8F4K

RT XFEL structure of the three-flash state of Photosystem II (3F, S0-rich) at 2.16 Angstrom resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.16 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.186 

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 
UniProt
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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 16 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DGD
Query on DGD

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BB [auth A]
IH [auth h]
LG [auth c]
MG [auth c]
NG [auth c]
BB [auth A],
IH [auth h],
LG [auth c],
MG [auth c],
NG [auth c],
PD [auth H],
QC [auth C],
RC [auth C],
SC [auth C],
TE [auth a]
DIGALACTOSYL DIACYL GLYCEROL (DGDG)
C51 H96 O15
LDQFLSUQYHBXSX-HXXRYREZSA-N
CLA
Query on CLA

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AD [auth D]
AF [auth b]
AG [auth c]
BC [auth C]
BF [auth b]
AD [auth D],
AF [auth b],
AG [auth c],
BC [auth C],
BF [auth b],
BG [auth c],
CB [auth B],
CC [auth C],
CF [auth b],
CG [auth c],
DB [auth B],
DC [auth C],
DF [auth b],
DG [auth c],
EB [auth B],
EC [auth C],
EF [auth b],
EG [auth c],
FB [auth B],
FC [auth C],
FF [auth b],
FG [auth c],
GB [auth B],
GC [auth C],
GF [auth b],
GG [auth c],
HB [auth B],
HC [auth C],
HF [auth b],
HG [auth c],
HH [auth h],
IB [auth B],
IC [auth C],
IF [auth b],
JB [auth B],
JC [auth C],
JF [auth b],
KB [auth B],
KC [auth C],
LB [auth B],
LC [auth C],
LE [auth a],
MB [auth B],
MC [auth C],
NB [auth B],
NC [auth C],
ND [auth H],
NE [auth a],
OB [auth B],
PB [auth B],
QB [auth B],
QE [auth a],
TA [auth A],
TG [auth d],
UA [auth A],
VE [auth b],
VF [auth c],
VG [auth d],
WA [auth A],
WE [auth b],
WF [auth c],
WG [auth d],
XE [auth b],
XF [auth c],
YE [auth b],
YF [auth c],
ZA [auth A],
ZC [auth D],
ZE [auth b],
ZF [auth c]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
PHO
Query on PHO

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ME [auth a],
UG [auth d],
VA [auth A],
YC [auth D]
PHEOPHYTIN A
C55 H74 N4 O5
CQIKWXUXPNUNDV-RCBXBCQGSA-N
SQD
Query on SQD

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AB [auth A]
BE [auth T]
ED [auth D]
GH [auth f]
NF [auth b]
AB [auth A],
BE [auth T],
ED [auth D],
GH [auth f],
NF [auth b],
RE [auth a],
SE [auth a],
WB [auth B]
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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BH [auth d]
CH [auth d]
DD [auth D]
HD [auth D]
ID [auth D]
BH [auth d],
CH [auth d],
DD [auth D],
HD [auth D],
ID [auth D],
OF [auth b],
OG [auth c],
PC [auth C],
QF [auth b],
QG [auth c],
SG [auth c],
TC [auth C],
VD [auth M]
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
PL9
Query on PL9

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CD [auth D],
PE [auth a],
YA [auth A],
YG [auth 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
LHG
Query on LHG

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AH [auth d]
FD [auth D]
FH [auth e]
GD [auth D]
KD [auth E]
AH [auth d],
FD [auth D],
FH [auth e],
GD [auth D],
KD [auth E],
LH [auth l],
RF [auth b],
UD [auth L],
VB [auth B],
ZG [auth d]
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
HEC
Query on HEC

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

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EH [auth e],
MD [auth F]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
BCR
Query on BCR

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BD [auth D]
DE [auth Y]
EE [auth Z]
IG [auth c]
JG [auth c]
BD [auth D],
DE [auth Y],
EE [auth Z],
IG [auth c],
JG [auth c],
KF [auth b],
KG [auth c],
KH [auth k],
LF [auth b],
MF [auth b],
OC [auth C],
OD [auth H],
OE [auth a],
OH [auth t],
RB [auth B],
SB [auth B],
SH [auth x],
TB [auth B],
TD [auth K],
XA [auth A],
XG [auth d],
ZD [auth T]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
OEY (Subject of Investigation/LOI)
Query on OEY

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GE [auth a],
PA [auth A]
CA-MN4-O6 CLUSTER
Ca Mn4 O6
VXLJVOKMVCJEPF-UHFFFAOYSA-N
OEX (Subject of Investigation/LOI)
Query on OEX

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

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AC [auth B]
AE [auth T]
DH [auth d]
JD [auth D]
JH [auth j]
AC [auth B],
AE [auth T],
DH [auth d],
JD [auth D],
JH [auth j],
LD [auth E],
MH [auth l],
NH [auth m],
PF [auth b],
PG [auth c],
PH [auth t],
QD [auth H],
QH [auth t],
RD [auth I],
RG [auth c],
SD [auth J],
SF [auth b],
TF [auth b],
TH [auth x],
UB [auth B],
UC [auth C],
UE [auth a],
UF [auth b],
VC [auth C],
WC [auth C],
WD [auth M],
XB [auth B],
XD [auth M],
YB [auth B],
YD [auth M],
ZB [auth B]
STEARIC ACID
C18 H36 O2
QIQXTHQIDYTFRH-UHFFFAOYSA-N
BCT
Query on BCT

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KE [auth a],
XC [auth D]
BICARBONATE ION
C H O3
BVKZGUZCCUSVTD-UHFFFAOYSA-M
FE2
Query on FE2

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

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IE [auth a],
JE [auth a],
RA [auth A],
SA [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 = 116.991α = 90
b = 221.755β = 90
c = 307.964γ = 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: 2023-05-17
    Changes: Database references
  • Version 1.2: 2023-05-31
    Changes: Database references
  • Version 1.3: 2023-08-16
    Changes: Data collection, Database references
  • Version 1.4: 2023-10-25
    Changes: Refinement description