4UB6

Native structure of photosystem II (dataset-1) by a femtosecond X-ray laser


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.200 

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Literature

Native structure of photosystem II at 1.95 angstrom resolution viewed by femtosecond X-ray pulses.

Suga, M.Akita, F.Hirata, K.Ueno, G.Murakami, H.Nakajima, Y.Shimizu, T.Yamashita, K.Yamamoto, M.Ago, H.Shen, J.R.

(2015) Nature 517: 99-103

  • DOI: https://doi.org/10.1038/nature13991
  • Primary Citation of Related Structures:  
    4UB6, 4UB8

  • PubMed Abstract: 

    Photosynthesis converts light energy into biologically useful chemical energy vital to life on Earth. The initial reaction of photosynthesis takes place in photosystem II (PSII), a 700-kilodalton homodimeric membrane protein complex that catalyses photo-oxidation of water into dioxygen through an S-state cycle of the oxygen evolving complex (OEC). The structure of PSII has been solved by X-ray diffraction (XRD) at 1.9 ångström resolution, which revealed that the OEC is a Mn4CaO5-cluster coordinated by a well defined protein environment. However, extended X-ray absorption fine structure (EXAFS) studies showed that the manganese cations in the OEC are easily reduced by X-ray irradiation, and slight differences were found in the Mn-Mn distances determined by XRD, EXAFS and theoretical studies. Here we report a 'radiation-damage-free' structure of PSII from Thermosynechococcus vulcanus in the S1 state at a resolution of 1.95 ångströms using femtosecond X-ray pulses of the SPring-8 ångström compact free-electron laser (SACLA) and hundreds of large, highly isomorphous PSII crystals. Compared with the structure from XRD, the OEC in the X-ray free electron laser structure has Mn-Mn distances that are shorter by 0.1-0.2 ångströms. The valences of each manganese atom were tentatively assigned as Mn1D(III), Mn2C(IV), Mn3B(IV) and Mn4A(III), based on the average Mn-ligand distances and analysis of the Jahn-Teller axis on Mn(III). One of the oxo-bridged oxygens, O5, has significantly longer distances to Mn than do the other oxo-oxygen atoms, suggesting that O5 is a hydroxide ion instead of a normal oxygen dianion and therefore may serve as one of the substrate oxygen atoms. These findings provide a structural basis for the mechanism of oxygen evolution, and we expect that this structure will provide a blueprint for the design of artificial catalysts for water oxidation.


  • Organizational Affiliation

    Photosynthesis Research Center, Graduate School of Natural Science and Technology, Okayama University, 3-1-1 Tsushima Naka, Okayama 700-8530, Japan.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem Q(B) proteinA,
U [auth a]
344Thermostichus vulcanusMutation(s): 0 
EC: 1.10.3.9
Membrane Entity: Yes 
UniProt
Find proteins for P51765 (Thermostichus vulcanus)
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II CP47 chlorophyll apoproteinB,
V [auth b]
505Thermostichus vulcanusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for D0VWR1 (Thermostichus vulcanus)
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II 44 kDa 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 
UniProt
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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
Find proteins for P12238 (Thermostichus vulcanus)
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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
Find proteins for P19052 (Thermostichus vulcanus)
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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
Find proteins for P12240 (Thermostichus vulcanus)
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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
Find proteins for Q7DGD4 (Thermostichus vulcanus)
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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
Find proteins for P19054 (Thermostichus vulcanus)
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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
Find proteins for P12312 (Thermostichus vulcanus)
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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
Find proteins for D0VWR2 (Thermostichus vulcanus)
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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
Find proteins for P12313 (Thermostichus vulcanus)
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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
Find proteins for P56152 (Thermostichus vulcanus)
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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 Ycf12KA [auth y],
Q [auth Y]
30Thermostichus vulcanusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for D0VWR3 (Thermostichus vulcanus)
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein XLA [auth x],
R [auth X]
40Thermostichus vulcanusMutation(s): 0 
Membrane Entity: Yes 
UniProt
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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
Find proteins for D0VWR5 (Thermostichus vulcanus)
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II protein YT [auth R]34Thermostichus vulcanusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P0DM37 (Thermostichus vulcanus)
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Small Molecules
Ligands 20 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DGD
Query on DGD

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CI [auth c]
DI [auth c]
EI [auth c]
HJ [auth h]
ID [auth C]
CI [auth c],
DI [auth c],
EI [auth c],
HJ [auth h],
ID [auth C],
JD [auth C],
KD [auth C],
KE [auth H],
SI [auth d],
WD [auth D]
DIGALACTOSYL DIACYL GLYCEROL (DGDG)
C51 H96 O15
LDQFLSUQYHBXSX-HXXRYREZSA-N
CLA
Query on CLA

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AD [auth C]
AI [auth c]
BD [auth C]
CD [auth C]
DD [auth C]
AD [auth C],
AI [auth c],
BD [auth C],
CD [auth C],
DD [auth C],
ED [auth C],
FD [auth C],
IB [auth B],
JB [auth B],
JG [auth b],
KB [auth B],
KG [auth b],
LB [auth B],
LG [auth b],
MB [auth B],
MG [auth b],
NB [auth B],
NG [auth b],
NI [auth d],
OB [auth B],
OG [auth b],
OH [auth c],
OI [auth d],
PB [auth B],
PG [auth b],
PH [auth c],
PI [auth d],
QB [auth B],
QF [auth a],
QG [auth b],
QH [auth c],
RA [auth A],
RB [auth B],
RF [auth a],
RG [auth b],
RH [auth c],
SA [auth A],
SB [auth B],
SD [auth D],
SG [auth b],
SH [auth c],
TA [auth A],
TB [auth B],
TC [auth C],
TD [auth D],
TF [auth a],
TG [auth b],
TH [auth c],
UB [auth B],
UC [auth C],
UG [auth b],
UH [auth c],
VB [auth B],
VC [auth C],
VG [auth b],
VH [auth c],
WA [auth A],
WB [auth B],
WC [auth C],
WG [auth b],
WH [auth c],
XB [auth B],
XC [auth C],
XG [auth b],
XH [auth c],
YC [auth C],
YG [auth b],
YH [auth c],
ZC [auth C],
ZH [auth c]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
PHO
Query on PHO

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EG [auth a],
SF [auth a],
UA [auth A],
VA [auth A]
PHEOPHYTIN A
C55 H74 N4 O5
CQIKWXUXPNUNDV-RCBXBCQGSA-N
SQD
Query on SQD

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BC [auth B]
CB [auth A]
DJ [auth f]
GE [auth F]
MF [auth a]
BC [auth B],
CB [auth A],
DJ [auth f],
GE [auth F],
MF [auth a],
TE [auth L],
VF [auth a],
YA [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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CC [auth B]
CH [auth b]
DK [auth z]
FI [auth c]
GI [auth c]
CC [auth B],
CH [auth b],
DK [auth z],
FI [auth c],
GI [auth c],
JJ [auth j],
KF [auth Z],
LD [auth C],
MD [auth C],
ME [auth J],
SC [auth C],
WF [auth a]
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
PL9
Query on PL9

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BG [auth a],
FB [auth A],
RI [auth d],
VD [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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AJ [auth e]
DE [auth E]
OJ [auth l]
SE [auth L]
TI [auth d]
AJ [auth e],
DE [auth E],
OJ [auth l],
SE [auth L],
TI [auth d],
UI [auth d],
VI [auth d],
XD [auth D],
YD [auth D],
ZD [auth D]
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
HEC
Query on HEC

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

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

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AC [auth B]
AF [auth T]
AH [auth b]
BH [auth b]
BI [auth c]
AC [auth B],
AF [auth T],
AH [auth b],
BH [auth b],
BI [auth c],
CK [auth y],
GD [auth C],
GJ [auth h],
HD [auth C],
JE [auth H],
MJ [auth k],
NJ [auth k],
QE [auth K],
QI [auth d],
RE [auth K],
UD [auth D],
UF [auth a],
VJ [auth t],
XA [auth A],
YB [auth B],
ZB [auth B],
ZG [auth b]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
LMT
Query on LMT

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DB [auth A]
DC [auth B]
DH [auth b]
EE [auth E]
EJ [auth f]
DB [auth A],
DC [auth B],
DH [auth b],
EE [auth E],
EJ [auth f],
FG [auth b],
HI [auth c],
LF [auth a],
ND [auth C],
QC [auth B],
QJ [auth m],
RJ [auth m],
SJ [auth m],
UE [auth M]
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
OEX
Query on OEX

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

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CE [auth D]
EC [auth B]
EF [auth V]
EH [auth b]
FC [auth B]
CE [auth D],
EC [auth B],
EF [auth V],
EH [auth b],
FC [auth B],
FH [auth b],
GC [auth B],
GG [auth b],
HG [auth b],
II [auth c],
JI [auth c],
NC [auth B],
OC [auth B],
OD [auth C],
PD [auth C],
YE [auth O],
YI [auth d]
heptyl 1-thio-beta-D-glucopyranoside
C13 H26 O5 S
HPEGNLMTTNTJSP-LBELIVKGSA-N
GOL
Query on GOL

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AB [auth A]
AK [auth v]
BB [auth A]
BF [auth T]
BK [auth v]
AB [auth A],
AK [auth v],
BB [auth A],
BF [auth T],
BK [auth v],
CJ [auth f],
FF [auth V],
GF [auth V],
GH [auth b],
HC [auth B],
HF [auth V],
HH [auth b],
IC [auth B],
IE [auth F],
IF [auth V],
IH [auth b],
JC [auth B],
JH [auth b],
KC [auth B],
KH [auth b],
KI [auth c],
LC [auth B],
LH [auth b],
LI [auth c],
MC [auth B],
QD [auth C],
RC [auth B],
RD [auth C],
UJ [auth o],
WJ [auth t],
XE [auth O],
XF [auth a],
YF [auth a],
ZA [auth A],
ZE [auth T],
ZF [auth a],
ZJ [auth v]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
BCT
Query on BCT

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

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

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FJ [auth f]
HB [auth B]
HE [auth F]
IG [auth b]
NH [auth c]
FJ [auth f],
HB [auth B],
HE [auth F],
IG [auth b],
NH [auth c],
TJ [auth o],
WE [auth O]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL
Query on CL

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CF [auth U]
OA [auth A]
OF [auth a]
PA [auth A]
PF [auth a]
CF [auth U],
OA [auth A],
OF [auth a],
PA [auth A],
PF [auth a],
XJ [auth v]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG
Query on MG

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

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AE [auth D]
BE [auth D]
CG [auth a]
GB [auth A]
IJ [auth i]
AE [auth D],
BE [auth D],
CG [auth a],
GB [auth A],
IJ [auth i],
JF [auth X],
KJ [auth j],
LE [auth I],
MH [auth b],
MI [auth c],
NE [auth J],
PC [auth B],
PE [auth K],
PJ [auth m],
VE [auth M],
WI [auth d],
XI [auth d],
ZI [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: 1.95 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.200 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 123.744α = 90
b = 229.989β = 90
c = 288.337γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan--

Revision History  (Full details and data files)

  • Version 1.0: 2014-12-03
    Type: Initial release
  • Version 1.1: 2015-04-15
    Changes: Database references
  • Version 1.2: 2017-07-26
    Changes: Advisory, Data collection, Database references, Derived calculations, Source and taxonomy
  • Version 2.0: 2019-10-02
    Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
  • Version 2.1: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Derived calculations, Structure summary
  • Version 3.0: 2024-03-20
    Changes: Data collection, Database references, Non-polymer description, Source and taxonomy, Structure summary