 Ligand Interaction
OEX
Query on OEX
Download Ideal Coordinates CCD File 
IE [auth a],
OA [auth A]		CA-MN4-O5 CLUSTER
Ca Mn4 O5
SEXWDHMBWJEXOJ-UHFFFAOYSA-N		 Ligand Interaction
BCT
Query on BCT
Download Ideal Coordinates CCD File 
ME [auth a],
SA [auth A]		BICARBONATE ION
C H O3
BVKZGUZCCUSVTD-UHFFFAOYSA-M		 Ligand Interaction
FE2
Query on FE2
Download Ideal Coordinates CCD File 
JE [auth a],
PA [auth A]		FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N		 Ligand Interaction
CL
Query on CL
Download Ideal Coordinates CCD File 
KE [auth a],
LE [auth a],
QA [auth A],
RA [auth A]		CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M		 Ligand Interaction
UNL
Query on UNL
Download Ideal Coordinates CCD File 
AF [auth a]
BC [auth B]
BE [auth M]
CB [auth A]
CD [auth C]
AF [auth a],
BC [auth B],
BE [auth M],
CB [auth A],
CD [auth C],
CE [auth M],
DD [auth C],
EB [auth A],
EE [auth T],
FE [auth T],
FH [auth d],
GC [auth B],
KH [auth i],
LH [auth j],
MH [auth j],
ND [auth D],
OD [auth D],
OH [auth m],
QD [auth E],
QH [auth m],
SH [auth t],
TD [auth H],
UD [auth I],
UG [auth c],
UH [auth x],
VD [auth I],
VG [auth c],
WD [auth J],
WF [auth b],
WG [auth c],
XD [auth J],
XF [auth b],
ZE [auth a]
Unknown ligand
VEXZGXHMUGYJMC-UHFFFAOYSA-M		 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D 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: 2.25 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.194 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 117.87α = 90
b = 223.14β = 90
c = 310.71γ = 90
Software Package:
Software NamePurpose
cctbx.xfeldata reduction
PHASERphasing
PHENIXrefinement

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


View more in-depth experimental data
Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Director, Office of Science, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences, and Biosciences, Department of EnergyDepartment of EnergyUnited 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 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
German Research Foundation (DFG)Germany--
Deutsche forschungs GemeinschaftGermanySfb1078, TP A5
Umea University, Solar Fuels Strong Research EnvironmentSweden--
K&A Wallenberg FoundationSweden2011.0055
EnergimyndighetenSweden36648-1
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
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
Brookhaven National Laboratory, Department of EnergyUnited StatesLaboratory Directed Research and Development grant 11-008
National Institutes of Health/National Center for Research Resources (NIH/NCRR)United States2-P41-RR012408
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States8P41GM103473-16
Department of Energy (DOE, United States)United StatesFWP BO-70
Biotechnology and Biological Sciences Research Council (BBSRC)United Kingdom102593
Department of Energy (DOE, United States)United StatesDE-AC02-98CH10886
Department of Energy (DOE, United States)United StatesDE-SC0012704
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesP41GM111244

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 1.5: 2020-01-01
    Changes: Author supporting evidence
  • Version 2.0: 2021-03-10
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary