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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This is version 2.1 of the entry. See complete history


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: 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) ...

    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
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem Q(B) proteinA, U [auth a]344Thermosynechococcus vulcanusMutation(s): 0 
Gene Names: psbApsbA-1
EC: 1.10.3.9
Membrane Entity: Yes 
UniProt
Find proteins for P51765 (Thermosynechococcus vulcanus)
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II CP47 chlorophyll apoproteinB, V [auth b]505Thermosynechococcus vulcanusMutation(s): 0 
Gene Names: psbB
Membrane Entity: Yes 
UniProt
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II 44 kDa reaction center proteinC, W [auth c]455Thermosynechococcus vulcanusMutation(s): 0 
Gene Names: psbC
Membrane Entity: Yes 
UniProt
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II D2 proteinD, X [auth d]342Thermosynechococcus vulcanusMutation(s): 0 
Gene Names: psbD
EC: 1.10.3.9
Membrane Entity: Yes 
UniProt
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome b559 subunit alphaE, Y [auth e]84Thermosynechococcus vulcanusMutation(s): 0 
Gene Names: psbE
Membrane Entity: Yes 
UniProt
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome b559 subunit betaF, Z [auth f]44Thermosynechococcus vulcanusMutation(s): 0 
Gene Names: psbF
Membrane Entity: Yes 
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II reaction center protein HG [auth H], AA [auth h]65Thermosynechococcus vulcanusMutation(s): 0 
Gene Names: psbH
Membrane Entity: Yes 
UniProt
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II reaction center protein IH [auth I], BA [auth i]38Thermosynechococcus vulcanusMutation(s): 0 
Gene Names: psbI
Membrane Entity: Yes 
UniProt
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II reaction center protein JI [auth J], CA [auth j]39Thermosynechococcus vulcanusMutation(s): 0 
Gene Names: psbJ
Membrane Entity: Yes 
UniProt
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II reaction center protein KJ [auth K], DA [auth k]37Thermosynechococcus vulcanusMutation(s): 0 
Gene Names: psbK
Membrane Entity: Yes 
UniProt
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II reaction center protein LK [auth L], EA [auth l]37Thermosynechococcus vulcanusMutation(s): 0 
Gene Names: psbL
Membrane Entity: Yes 
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II reaction center protein ML [auth M], FA [auth m]36Thermosynechococcus vulcanusMutation(s): 0 
Gene Names: psbM
Membrane Entity: Yes 
UniProt
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II manganese-stabilizing polypeptideM [auth O], GA [auth o]244Thermosynechococcus vulcanusMutation(s): 0 
Gene Names: psbO
Membrane Entity: Yes 
UniProt
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II reaction center protein TN [auth T], HA [auth t]32Thermosynechococcus vulcanusMutation(s): 0 
Gene Names: psbT
Membrane Entity: Yes 
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II 12 kDa extrinsic proteinO [auth U], IA [auth u]104Thermosynechococcus vulcanusMutation(s): 0 
Gene Names: psbU
Membrane Entity: Yes 
UniProt
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome c-550P [auth V], JA [auth v]137Thermosynechococcus vulcanusMutation(s): 0 
Gene Names: psbV
Membrane Entity: Yes 
UniProt
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II reaction center protein Ycf12Q [auth Y], KA [auth y]30Thermosynechococcus vulcanusMutation(s): 0 
Gene Names: ycf12psbY
Membrane Entity: Yes 
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II reaction center protein XR [auth X], LA [auth x]40Thermosynechococcus vulcanusMutation(s): 0 
Gene Names: psbX
Membrane Entity: Yes 
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II reaction center protein ZS [auth Z], MA [auth z]62Thermosynechococcus vulcanusMutation(s): 0 
Gene Names: psbZ
Membrane Entity: Yes 
UniProt
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II protein YT [auth R]34Thermosynechococcus vulcanusMutation(s): 0 
Gene Names: psbY
Membrane Entity: Yes 
UniProt
Find proteins for P0DM37 (Thermosynechococcus vulcanus)
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  • Reference Sequence
Small Molecules
Ligands 20 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DGD (Subject of Investigation/LOI)
Query on DGD

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CI [auth c] , DI [auth c] , EI [auth c] , HJ [auth h] , ID [auth C] , JD [auth C] , KD [auth C] , KE [auth H] , 
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
 Ligand Interaction
CLA (Subject of Investigation/LOI)
Query on CLA

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AD [auth C] , AI [auth c] , BD [auth C] , CD [auth C] , DD [auth C] , ED [auth C] , FD [auth C] , IB [auth B] , 
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
 Ligand Interaction
PHO (Subject of Investigation/LOI)
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
 Ligand Interaction
SQD (Subject of Investigation/LOI)
Query on SQD

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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
 Ligand Interaction
LMG (Subject of Investigation/LOI)
Query on LMG

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CC [auth B] , CH [auth b] , DK [auth z] , FI [auth c] , GI [auth c] , JJ [auth j] , KF [auth Z] , LD [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
 Ligand Interaction
PL9 (Subject of Investigation/LOI)
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
 Ligand Interaction
LHG (Subject of Investigation/LOI)
Query on LHG

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AJ [auth e] , DE [auth E] , OJ [auth l] , SE [auth L] , TI [auth d] , UI [auth d] , VI [auth d] , XD [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
 Ligand Interaction
HEC (Subject of Investigation/LOI)
Query on HEC

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DF [auth V], YJ [auth v]HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
 Ligand Interaction
HEM (Subject of Investigation/LOI)
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
 Ligand Interaction
BCR (Subject of Investigation/LOI)
Query on BCR

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AC [auth B] , AF [auth T] , AH [auth b] , BH [auth b] , BI [auth c] , CK [auth y] , GD [auth C] , GJ [auth h] , 
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
 Ligand Interaction
LMT (Subject of Investigation/LOI)
Query on LMT

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DB [auth A] , DC [auth B] , DH [auth b] , EE [auth E] , EJ [auth f] , FG [auth b] , HI [auth c] , LF [auth a] , 
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
 Ligand Interaction
OEX (Subject of Investigation/LOI)
Query on OEX

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AG [auth a], EB [auth A]CA-MN4-O5 CLUSTER
Ca Mn4 O5
SEXWDHMBWJEXOJ-UHFFFAOYSA-N
 Ligand Interaction
HTG (Subject of Investigation/LOI)
Query on HTG

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CE [auth D] , EC [auth B] , EF [auth V] , EH [auth b] , FC [auth B] , FH [auth b] , GC [auth B] , GG [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
 Ligand Interaction
GOL
Query on GOL

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AB [auth A] , AK [auth v] , BB [auth A] , BF [auth T] , BK [auth v] , CJ [auth f] , FF [auth V] , GF [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
 Ligand Interaction
BCT
Query on BCT

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

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

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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
 Ligand Interaction
CL
Query on CL

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

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

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AE [auth D] , BE [auth D] , CG [auth a] , GB [auth A] , IJ [auth i] , JF [auth X] , KJ [auth j] , LE [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
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D 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