7RF1

RT XFEL structure of Photosystem II averaged across all S-states at 1.89 Angstrom resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.89 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.171 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural dynamics in the water and proton channels of photosystem II during the S 2 to S 3 transition.

Hussein, R.Ibrahim, M.Bhowmick, A.Simon, P.S.Chatterjee, R.Lassalle, L.Doyle, M.Bogacz, I.Kim, I.S.Cheah, M.H.Gul, S.de Lichtenberg, C.Chernev, P.Pham, C.C.Young, I.D.Carbajo, S.Fuller, F.D.Alonso-Mori, R.Batyuk, A.Sutherlin, K.D.Brewster, A.S.Bolotovsky, R.Mendez, D.Holton, J.M.Moriarty, N.W.Adams, P.D.Bergmann, U.Sauter, N.K.Dobbek, H.Messinger, J.Zouni, A.Kern, J.Yachandra, V.K.Yano, J.

(2021) Nat Commun 12: 6531-6531

  • DOI: https://doi.org/10.1038/s41467-021-26781-z
  • Primary Citation of Related Structures:  
    7RF1, 7RF2, 7RF3, 7RF4, 7RF5, 7RF6, 7RF7, 7RF8

  • PubMed Abstract: 

    Light-driven oxidation of water to molecular oxygen is catalyzed by the oxygen-evolving complex (OEC) in Photosystem II (PS II). This multi-electron, multi-proton catalysis requires the transport of two water molecules to and four protons from the OEC. A high-resolution 1.89 Å structure obtained by averaging all the S states and refining the data of various time points during the S 2 to S 3 transition has provided better visualization of the potential pathways for substrate water insertion and proton release. Our results indicate that the O1 channel is the likely water intake pathway, and the Cl1 channel is the likely proton release pathway based on the structural rearrangements of water molecules and amino acid side chains along these channels. In particular in the Cl1 channel, we suggest that residue D1-E65 serves as a gate for proton transport by minimizing the back reaction. The results show that the water oxidation reaction at the OEC is well coordinated with the amino acid side chains and the H-bonding network over the entire length of the channels, which is essential in shuttling substrate waters and protons.


  • Organizational Affiliation

    Institut für Biologie, Humboldt-Universität zu Berlin, 10115, Berlin, 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
UniProt
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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
Find proteins for Q8DIQ1 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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UniProt GroupQ8DIQ1
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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 
UniProt
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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
UniProt
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b559 subunit alphaE,
Y [auth e]
84Thermosynechococcus vestitus BP-1Mutation(s): 0 
UniProt
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b559 subunit betaF,
Z [auth f]
45Thermosynechococcus vestitus BP-1Mutation(s): 0 
UniProt
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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 
UniProt
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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 
UniProt
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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 
UniProt
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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 
UniProt
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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 
UniProt
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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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UniProt GroupP0A431
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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 
UniProt
Find proteins for P0A386 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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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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UniProt GroupQ8DJI1
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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 
UniProt
Find proteins for Q9F1R6 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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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
Find proteins for Q8DHJ2 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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UniProt GroupQ8DHJ2
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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 
UniProt
Find proteins for Q8DKM3 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 15 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DGD
Query on DGD

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AH [auth c]
BB [auth A]
BE [auth H]
BH [auth c]
CH [auth c]
AH [auth c],
BB [auth A],
BE [auth H],
BH [auth c],
CH [auth c],
XC [auth C],
YC [auth C],
ZC [auth C],
ZH [auth h]
DIGALACTOSYL DIACYL GLYCEROL (DGDG)
C51 H96 O15
LDQFLSUQYHBXSX-HXXRYREZSA-N
CLA
Query on CLA

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DC [auth C]
EC [auth C]
FC [auth C]
GB [auth B]
GC [auth C]
DC [auth C],
EC [auth C],
FC [auth C],
GB [auth B],
GC [auth C],
HB [auth B],
HC [auth C],
HF [auth b],
HH [auth d],
IB [auth B],
IC [auth C],
ID [auth D],
IF [auth b],
IG [auth c],
IH [auth d],
JB [auth B],
JC [auth C],
JD [auth D],
JF [auth b],
JG [auth c],
KB [auth B],
KC [auth C],
KD [auth D],
KF [auth b],
KG [auth c],
LB [auth B],
LC [auth C],
LF [auth b],
LG [auth c],
MB [auth B],
MC [auth C],
MF [auth b],
MG [auth c],
NB [auth B],
NC [auth C],
NF [auth b],
NG [auth c],
OB [auth B],
OC [auth C],
OF [auth b],
OG [auth c],
PB [auth B],
PC [auth C],
PF [auth b],
PG [auth c],
QB [auth B],
QF [auth b],
QG [auth c],
RA [auth A],
RB [auth B],
RF [auth b],
RG [auth c],
SA [auth A],
SB [auth B],
SF [auth b],
SG [auth c],
TB [auth B],
TE [auth a],
TF [auth b],
TG [auth c],
UA [auth A],
UB [auth B],
UE [auth a],
UF [auth b],
UG [auth c],
VB [auth B],
VF [auth b],
WE [auth a],
YH [auth h],
ZE [auth a]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
PHO
Query on PHO

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GH [auth d],
HD [auth D],
TA [auth A],
VE [auth a]
PHEOPHYTIN A
C55 H74 N4 O5
CQIKWXUXPNUNDV-RCBXBCQGSA-N
SQD
Query on SQD

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AB [auth A]
AF [auth a]
AG [auth b]
CF [auth a]
GI [auth l]
AB [auth A],
AF [auth a],
AG [auth b],
CF [auth a],
GI [auth l],
XH [auth f],
ZA [auth A],
ZD [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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AD [auth C]
BG [auth b]
DF [auth a]
DG [auth b]
DH [auth c]
AD [auth C],
BG [auth b],
DF [auth a],
DG [auth b],
DH [auth c],
EH [auth c],
FH [auth c],
IE [auth M],
ND [auth D],
OD [auth D],
OH [auth d],
TC [auth C],
YA [auth A],
ZB [auth B],
ZF [auth b],
ZG [auth c]
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
PL9
Query on PL9

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KH [auth d],
MD [auth D],
WA [auth A],
YE [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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BF [auth a]
HE [auth L]
HI [auth l]
LH [auth d]
MH [auth d]
BF [auth a],
HE [auth L],
HI [auth l],
LH [auth d],
MH [auth d],
NH [auth d],
PD [auth D],
QD [auth D],
RD [auth D],
UD [auth E]
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
HEC
Query on HEC

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

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WH [auth f],
YD [auth F]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
BCR
Query on BCR

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AE [auth H]
EI [auth k]
FI [auth k]
GE [auth K]
JH [auth d]
AE [auth H],
EI [auth k],
FI [auth k],
GE [auth K],
JH [auth d],
LD [auth D],
LE [auth T],
LI [auth t],
PI [auth x],
QC [auth C],
RC [auth C],
VA [auth A],
VG [auth c],
WB [auth B],
WC [auth C],
WF [auth b],
WG [auth c],
XB [auth B],
XE [auth a],
XF [auth b],
YB [auth B],
YF [auth b]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
OEX (Subject of Investigation/LOI)
Query on OEX

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

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AC [auth B]
AI [auth i]
BC [auth B]
BD [auth C]
BI [auth i]
AC [auth B],
AI [auth i],
BC [auth B],
BD [auth C],
BI [auth i],
CB [auth A],
CC [auth B],
CD [auth C],
CE [auth H],
CG [auth b],
CI [auth j],
DB [auth A],
DD [auth C],
DE [auth I],
DI [auth j],
EB [auth A],
ED [auth C],
EE [auth I],
EF [auth a],
EG [auth b],
FD [auth C],
FE [auth J],
FF [auth a],
FG [auth b],
GG [auth b],
HG [auth b],
II [auth l],
JE [auth M],
JI [auth m],
KE [auth M],
KI [auth m],
ME [auth T],
MI [auth t],
NI [auth t],
OE [auth Z],
PH [auth d],
QH [auth d],
QI [auth x],
RH [auth d],
RI [auth z],
SC [auth C],
SD [auth D],
SH [auth e],
TD [auth D],
TH [auth e],
UC [auth C],
UH [auth e],
VC [auth C],
VD [auth E],
VH [auth e],
WD [auth E],
XA [auth A],
XD [auth E],
XG [auth c],
YG [auth c]
STEARIC ACID
C18 H36 O2
QIQXTHQIDYTFRH-UHFFFAOYSA-N
BCT
Query on BCT

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

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

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PA [auth A],
QA [auth A],
QE [auth a],
RE [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

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.89 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.171 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 117α = 90
b = 221.6β = 90
c = 307.7γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
cctbx.xfeldata reduction
PHASERphasing
cxi.mergedata scaling

Structure Validation

View Full Validation Report



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 CouncilSweden2017-00356
Department of Energy (DOE, United States)United StatesDE-AC02-05CH11231
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesP41GM103393

Revision History  (Full details and data files)

  • Version 1.0: 2021-11-10
    Type: Initial release
  • Version 1.1: 2021-12-01
    Changes: Database references
  • Version 1.2: 2023-10-18
    Changes: Data collection, Refinement description