8IRF

XFEL structure of cyanobacterial photosystem II following two flashes (2F) with a 1-microsecond delay


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.177 
  • R-Value Work: 0.140 
  • R-Value Observed: 0.141 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 2.0 of the entry. See complete history


Literature

Oxygen-evolving photosystem II structures during S 1 -S 2 -S 3 transitions.

Li, H.Nakajima, Y.Nango, E.Owada, S.Yamada, D.Hashimoto, K.Luo, F.Tanaka, R.Akita, F.Kato, K.Kang, J.Saitoh, Y.Kishi, S.Yu, H.Matsubara, N.Fujii, H.Sugahara, M.Suzuki, M.Masuda, T.Kimura, T.Thao, T.N.Yonekura, S.Yu, L.J.Tosha, T.Tono, K.Joti, Y.Hatsui, T.Yabashi, M.Kubo, M.Iwata, S.Isobe, H.Yamaguchi, K.Suga, M.Shen, J.R.

(2024) Nature 626: 670-677

  • DOI: https://doi.org/10.1038/s41586-023-06987-5
  • Primary Citation of Related Structures:  
    8IR5, 8IR6, 8IR7, 8IR8, 8IR9, 8IRA, 8IRB, 8IRC, 8IRD, 8IRE, 8IRF, 8IRG, 8IRH, 8IRI

  • PubMed Abstract: 

    Photosystem II (PSII) catalyses the oxidation of water through a four-step cycle of S i states (i = 0-4) at the Mn 4 CaO 5 cluster 1-3 , during which an extra oxygen (O6) is incorporated at the S 3 state to form a possible dioxygen 4-7 . Structural changes of the metal cluster and its environment during the S-state transitions have been studied on the microsecond timescale. Here we use pump-probe serial femtosecond crystallography to reveal the structural dynamics of PSII from nanoseconds to milliseconds after illumination with one flash (1F) or two flashes (2F). Y Z , a tyrosine residue that connects the reaction centre P680 and the Mn 4 CaO 5 cluster, showed structural changes on a nanosecond timescale, as did its surrounding amino acid residues and water molecules, reflecting the fast transfer of electrons and protons after flash illumination. Notably, one water molecule emerged in the vicinity of Glu189 of the D1 subunit of PSII (D1-E189), and was bound to the Ca 2+ ion on a sub-microsecond timescale after 2F illumination. This water molecule disappeared later with the concomitant increase of O6, suggesting that it is the origin of O6. We also observed concerted movements of water molecules in the O1, O4 and Cl-1 channels and their surrounding amino acid residues to complete the sequence of electron transfer, proton release and substrate water delivery. These results provide crucial insights into the structural dynamics of PSII during S-state transitions as well as O-O bond formation.


  • Organizational Affiliation

    Research Institute for Interdisciplinary Science, Graduate School of Natural Science and Technology, Okayama University, Okayama, Japan.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II protein D1A,
S [auth a]
344Thermostichus vulcanusMutation(s): 0 
Gene Names: psbApsbA-1
EC: 1.10.3.9
Membrane Entity: Yes 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II CP47 reaction center proteinB,
T [auth b]
505Thermostichus vulcanusMutation(s): 0 
Gene Names: psbB
Membrane Entity: Yes 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II CP43 reaction center proteinC,
U [auth c]
455Thermostichus vulcanusMutation(s): 0 
Gene Names: psbC
Membrane Entity: Yes 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II D2 proteinD,
V [auth d]
342Thermostichus vulcanusMutation(s): 0 
Gene Names: psbD
Membrane Entity: Yes 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b559 subunit alphaE,
W [auth e]
84Thermostichus vulcanusMutation(s): 0 
Gene Names: psbE
Membrane Entity: Yes 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b559 subunit betaF,
X [auth f]
44Thermostichus vulcanusMutation(s): 0 
Gene Names: psbF
Membrane Entity: Yes 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein HG [auth H],
Y [auth h]
65Thermostichus vulcanusMutation(s): 0 
Gene Names: psbH
Membrane Entity: Yes 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein IH [auth I],
Z [auth i]
38Thermostichus vulcanusMutation(s): 0 
Gene Names: psbI
Membrane Entity: Yes 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein JAA [auth j],
I [auth J]
39Thermostichus vulcanusMutation(s): 0 
Gene Names: psbJ
Membrane Entity: Yes 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein KBA [auth k],
J [auth K]
37Thermostichus vulcanusMutation(s): 0 
Gene Names: psbK
Membrane Entity: Yes 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein LCA [auth l],
K [auth L]
37Thermostichus vulcanusMutation(s): 0 
Gene Names: psbL
Membrane Entity: Yes 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein MDA [auth m],
L [auth M]
36Thermostichus vulcanusMutation(s): 0 
Gene Names: psbM
Membrane Entity: Yes 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II manganese-stabilizing polypeptideEA [auth o],
M [auth O]
244Thermostichus vulcanusMutation(s): 0 
Gene Names: psbO
Membrane Entity: Yes 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein TFA [auth t],
N [auth T]
32Thermostichus vulcanusMutation(s): 0 
Gene Names: psbT
Membrane Entity: Yes 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II 12 kDa extrinsic proteinGA [auth u],
O [auth U]
104Thermostichus vulcanusMutation(s): 0 
Gene Names: psbU
Membrane Entity: Yes 
UniProt
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c-550HA [auth v],
P [auth V]
137Thermostichus vulcanusMutation(s): 0 
Gene Names: psbV
Membrane Entity: Yes 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein XIA [auth x],
Q [auth X]
40Thermostichus vulcanusMutation(s): 0 
Gene Names: psbX
Membrane Entity: Yes 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein Ycf12JA [auth y],
R [auth Y]
30Thermostichus vulcanusMutation(s): 0 
Gene Names: ycf12psbY
Membrane Entity: Yes 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein ZKA [auth Z],
MA [auth z]
62Thermostichus vulcanusMutation(s): 0 
Gene Names: psbZ
Membrane Entity: Yes 
UniProt
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II protein YLA [auth R]34Thermostichus vulcanusMutation(s): 0 
Gene Names: psbY
Membrane Entity: Yes 
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Small Molecules
Ligands 20 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DGD
Query on DGD

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CD [auth C]
CE [auth H]
DD [auth C]
ED [auth C]
HH [auth c]
CD [auth C],
CE [auth H],
DD [auth C],
ED [auth C],
HH [auth c],
IH [auth c],
JH [auth c],
KI [auth h]
DIGALACTOSYL DIACYL GLYCEROL (DGDG)
C51 H96 O15
LDQFLSUQYHBXSX-HXXRYREZSA-N
CLA (Subject of Investigation/LOI)
Query on CLA

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AF [auth a]
AG [auth b]
AH [auth c]
BG [auth b]
BH [auth c]
AF [auth a],
AG [auth b],
AH [auth c],
BG [auth b],
BH [auth c],
CF [auth a],
CG [auth b],
CH [auth c],
DG [auth b],
DH [auth c],
EG [auth b],
EH [auth c],
HB [auth B],
IB [auth B],
JB [auth B],
KB [auth B],
LB [auth B],
LD [auth D],
MB [auth B],
MD [auth D],
NB [auth B],
NC [auth C],
OB [auth B],
OC [auth C],
PB [auth B],
PC [auth C],
PF [auth b],
QA [auth A],
QB [auth B],
QC [auth C],
QF [auth b],
RA [auth A],
RB [auth B],
RC [auth C],
RF [auth b],
SA [auth A],
SB [auth B],
SC [auth C],
SF [auth b],
SG [auth c],
TB [auth B],
TC [auth C],
TF [auth b],
TG [auth c],
TH [auth d],
UA [auth A],
UB [auth B],
UC [auth C],
UF [auth b],
UG [auth c],
UH [auth d],
VB [auth B],
VC [auth C],
VF [auth b],
VG [auth c],
WB [auth B],
WC [auth C],
WF [auth b],
WG [auth c],
XC [auth C],
XF [auth b],
XG [auth c],
YC [auth C],
YE [auth a],
YF [auth b],
YG [auth c],
ZC [auth C],
ZE [auth a],
ZF [auth b],
ZG [auth c]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
PHO
Query on PHO

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BF [auth a],
CB [auth A],
JF [auth a],
TA [auth A]
PHEOPHYTIN A
C55 H74 N4 O5
CQIKWXUXPNUNDV-RCBXBCQGSA-N
SQD
Query on SQD

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AC [auth B]
EF [auth a]
FF [auth a]
HI [auth f]
IG [auth b]
AC [auth B],
EF [auth a],
FF [auth a],
HI [auth f],
IG [auth b],
WA [auth A],
YA [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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BC [auth B]
CI [auth d]
CJ [auth Z]
DJ [auth z]
FD [auth C]
BC [auth B],
CI [auth d],
CJ [auth Z],
DJ [auth z],
FD [auth C],
GD [auth C],
KF [auth a],
KH [auth c],
LH [auth c],
MC [auth C],
PI [auth m],
UD [auth D]
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
PL9 (Subject of Investigation/LOI)
Query on PL9

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AB [auth A],
HF [auth a],
OD [auth D],
WH [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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EI [auth d]
FB [auth A]
IE [auth L]
OF [auth a]
PD [auth D]
EI [auth d],
FB [auth A],
IE [auth L],
OF [auth a],
PD [auth D],
QD [auth D],
RG [auth b],
WD [auth E],
XH [auth d],
YH [auth d]
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
HEC
Query on HEC

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

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GI [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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AD [auth C]
BD [auth C]
BE [auth H]
BJ [auth y]
DF [auth a]
AD [auth C],
BD [auth C],
BE [auth H],
BJ [auth y],
DF [auth a],
FG [auth b],
FH [auth c],
GG [auth b],
GH [auth c],
HE [auth K],
HG [auth b],
JI [auth h],
ND [auth D],
NI [auth k],
PE [auth T],
UE [auth Y],
VA [auth A],
VH [auth d],
XB [auth B],
XI [auth t],
YB [auth B],
ZB [auth B]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
LMT
Query on LMT

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DB [auth A]
FI [auth e]
GB [auth A]
HC [auth B]
JC [auth B]
DB [auth A],
FI [auth e],
GB [auth A],
HC [auth B],
JC [auth B],
JE [auth M],
JG [auth b],
LC [auth B],
LE [auth M],
LF [auth a],
PG [auth b],
RI [auth m],
WI [auth t],
XD [auth F]
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
OEX (Subject of Investigation/LOI)
Query on OEX

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

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BI [auth d]
CC [auth B]
EC [auth B]
HD [auth C]
KG [auth b]
BI [auth d],
CC [auth B],
EC [auth B],
HD [auth C],
KG [auth b],
LG [auth b],
MH [auth c],
NG [auth b],
RE [auth V],
SI [auth o],
TD [auth D]
heptyl 1-thio-beta-D-glucopyranoside
C13 H26 O5 S
HPEGNLMTTNTJSP-LBELIVKGSA-N
GOL
Query on GOL

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DC [auth B]
DI [auth d]
EB [auth A]
GC [auth B]
IC [auth B]
DC [auth B],
DI [auth d],
EB [auth A],
GC [auth B],
IC [auth B],
ID [auth C],
MF [auth a],
MG [auth b],
NE [auth O],
NF [auth a],
OE [auth O],
OI [auth l],
QG [auth b],
QH [auth c],
RH [auth c],
SE [auth V],
UI [auth o],
VD [auth D],
VI [auth o],
XA [auth A],
ZI [auth v]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
BCT (Subject of Investigation/LOI)
Query on BCT

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KD [auth D],
SH [auth d]
BICARBONATE ION
C H O3
BVKZGUZCCUSVTD-UHFFFAOYSA-M
FE2 (Subject of Investigation/LOI)
Query on FE2

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NA [auth A],
VE [auth a]
FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
CA
Query on CA

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AE [auth F]
II [auth f]
JD [auth C]
ME [auth O]
NH [auth c]
AE [auth F],
II [auth f],
JD [auth C],
ME [auth O],
NH [auth c],
OH [auth c],
TI [auth o]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL (Subject of Investigation/LOI)
Query on CL

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OA [auth A],
PA [auth A],
WE [auth a],
XE [auth a]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG
Query on MG

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FE [auth J],
MI [auth j]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
UNL
Query on UNL

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AI [auth d]
AJ [auth x]
BB [auth A]
DE [auth I]
EE [auth J]
AI [auth d],
AJ [auth x],
BB [auth A],
DE [auth I],
EE [auth J],
FC [auth B],
GE [auth K],
IF [auth a],
KC [auth B],
KE [auth M],
LI [auth j],
OG [auth b],
PH [auth c],
QI [auth m],
RD [auth D],
SD [auth D],
TE [auth X],
ZH [auth d]
Unknown ligand
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
FME
Query on FME
H [auth I],
Z [auth i]
L-PEPTIDE LINKINGC6 H11 N O3 SMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.177 
  • R-Value Work: 0.140 
  • R-Value Observed: 0.141 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 125.77α = 90
b = 231.76β = 90
c = 288.58γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
cctbx.xfeldata reduction
cxi.mergedata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)JapanJP17H06434, JP22H04916

Revision History  (Full details and data files)

  • Version 1.0: 2024-01-17
    Type: Initial release
  • Version 1.1: 2024-02-14
    Changes: Database references
  • Version 1.2: 2024-02-28
    Changes: Database references
  • Version 2.0: 2024-03-20
    Type: Coordinate replacement
    Reason: Model completeness
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Refinement description, Structure summary