7RF5 | pdb_00007rf5

RT XFEL structure of Photosystem II 150 microseconds after the second illumination at 2.23 Angstrom resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.23 Å
  • R-Value Free: 
    0.233 (Depositor), 0.234 (DCC) 
  • R-Value Work: 
    0.176 (Depositor), 0.177 (DCC) 
  • R-Value Observed: 
    0.176 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.4 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 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.

Macromolecule Content 

  • Total Structure Weight: 759.05 kDa 
  • Atom Count: 52,802 
  • Modeled Residue Count: 5,299 
  • Deposited Residue Count: 5,700 
  • Unique protein chains: 20

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 
UniProt
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Reference Sequence
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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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Reference Sequence
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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 
UniProt
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Reference Sequence
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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 
UniProt
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Reference Sequence
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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 
UniProt
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Reference Sequence
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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 
UniProt
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Reference Sequence
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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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Reference Sequence
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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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Reference Sequence
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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 
UniProt
Find proteins for P59087 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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Reference Sequence
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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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Reference Sequence
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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 
UniProt
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Reference Sequence
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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 
UniProt
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Reference Sequence
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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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Reference Sequence
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Entity ID: 14
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II protein YHA [auth r],
N [auth R]
41Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q8DKM3 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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Reference Sequence
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Entity ID: 15
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein TIA [auth t],
O [auth T]
32Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
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Reference Sequence
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Entity ID: 16
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II 12 kDa extrinsic proteinJA [auth u],
P [auth U]
134Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q9F1L5 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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Reference Sequence
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Entity ID: 17
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome c-550KA [auth v],
Q [auth V]
163Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P0A386 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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Reference Sequence
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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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Reference Sequence
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Entity ID: 19
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein Ycf12MA [auth y],
S [auth Y]
46Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q8DJI1 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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Reference Sequence
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Entity ID: 20
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein ZNA [auth z],
T [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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Reference Sequence

Small Molecules

Ligands 16 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DGD

Query on DGD



Download:Ideal Coordinates CCD File
DB [auth A]
NH [auth h]
OD [auth H]
QG [auth c]
RG [auth c]
DB [auth A],
NH [auth h],
OD [auth H],
QG [auth c],
RG [auth c],
SG [auth c],
TC [auth C],
UC [auth C],
VC [auth C]
DIGALACTOSYL DIACYL GLYCEROL (DGDG)
C51 H96 O15
LDQFLSUQYHBXSX-HXXRYREZSA-N
CLA

Query on CLA



Download:Ideal Coordinates CCD File
AH [auth d]
BD [auth D]
BG [auth c]
CD [auth D]
CF [auth b]
AH [auth d],
BD [auth D],
BG [auth c],
CD [auth D],
CF [auth b],
CG [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],
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],
LG [auth c],
MB [auth B],
MC [auth C],
ME [auth a],
MF [auth b],
MG [auth c],
NB [auth B],
NC [auth C],
ND [auth H],
NE [auth a],
NF [auth b],
NG [auth c],
OB [auth B],
OC [auth C],
OF [auth b],
PB [auth B],
PC [auth C],
PE [auth a],
PF [auth b],
QB [auth B],
QC [auth C],
QF [auth b],
RA [auth A],
RB [auth B],
RF [auth b],
SA [auth A],
SB [auth B],
UA [auth A],
VE [auth a],
ZA [auth A],
ZG [auth d]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
PHO

Query on PHO



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OE [auth a],
TA [auth A],
YG [auth d],
ZC [auth D]
PHEOPHYTIN A
C55 H74 N4 O5
CQIKWXUXPNUNDV-RCBXBCQGSA-N
SQD

Query on SQD



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AB [auth A]
CB [auth A]
GD [auth D]
LH [auth f]
VF [auth b]
AB [auth A],
CB [auth A],
GD [auth D],
LH [auth f],
VF [auth b],
XB [auth B],
XE [auth a],
YE [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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BF [auth a]
FD [auth D]
FH [auth d]
HE [auth Y]
JD [auth D]
BF [auth a],
FD [auth D],
FH [auth d],
HE [auth Y],
JD [auth D],
KD [auth D],
SC [auth C],
TG [auth c],
TH [auth m],
VG [auth c],
WD [auth M],
WG [auth c],
XF [auth b]
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
PL9

Query on PL9



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CH [auth d],
ED [auth D],
UE [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
LHG

Query on LHG



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BB [auth A]
DH [auth d]
EH [auth d]
HD [auth D]
ID [auth D]
BB [auth A],
DH [auth d],
EH [auth d],
HD [auth D],
ID [auth D],
JH [auth e],
LD [auth D],
SH [auth l],
UD [auth L],
WE [auth a]
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
HEC

Query on HEC



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

Query on HEM



Download:Ideal Coordinates CCD File
KH [auth f],
MD [auth F]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
BCR

Query on BCR



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BE [auth T]
BH [auth d]
DD [auth D]
FE [auth X]
MH [auth h]
BE [auth T],
BH [auth d],
DD [auth D],
FE [auth X],
MH [auth h],
OG [auth c],
PG [auth c],
QE [auth a],
QH [auth k],
RC [auth C],
RD [auth K],
RH [auth k],
SD [auth K],
SF [auth b],
TB [auth B],
TD [auth K],
TF [auth b],
UB [auth B],
UF [auth b],
UH [auth t],
VA [auth A],
VB [auth B]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
OEY
(Subject of Investigation/LOI)

Query on OEY



Download:Ideal Coordinates CCD File
JE [auth a],
OA [auth A]
CA-MN4-O6 CLUSTER
Ca Mn4 O6
VXLJVOKMVCJEPF-UHFFFAOYSA-N
OEX
(Subject of Investigation/LOI)

Query on OEX



Download:Ideal Coordinates CCD File
KE [auth a],
PA [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 R]
AF [auth a]
AG [auth b]
BC [auth B]
AC [auth B],
AE [auth R],
AF [auth a],
AG [auth b],
BC [auth B],
CC [auth B],
CE [auth T],
DC [auth B],
DE [auth T],
GE [auth X],
GH [auth d],
HH [auth d],
IE [auth Z],
IH [auth d],
OH [auth h],
PD [auth I],
PH [auth j],
QD [auth J],
UG [auth c],
VD [auth L],
VH [auth t],
WB [auth B],
WC [auth C],
WF [auth b],
XC [auth C],
XD [auth M],
XG [auth c],
YB [auth B],
YC [auth C],
YD [auth M],
YF [auth b],
ZB [auth B],
ZD [auth M],
ZE [auth a],
ZF [auth b]
STEARIC ACID
C18 H36 O2
QIQXTHQIDYTFRH-UHFFFAOYSA-N
BCT

Query on BCT



Download:Ideal Coordinates CCD File
AD [auth D],
TE [auth a]
BICARBONATE ION
C H O3
BVKZGUZCCUSVTD-UHFFFAOYSA-M
FE2

Query on FE2



Download:Ideal Coordinates CCD File
LE [auth a],
QA [auth A]
FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
CL

Query on CL



Download:Ideal Coordinates CCD File
RE [auth a],
SE [auth a],
WA [auth A],
XA [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: 2.23 Å
  • R-Value Free:  0.233 (Depositor), 0.234 (DCC) 
  • R-Value Work:  0.176 (Depositor), 0.177 (DCC) 
  • R-Value Observed: 0.176 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 117.018α = 90
b = 221.781β = 90
c = 308.191γ = 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: 2021-11-17
    Changes: Database references
  • Version 1.2: 2021-12-01
    Changes: Database references
  • Version 1.3: 2023-10-18
    Changes: Data collection, Refinement description
  • Version 1.4: 2024-11-13
    Changes: Structure summary