6W1V

RT XFEL structure of the two-flash state of Photosystem II (2F, S3-rich) at 2.09 Angstrom resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.09 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.183 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 2.0 of the entry. See complete history

Re-refinement Note

A newer entry is available that reflects an alternative modeling of the original data: 8EZ5


Literature

Untangling the sequence of events during the S2→ S3transition in photosystem II and implications for the water oxidation mechanism.

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

(2020) Proc Natl Acad Sci U S A 117: 12624-12635

  • DOI: https://doi.org/10.1073/pnas.2000529117
  • Primary Citation of Related Structures:  
    6W1O, 6W1P, 6W1Q, 6W1R, 6W1T, 6W1U, 6W1V

  • PubMed Abstract: 

    In oxygenic photosynthesis, light-driven oxidation of water to molecular oxygen is carried out by the oxygen-evolving complex (OEC) in photosystem II (PS II). Recently, we reported the room-temperature structures of PS II in the four (semi)stable S-states, S 1 , S 2 , S 3 , and S 0 , showing that a water molecule is inserted during the S 2 → S 3 transition, as a new bridging O(H)-ligand between Mn1 and Ca. To understand the sequence of events leading to the formation of this last stable intermediate state before O 2 formation, we recorded diffraction and Mn X-ray emission spectroscopy (XES) data at several time points during the S 2 → S 3 transition. At the electron acceptor site, changes due to the two-electron redox chemistry at the quinones, Q A and Q B , are observed. At the donor site, tyrosine Y Z and His190 H-bonded to it move by 50 µs after the second flash, and Glu189 moves away from Ca. This is followed by Mn1 and Mn4 moving apart, and the insertion of O X (H) at the open coordination site of Mn1. This water, possibly a ligand of Ca, could be supplied via a "water wheel"-like arrangement of five waters next to the OEC that is connected by a large channel to the bulk solvent. XES spectra show that Mn oxidation (τ of ∼350 µs) during the S 2 → S 3 transition mirrors the appearance of O X electron density. This indicates that the oxidation state change and the insertion of water as a bridging atom between Mn1 and Ca are highly correlated.


  • Organizational Affiliation

    Institut für Biologie, Humboldt-Universität zu Berlin, D-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
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 
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
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 
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 
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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 
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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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II protein YHA [auth r],
N [auth R]
41Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
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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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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
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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
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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 Ycf12MA [auth y],
S [auth Y]
46Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
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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
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Small Molecules
Ligands 15 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DGD
Query on DGD

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AB [auth A]
OH [auth h]
TD [auth H]
VC [auth C]
VG [auth c]
AB [auth A],
OH [auth h],
TD [auth H],
VC [auth C],
VG [auth c],
WC [auth C],
WG [auth c],
XC [auth C],
XG [auth c]
DIGALACTOSYL DIACYL GLYCEROL (DGDG)
C51 H96 O15
LDQFLSUQYHBXSX-HXXRYREZSA-N
CLA
Query on CLA

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CD [auth D]
CH [auth d]
DD [auth D]
DH [auth d]
ED [auth D]
CD [auth D],
CH [auth d],
DD [auth D],
DH [auth d],
ED [auth D],
EF [auth b],
FF [auth b],
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],
JE [auth a],
JF [auth b],
JG [auth c],
KB [auth B],
KC [auth C],
KF [auth b],
KG [auth c],
LB [auth B],
LC [auth C],
LE [auth a],
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],
NF [auth b],
NG [auth c],
OB [auth B],
OC [auth C],
OE [auth a],
OF [auth b],
OG [auth c],
PA [auth A],
PB [auth B],
PC [auth C],
PF [auth b],
PG [auth c],
QA [auth A],
QB [auth B],
QC [auth C],
QF [auth b],
QG [auth c],
RA [auth A],
RB [auth B],
RC [auth C],
RF [auth b],
RG [auth c],
SB [auth B],
SC [auth C],
SD [auth H],
SF [auth b],
SG [auth c],
TB [auth B],
TF [auth b],
UB [auth B]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
PHO
Query on PHO

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

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BC [auth B]
KD [auth D]
MH [auth f]
VE [auth a]
WA [auth A]
BC [auth B],
KD [auth D],
MH [auth f],
VE [auth a],
WA [auth A],
XE [auth a],
XF [auth b],
ZA [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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AE [auth M]
AG [auth b]
AH [auth c]
BF [auth a]
BH [auth c]
AE [auth M],
AG [auth b],
AH [auth c],
BF [auth a],
BH [auth c],
JD [auth D],
JH [auth d],
ND [auth D],
UC [auth C],
YC [auth C],
YF [auth b],
YG [auth c],
ZB [auth B]
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
PL9
Query on PL9

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FH [auth d],
GD [auth D],
TE [auth a],
VA [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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AC [auth B]
HH [auth d]
IH [auth d]
LD [auth D]
MD [auth D]
AC [auth B],
HH [auth d],
IH [auth d],
LD [auth D],
MD [auth D],
TH [auth l],
UE [auth a],
WE [auth a],
XA [auth A],
ZD [auth L]
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
HEC
Query on HEC

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FE [auth V],
LH [auth e],
QD [auth E],
YH [auth v]
HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
BCR
Query on BCR

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DE [auth T]
EH [auth d]
FC [auth C]
FD [auth D]
HE [auth Y]
DE [auth T],
EH [auth d],
FC [auth C],
FD [auth D],
HE [auth Y],
NH [auth h],
PE [auth a],
RD [auth H],
RH [auth k],
SA [auth A],
SH [auth k],
TC [auth C],
TG [auth c],
UF [auth b],
UG [auth c],
VB [auth B],
VF [auth b],
WB [auth B],
WF [auth b],
WH [auth t],
XB [auth B],
YD [auth K]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
OEY
Query on OEY

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DB [auth A],
DF [auth a]
CA-MN4-O6 CLUSTER
Ca Mn4 O6
VXLJVOKMVCJEPF-UHFFFAOYSA-N
OEX
Query on OEX

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

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AD [auth C]
AF [auth a]
BB [auth A]
BD [auth C]
BE [auth M]
AD [auth C],
AF [auth a],
BB [auth A],
BD [auth C],
BE [auth M],
BG [auth b],
CC [auth B],
CE [auth M],
CG [auth b],
DC [auth B],
DG [auth b],
EC [auth B],
EE [auth T],
EG [auth b],
FB [auth B],
FG [auth c],
GE [auth X],
IE [auth Z],
KH [auth d],
OD [auth E],
PD [auth E],
PH [auth h],
QH [auth j],
UD [auth H],
UH [auth l],
VD [auth H],
VH [auth m],
WD [auth I],
XD [auth J],
XH [auth t],
YA [auth A],
YB [auth B],
YE [auth a],
ZC [auth C],
ZE [auth a],
ZF [auth b],
ZG [auth c],
ZH [auth x]
STEARIC ACID
C18 H36 O2
QIQXTHQIDYTFRH-UHFFFAOYSA-N
BCT
Query on BCT

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

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

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QE [auth a],
RE [auth a],
TA [auth A],
UA [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: 2.09 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.183 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 116.958α = 90
b = 221.646β = 90
c = 307.786γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
cctbx.xfeldata reduction
PHASERphasing
cxi.mergedata scaling

Structure Validation

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Ligand Structure Quality Assessment 


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
Department of Energy (DOE, United States)United States--
German Research Foundation (DFG)GermanySFB1078
German Research Foundation (DFG)GermanyEXEC 2008/1 - 390540038
Swedish Research CouncilSweden2016-05183
Swedish Research CouncilSweden2017-00356
Biotechnology and Biological Sciences Research Council (BBSRC)United Kingdom102593
Wellcome TrustUnited Kingdom210734/Z/18/Z
Royal SocietyUnited KingdomRSWF R2 182017

Revision History  (Full details and data files)

  • Version 1.0: 2020-06-03
    Type: Initial release
  • Version 1.1: 2020-06-24
    Changes: Database references
  • Version 2.0: 2023-10-18
    Changes: Data collection, Database references, Derived calculations, Non-polymer description, Refinement description