8F4F

RT XFEL structure of Photosystem II 500 microseconds after the third illumination at 2.03 Angstrom resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.03 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.200 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Structural evidence for intermediates during O 2 formation in photosystem II.

Bhowmick, A.Hussein, R.Bogacz, I.Simon, P.S.Ibrahim, M.Chatterjee, R.Doyle, M.D.Cheah, M.H.Fransson, T.Chernev, P.Kim, I.S.Makita, H.Dasgupta, M.Kaminsky, C.J.Zhang, M.Gatcke, J.Haupt, S.Nangca, I.I.Keable, S.M.Aydin, A.O.Tono, K.Owada, S.Gee, L.B.Fuller, F.D.Batyuk, A.Alonso-Mori, R.Holton, J.M.Paley, D.W.Moriarty, N.W.Mamedov, F.Adams, P.D.Brewster, A.S.Dobbek, H.Sauter, N.K.Bergmann, U.Zouni, A.Messinger, J.Kern, J.Yano, J.Yachandra, V.K.

(2023) Nature 617: 629-636

  • DOI: https://doi.org/10.1038/s41586-023-06038-z
  • Primary Citation of Related Structures:  
    8EZ5, 8F4C, 8F4D, 8F4E, 8F4F, 8F4G, 8F4H, 8F4I, 8F4J, 8F4K

  • PubMed Abstract: 

    In natural photosynthesis, the light-driven splitting of water into electrons, protons and molecular oxygen forms the first step of the solar-to-chemical energy conversion process. The reaction takes place in photosystem II, where the Mn 4 CaO 5 cluster first stores four oxidizing equivalents, the S 0 to S 4 intermediate states in the Kok cycle, sequentially generated by photochemical charge separations in the reaction center and then catalyzes the O-O bond formation chemistry 1-3 . Here, we report room temperature snapshots by serial femtosecond X-ray crystallography to provide structural insights into the final reaction step of Kok's photosynthetic water oxidation cycle, the S 3 →[S 4 ]→S 0 transition where O 2 is formed and Kok's water oxidation clock is reset. Our data reveal a complex sequence of events, which occur over micro- to milliseconds, comprising changes at the Mn 4 CaO 5 cluster, its ligands and water pathways as well as controlled proton release through the hydrogen-bonding network of the Cl1 channel. Importantly, the extra O atom O x , which was introduced as a bridging ligand between Ca and Mn1 during the S 2 →S 3 transition 4-6 , disappears or relocates in parallel with Y z reduction starting at approximately 700 μs after the third flash. The onset of O 2 evolution, as indicated by the shortening of the Mn1-Mn4 distance, occurs at around 1,200 μs, signifying the presence of a reduced intermediate, possibly a bound peroxide.


  • Organizational Affiliation

    Institute of Molecular Medicine, University of Lübeck, Lübeck, Germany.


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 
UniProt
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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 
UniProt
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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 
UniProt
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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 
UniProt
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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 
UniProt
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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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DB [auth A]
FH [auth h]
HG [auth c]
IG [auth c]
JG [auth c]
DB [auth A],
FH [auth h],
HG [auth c],
IG [auth c],
JG [auth c],
QD [auth H],
SE [auth a],
TD [auth J],
UC [auth C],
VC [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]
CD [auth D]
AF [auth b],
AG [auth c],
BF [auth b],
BG [auth c],
CD [auth D],
CF [auth b],
CG [auth c],
DD [auth D],
DF [auth b],
DG [auth c],
EF [auth b],
EG [auth c],
FB [auth B],
FF [auth b],
FG [auth c],
GB [auth B],
GC [auth C],
GF [auth b],
HB [auth B],
HC [auth C],
HF [auth b],
IB [auth B],
IC [auth C],
IF [auth b],
JB [auth B],
JC [auth C],
JE [auth a],
JF [auth b],
KB [auth B],
KC [auth C],
KE [auth a],
LB [auth B],
LC [auth C],
MB [auth B],
MC [auth C],
ME [auth a],
NB [auth B],
NC [auth C],
OB [auth B],
OC [auth C],
PB [auth B],
PC [auth C],
PE [auth a],
QB [auth B],
QC [auth C],
QG [auth d],
RB [auth B],
RC [auth C],
RG [auth d],
SB [auth B],
SC [auth C],
TA [auth A],
TB [auth B],
TF [auth c],
UA [auth A],
UB [auth B],
UE [auth b],
UF [auth c],
VA [auth A],
VE [auth b],
VF [auth c],
WE [auth b],
WF [auth c],
XE [auth b],
XF [auth c],
YA [auth A],
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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AD [auth D],
BD [auth D],
LE [auth a],
PG [auth d]
PHEOPHYTIN A
C55 H74 N4 O5
CQIKWXUXPNUNDV-RCBXBCQGSA-N
SQD
Query on SQD

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AB [auth A]
BC [auth B]
CB [auth A]
DH [auth f]
HD [auth D]
AB [auth A],
BC [auth B],
CB [auth A],
DH [auth f],
HD [auth D],
NF [auth b],
QE [auth a],
RE [auth a]
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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AC [auth B]
GD [auth D]
KD [auth D]
KG [auth c]
MG [auth c]
AC [auth B],
GD [auth D],
KD [auth D],
KG [auth c],
MG [auth c],
MH [auth m],
NG [auth c],
PF [auth b],
WC [auth C],
XG [auth d],
YB [auth B],
YG [auth d],
ZA [auth A]
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
PL9
Query on PL9

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FD [auth D],
OE [auth a],
TG [auth d],
XA [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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BB [auth A]
BH [auth e]
ID [auth D]
JD [auth D]
LD [auth D]
BB [auth A],
BH [auth e],
ID [auth D],
JD [auth D],
LD [auth D],
LH [auth l],
UG [auth d],
VG [auth d],
WG [auth d],
YD [auth L]
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
HEC
Query on HEC

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

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

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CE [auth T]
ED [auth D]
EH [auth h]
GG [auth c]
HH [auth k]
CE [auth T],
ED [auth D],
EH [auth h],
GG [auth c],
HH [auth k],
IH [auth k],
JH [auth k],
KF [auth b],
LF [auth b],
MF [auth b],
NE [auth a],
OH [auth t],
PD [auth H],
SG [auth d],
TC [auth C],
VB [auth B],
VD [auth K],
WA [auth A],
WB [auth B],
WD [auth K],
XB [auth B],
XD [auth K]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
OEY (Subject of Investigation/LOI)
Query on OEY

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FE [auth a],
OA [auth A]
CA-MN4-O6 CLUSTER
Ca Mn4 O6
VXLJVOKMVCJEPF-UHFFFAOYSA-N
STE
Query on STE

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AE [auth M]
AH [auth d]
BE [auth M]
CC [auth B]
DC [auth B]
AE [auth M],
AH [auth d],
BE [auth M],
CC [auth B],
DC [auth B],
DE [auth T],
EB [auth A],
EC [auth B],
FC [auth B],
GH [auth j],
KH [auth k],
LG [auth c],
MD [auth D],
NH [auth m],
OD [auth E],
OF [auth b],
PH [auth t],
QF [auth b],
QH [auth t],
RD [auth H],
RF [auth b],
SD [auth I],
SF [auth b],
TE [auth a],
UD [auth J],
XC [auth C],
YC [auth C],
ZB [auth B],
ZC [auth C],
ZD [auth L],
ZG [auth d]
STEARIC ACID
C18 H36 O2
QIQXTHQIDYTFRH-UHFFFAOYSA-N
BCT
Query on BCT

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OG [auth d],
SA [auth A]
BICARBONATE ION
C H O3
BVKZGUZCCUSVTD-UHFFFAOYSA-M
FE2
Query on FE2

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

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HE [auth a],
IE [auth a],
QA [auth A],
RA [auth A]
CHLORIDE ION
Cl
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

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 117.534α = 90
b = 222.832β = 90
c = 309.505γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
cctbx.xfeldata reduction
cctbx.xfel.mergedata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
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 StatesGM124149
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM124169
German Research Foundation (DFG)GermanyUniCat
German Research Foundation (DFG)GermanySfb1078 TP A5
Swedish Research CouncilSweden2016-05183
Swedish Research CouncilSweden2020-03809
Department of Energy (DOE, United States)United StatesDE-AC02-05CH11231
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesP41GM103393
Swedish Energy AgencySweden45421-1
Department of Energy (DOE, United States)United StatesDE-AC02-76SF00515
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesP41GM139687
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesS10 OD023453
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesP30 GM124169-01
Swedish Research CouncilSweden2017-00356

Revision History  (Full details and data files)

  • Version 1.0: 2023-03-22
    Type: Initial release
  • Version 1.1: 2023-05-03
    Changes: Database references
  • Version 1.2: 2023-05-17
    Changes: Database references
  • Version 1.3: 2023-05-31
    Changes: Database references
  • Version 1.4: 2023-08-16
    Changes: Data collection, Database references