7CJI

Photosystem II structure in the S1 state


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.160 
  • R-Value Observed: 0.163 

Starting Model: experimental
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This is version 2.0 of the entry. See complete history


Literature

Capturing structural changes of the S 1 to S 2 transition of photosystem II using time-resolved serial femtosecond crystallography.

Li, H.Nakajima, Y.Nomura, T.Sugahara, M.Yonekura, S.Chan, S.K.Nakane, T.Yamane, T.Umena, Y.Suzuki, M.Masuda, T.Motomura, T.Naitow, H.Matsuura, Y.Kimura, T.Tono, K.Owada, S.Joti, Y.Tanaka, R.Nango, E.Akita, F.Kubo, M.Iwata, S.Shen, J.R.Suga, M.

(2021) IUCrJ 8: 431-443

  • DOI: https://doi.org/10.1107/S2052252521002177
  • Primary Citation of Related Structures:  
    7CJI, 7CJJ, 7COU

  • PubMed Abstract: 

    Photosystem II (PSII) catalyzes light-induced water oxidation through an S i -state cycle, leading to the generation of di-oxygen, protons and electrons. Pump-probe time-resolved serial femtosecond crystallography (TR-SFX) has been used to capture structural dynamics of light-sensitive proteins. In this approach, it is crucial to avoid light contamination in the samples when analyzing a particular reaction intermediate. Here, a method for determining a condition that avoids light contamination of the PSII microcrystals while minimizing sample consumption in TR-SFX is described. By swapping the pump and probe pulses with a very short delay between them, the structural changes that occur during the S 1 -to-S 2 transition were examined and a boundary of the excitation region was accurately determined. With the sample flow rate and concomitant illumination conditions determined, the S 2 -state structure of PSII could be analyzed at room temperature, revealing the structural changes that occur during the S 1 -to-S 2 transition at ambient temperature. Though the structure of the manganese cluster was similar to previous studies, the behaviors of the water molecules in the two channels (O1 and O4 channels) were found to be different. By comparing with the previous studies performed at low temperature or with a different delay time, the possible channels for water inlet and structural changes important for the water-splitting reaction were revealed.


  • Organizational Affiliation

    Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University, 3-1-1 Tsushima-naka, Kitaku, Okayama, Okayama 700-8530, Japan.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II protein D1A,
U [auth a]
344Thermostichus vulcanusMutation(s): 0 
EC: 1.10.3.9
Membrane Entity: Yes 
UniProt
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II CP47 reaction center proteinB,
V [auth b]
505Thermostichus vulcanusMutation(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]
455Thermostichus vulcanusMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II D2 proteinD,
X [auth d]
342Thermostichus vulcanusMutation(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]
84Thermostichus vulcanusMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b559 subunit betaF,
Z [auth f]
44Thermostichus vulcanusMutation(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]
65Thermostichus vulcanusMutation(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]
38Thermostichus vulcanusMutation(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]
39Thermostichus vulcanusMutation(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]
37Thermostichus vulcanusMutation(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]
37Thermostichus vulcanusMutation(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]
36Thermostichus vulcanusMutation(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]
244Thermostichus vulcanusMutation(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]
32Thermostichus vulcanusMutation(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]
104Thermostichus vulcanusMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c-550JA [auth v],
P [auth V]
137Thermostichus vulcanusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P0A387 (Thermostichus vulcanus)
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein XKA [auth x],
Q [auth X]
40Thermostichus vulcanusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein Ycf12LA [auth y],
R [auth Y]
30Thermostichus vulcanusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein ZMA [auth z],
S [auth Z]
62Thermostichus vulcanusMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II protein YT [auth R]34Thermostichus vulcanusMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Small Molecules
Ligands 20 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DGD
Query on DGD

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DH [auth c]
EH [auth c]
EI [auth h]
FH [auth c]
VC [auth C]
DH [auth c],
EH [auth c],
EI [auth h],
FH [auth c],
VC [auth C],
WC [auth C],
XC [auth C],
ZD [auth H]
DIGALACTOSYL DIACYL GLYCEROL (DGDG)
C51 H96 O15
LDQFLSUQYHBXSX-HXXRYREZSA-N
CLA
Query on CLA

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AG [auth b]
AH [auth c]
DB [auth B]
EB [auth B]
FB [auth B]
AG [auth b],
AH [auth c],
DB [auth B],
EB [auth B],
FB [auth B],
GB [auth B],
GC [auth C],
HB [auth B],
HC [auth C],
IB [auth B],
IC [auth C],
JB [auth B],
JC [auth C],
JD [auth D],
KB [auth B],
KC [auth C],
KD [auth D],
LB [auth B],
LC [auth C],
LF [auth b],
MB [auth B],
MC [auth C],
MF [auth b],
NB [auth B],
NC [auth C],
NF [auth b],
OB [auth B],
OC [auth C],
OF [auth b],
OG [auth c],
OH [auth d],
PB [auth B],
PC [auth C],
PF [auth b],
PG [auth c],
PH [auth d],
QA [auth A],
QB [auth B],
QC [auth C],
QF [auth b],
QG [auth c],
QH [auth d],
RA [auth A],
RB [auth B],
RC [auth C],
RF [auth b],
RG [auth c],
SA [auth A],
SB [auth B],
SC [auth C],
SF [auth b],
SG [auth c],
TF [auth b],
TG [auth c],
UA [auth A],
UF [auth b],
UG [auth c],
VE [auth a],
VF [auth b],
VG [auth c],
WE [auth a],
WF [auth b],
WG [auth c],
XF [auth b],
XG [auth c],
YE [auth a],
YF [auth b],
YG [auth c],
ZF [auth b],
ZG [auth c]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
PHO
Query on PHO

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GD [auth D],
HF [auth a],
TA [auth A],
XE [auth a]
PHEOPHYTIN A
C55 H74 N4 O5
CQIKWXUXPNUNDV-RCBXBCQGSA-N
SQD
Query on SQD

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AF [auth a]
BI [auth f]
CF [auth a]
FC [auth C]
FE [auth L]
AF [auth a],
BI [auth f],
CF [auth a],
FC [auth C],
FE [auth L],
TD [auth D],
WB [auth B],
XA [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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BB [auth A]
GE [auth M]
GH [auth c]
HH [auth c]
IF [auth a]
BB [auth A],
GE [auth M],
GH [auth c],
HH [auth c],
IF [auth a],
KI [auth m],
RE [auth Z],
SD [auth D],
UI [auth z],
YC [auth C],
YH [auth d],
ZC [auth C]
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
PL9
Query on PL9

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FF [auth a],
MD [auth D],
SH [auth d],
ZA [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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CB [auth A]
EE [auth L]
KF [auth a]
MG [auth b]
ND [auth D]
CB [auth A],
EE [auth L],
KF [auth a],
MG [auth b],
ND [auth D],
OD [auth D],
TH [auth d],
UD [auth E],
UH [auth d],
VH [auth d]
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
HEC
Query on HEC

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

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AI [auth f],
WD [auth E]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
BCR
Query on BCR

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BG [auth b]
BH [auth c]
CG [auth b]
CH [auth c]
DE [auth K]
BG [auth b],
BH [auth c],
CG [auth b],
CH [auth c],
DE [auth K],
DG [auth b],
DI [auth h],
II [auth k],
JI [auth k],
LD [auth D],
ME [auth T],
PI [auth t],
QE [auth Y],
RH [auth d],
TB [auth B],
TC [auth C],
UB [auth B],
UC [auth C],
VA [auth A],
VB [auth B],
YD [auth H],
ZE [auth a]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
LMT
Query on LMT

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DD [auth C]
DF [auth a]
EC [auth B]
EG [auth b]
HD [auth D]
DD [auth C],
DF [auth a],
EC [auth B],
EG [auth b],
HD [auth D],
HE [auth M],
ID [auth D],
JE [auth M],
JF [auth a],
KG [auth b],
MI [auth m],
OI [auth t],
VD [auth E],
ZH [auth e]
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
OEX
Query on OEX

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

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AC [auth B]
AD [auth C]
CI [auth h]
FG [auth b]
GG [auth b]
AC [auth B],
AD [auth C],
CI [auth h],
FG [auth b],
GG [auth b],
IG [auth b],
IH [auth c],
OE [auth V],
RD [auth D],
XB [auth B],
YB [auth B]
heptyl 1-thio-beta-D-glucopyranoside
C13 H26 O5 S
HPEGNLMTTNTJSP-LBELIVKGSA-N
GOL
Query on GOL

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BD [auth C]
BF [auth a]
CC [auth B]
DC [auth B]
HG [auth b]
BD [auth C],
BF [auth a],
CC [auth B],
DC [auth B],
HG [auth b],
LE [auth O],
LG [auth b],
MH [auth c],
NG [auth c],
RI [auth v],
WA [auth A],
ZB [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
BCT
Query on BCT

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FD [auth D],
NH [auth d]
BICARBONATE ION
C H O3
BVKZGUZCCUSVTD-UHFFFAOYSA-M
FE2
Query on FE2

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

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CD [auth C]
JH [auth c]
KE [auth O]
KH [auth c]
NI [auth o]
CD [auth C],
JH [auth c],
KE [auth O],
KH [auth c],
NI [auth o],
QI [auth v],
XD [auth F]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL
Query on CL

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

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

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AB [auth A]
AE [auth I]
BC [auth B]
BE [auth J]
ED [auth C]
AB [auth A],
AE [auth I],
BC [auth B],
BE [auth J],
ED [auth C],
FI [auth i],
GF [auth a],
GI [auth j],
IE [auth M],
JG [auth b],
LH [auth c],
LI [auth m],
PD [auth D],
PE [auth X],
QD [auth D],
TI [auth x],
WH [auth d],
XH [auth d]
Unknown ligand
JLVVSXFLKOJNIY-UHFFFAOYSA-N
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: 2.35 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.160 
  • R-Value Observed: 0.163 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 126.02α = 90
b = 231.7β = 90
c = 288.32γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Cheetahdata collection
CrystFELdata processing
PHENIXmodel building
PHASERphasing
DIALSdata reduction
DIALSdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)Japan--

Revision History  (Full details and data files)

  • Version 1.0: 2021-04-28
    Type: Initial release
  • Version 1.1: 2021-05-19
    Changes: Database references
  • Version 2.0: 2023-11-29
    Changes: Data collection, Database references, Non-polymer description, Refinement description