5WS6

Native XFEL structure of Photosystem II (preflash two-flash dataset


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.175 
  • R-Value Work: 0.129 
  • R-Value Observed: 0.131 

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Ligand Structure Quality Assessment 


This is version 2.1 of the entry. See complete history


Literature

Light-induced structural changes and the site of O=O bond formation in PSII caught by XFEL.

Suga, M.Akita, F.Sugahara, M.Kubo, M.Nakajima, Y.Nakane, T.Yamashita, K.Umena, Y.Nakabayashi, M.Yamane, T.Nakano, T.Suzuki, M.Masuda, T.Inoue, S.Kimura, T.Nomura, T.Yonekura, S.Yu, L.J.Sakamoto, T.Motomura, T.Chen, J.H.Kato, Y.Noguchi, T.Tono, K.Joti, Y.Kameshima, T.Hatsui, T.Nango, E.Tanaka, R.Naitow, H.Matsuura, Y.Yamashita, A.Yamamoto, M.Nureki, O.Yabashi, M.Ishikawa, T.Iwata, S.Shen, J.R.

(2017) Nature 543: 131-135

  • DOI: 10.1038/nature21400
  • Primary Citation of Related Structures:  
    5GTH, 5GTI, 5WS5, 5WS6

  • PubMed Abstract: 
  • Photosystem II (PSII) is a huge membrane-protein complex consisting of 20 different subunits with a total molecular mass of 350 kDa for a monomer. It catalyses light-driven water oxidation at its catalytic centre, the oxygen-evolving complex (OEC). The structure of PSII has been analysed at 1 ...

    Photosystem II (PSII) is a huge membrane-protein complex consisting of 20 different subunits with a total molecular mass of 350 kDa for a monomer. It catalyses light-driven water oxidation at its catalytic centre, the oxygen-evolving complex (OEC). The structure of PSII has been analysed at 1.9 Å resolution by synchrotron radiation X-rays, which revealed that the OEC is a Mn 4 CaO 5 cluster organized in an asymmetric, 'distorted-chair' form. This structure was further analysed with femtosecond X-ray free electron lasers (XFEL), providing the 'radiation damage-free' structure. The mechanism of O=O bond formation, however, remains obscure owing to the lack of intermediate-state structures. Here we describe the structural changes in PSII induced by two-flash illumination at room temperature at a resolution of 2.35 Å using time-resolved serial femtosecond crystallography with an XFEL provided by the SPring-8 ångström compact free-electron laser. An isomorphous difference Fourier map between the two-flash and dark-adapted states revealed two areas of apparent changes: around the Q B /non-haem iron and the Mn 4 CaO 5 cluster. The changes around the Q B /non-haem iron region reflected the electron and proton transfers induced by the two-flash illumination. In the region around the OEC, a water molecule located 3.5 Å from the Mn 4 CaO 5 cluster disappeared from the map upon two-flash illumination. This reduced the distance between another water molecule and the oxygen atom O4, suggesting that proton transfer also occurred. Importantly, the two-flash-minus-dark isomorphous difference Fourier map showed an apparent positive peak around O5, a unique μ 4 -oxo-bridge located in the quasi-centre of Mn1 and Mn4 (refs 4,5). This suggests the insertion of a new oxygen atom (O6) close to O5, providing an O=O distance of 1.5 Å between these two oxygen atoms. This provides a mechanism for the O=O bond formation consistent with that proposed previously.


    Organizational Affiliation

    Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, No.20 Nanxincun, Xiangshan, Beijing 100093, China.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II D1 proteinA, U [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
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II CP47 reaction center proteinB, V [auth b]505Thermostichus vulcanusMutation(s): 0 
Gene Names: psbB
Membrane Entity: Yes 
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II CP43 chlorophyll proteinC, W [auth c]455Thermostichus vulcanusMutation(s): 0 
Gene Names: psbC
Membrane Entity: Yes 
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II D2 proteinD, X [auth d]342Thermostichus vulcanusMutation(s): 0 
Gene Names: psbD
EC: 1.10.3.9
Membrane Entity: Yes 
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome b559 subunit alphaE, Y [auth e]84Thermostichus vulcanusMutation(s): 0 
Gene Names: psbE
Membrane Entity: Yes 
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome b559 subunit betaF, Z [auth f]44Thermostichus 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]65Thermostichus vulcanusMutation(s): 0 
Gene Names: psbH
Membrane Entity: Yes 
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II reaction center protein IH [auth I], BA [auth i]38Thermostichus vulcanusMutation(s): 0 
Gene Names: psbI
Membrane Entity: Yes 
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II reaction center protein JI [auth J], CA [auth j]39Thermostichus vulcanusMutation(s): 0 
Gene Names: psbJ
Membrane Entity: Yes 
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II reaction center protein KJ [auth K], DA [auth k]37Thermostichus vulcanusMutation(s): 0 
Gene Names: psbK
Membrane Entity: Yes 
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II reaction center protein LK [auth L], EA [auth l]37Thermostichus 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]36Thermostichus vulcanusMutation(s): 0 
Gene Names: psbM
Membrane Entity: Yes 
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II manganese-stabilizing polypeptideM [auth O], GA [auth o]244Thermostichus vulcanusMutation(s): 0 
Gene Names: psbO
Membrane Entity: Yes 
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II reaction center protein TN [auth T], HA [auth t]32Thermostichus 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]104Thermostichus vulcanusMutation(s): 0 
Gene Names: psbU
Membrane Entity: Yes 
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome c-550P [auth V], JA [auth v]137Thermostichus vulcanusMutation(s): 0 
Gene Names: psbV
Membrane Entity: Yes 
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II reaction center protein XQ [auth X], KA [auth x]40Thermostichus vulcanusMutation(s): 0 
Gene Names: psbX
Membrane Entity: Yes 
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II reaction center protein Ycf12R [auth Y], LA [auth y]30Thermostichus vulcanusMutation(s): 0 
Gene Names: ycf12psbY
Membrane Entity: Yes 
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II reaction center protein ZS [auth Z], MA [auth z]62Thermostichus vulcanusMutation(s): 0 
Gene Names: psbZ
Membrane Entity: Yes 
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II protein YT [auth R]34Thermostichus vulcanusMutation(s): 0 
Gene Names: psbY
Membrane Entity: Yes 
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  • Reference Sequence
Small Molecules
Ligands 21 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DGD (Subject of Investigation/LOI)
Query on DGD

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AD [auth C], BD [auth C], CD [auth C], II [auth h], KH [auth c], LH [auth c], MH [auth c], YD [auth H]DIGALACTOSYL DIACYL GLYCEROL (DGDG)
C51 H96 O15
LDQFLSUQYHBXSX-HXXRYREZSA-N
 Ligand Interaction
CLA (Subject of Investigation/LOI)
Query on CLA

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AG [auth b] , AH [auth c] , BG [auth b] , BH [auth c] , CG [auth b] , CH [auth c] , DG [auth b] , DH [auth c] , 
AG [auth b], AH [auth c], BG [auth b], BH [auth c], CG [auth b], CH [auth c], DG [auth b], DH [auth c], EG [auth b], EH [auth c], FG [auth b], FH [auth c], GH [auth c], HB [auth B], HH [auth c], IB [auth B], JB [auth B], JD [auth D], KB [auth B], KD [auth D], LB [auth B], LC [auth C], MB [auth B], MC [auth C], NB [auth B], NC [auth C], OB [auth B], OC [auth C], OF [auth a], PB [auth B], PC [auth C], 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], TB [auth B], TC [auth C], TF [auth b], UB [auth B], UC [auth C], UF [auth b], UH [auth d], VA [auth A], VB [auth B], VC [auth C], VE [auth a], VF [auth b], VG [auth c], VH [auth d], WB [auth B], WC [auth C], WE [auth a], WF [auth b], WG [auth c], XC [auth C], XF [auth b], XG [auth c], YF [auth b], YG [auth c], ZE [auth a], ZF [auth b], ZG [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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TA [auth A], UA [auth A], XE [auth a], YE [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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AC [auth B], BF [auth a], DF [auth a], FI [auth f], JG [auth b], WD [auth F], XA [auth A], 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
 Ligand Interaction
LMG (Subject of Investigation/LOI)
Query on LMG

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BC [auth B] , BE [auth J] , DD [auth C] , EB [auth A] , ED [auth C] , JF [auth a] , KG [auth b] , KI [auth j] , 
BC [auth B], BE [auth J], DD [auth C], EB [auth A], ED [auth C], JF [auth a], KG [auth b], KI [auth j], NH [auth c], OH [auth c], SE [auth Z], ZI [auth z]
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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CB [auth A], GF [auth a], MD [auth D], XH [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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AI [auth d] , GE [auth L] , LF [auth a] , ND [auth D] , OD [auth D] , OI [auth l] , SD [auth D] , TD [auth E] , 
AI [auth d], GE [auth L], LF [auth a], ND [auth D], OD [auth D], OI [auth l], SD [auth D], TD [auth E], YH [auth d], ZH [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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OE [auth V], WI [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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EI [auth e], VD [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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AF [auth a] , FE [auth K] , GG [auth b] , HG [auth b] , HI [auth h] , IG [auth b] , IH [auth c] , JH [auth c] , 
AF [auth a], FE [auth K], GG [auth b], HG [auth b], HI [auth h], IG [auth b], IH [auth c], JH [auth c], LD [auth D], LE [auth T], NI [auth k], RE [auth Y], TI [auth t], WA [auth A], WH [auth d], XB [auth B], XD [auth H], YB [auth B], YC [auth C], YI [auth y], ZB [auth B], ZC [auth C]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
 Ligand Interaction
LMT (Subject of Investigation/LOI)
Query on LMT

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CC [auth B] , DI [auth e] , GB [auth A] , HE [auth M] , JE [auth M] , KC [auth B] , KF [auth a] , LG [auth b] , 
CC [auth B], DI [auth e], GB [auth A], HE [auth M], JE [auth M], KC [auth B], KF [auth a], LG [auth b], PF [auth a], QI [auth m], SI [auth t], TG [auth b], UD [auth E], ZD [auth I]
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
 Ligand Interaction
OEY (Subject of Investigation/LOI)
Query on OEY

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BB [auth A], FF [auth a]CA-MN4-O6 CLUSTER
Ca Mn4 O6
VXLJVOKMVCJEPF-UHFFFAOYSA-N
 Ligand Interaction
OEX (Subject of Investigation/LOI)
Query on OEX

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AB [auth A], EF [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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DC [auth B] , EC [auth B] , FC [auth B] , FD [auth C] , GD [auth C] , GI [auth h] , IC [auth B] , MG [auth b] , 
DC [auth B], EC [auth B], FC [auth B], FD [auth C], GD [auth C], GI [auth h], IC [auth B], MG [auth b], NG [auth b], OG [auth b], PE [auth V], PH [auth c], RD [auth D], RG [auth b], SH [auth c]
heptyl 1-thio-beta-D-glucopyranoside
C13 H26 O5 S
HPEGNLMTTNTJSP-LBELIVKGSA-N
 Ligand Interaction
GOL
Query on GOL

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CF [auth a] , GC [auth B] , HC [auth B] , ID [auth C] , IF [auth a] , NE [auth V] , QG [auth b] , UG [auth c] , 
CF [auth a], GC [auth B], HC [auth B], ID [auth C], IF [auth a], NE [auth V], QG [auth b], UG [auth c], VI [auth v], YA [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
BCT
Query on BCT

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

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

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HD [auth C], KE [auth O], ME [auth V], PG [auth b], QH [auth c], RH [auth c], RI [auth o], UI [auth v]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

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FB [auth A], NF [auth a], OA [auth A], UE [auth a]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
MG
Query on MG

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

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AE [auth I] , BI [auth d] , CE [auth J] , CI [auth d] , DB [auth A] , EE [auth K] , HF [auth a] , IE [auth M] , 
AE [auth I], BI [auth d], CE [auth J], CI [auth d], DB [auth A], EE [auth K], HF [auth a], IE [auth M], JC [auth B], JI [auth i], LI [auth j], PD [auth D], PI [auth m], QD [auth D], QE [auth X], SG [auth b], TH [auth c], XI [auth x]
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: 2.35 Å
  • R-Value Free: 0.175 
  • R-Value Work: 0.129 
  • R-Value Observed: 0.131 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 124.96α = 90
b = 230.22β = 90
c = 286.02γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
CrystFELdata reduction
CrystFELdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

  • Deposited Date: 2016-12-05 
  • Released Date: 2017-03-15 
  • Deposition Author(s): Suga, M., Shen, J.R.

Revision History  (Full details and data files)

  • Version 1.0: 2017-03-15
    Type: Initial release
  • 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