4PBU

Serial Time-resolved crystallography of Photosystem II using a femtosecond X-ray laser The S1 state


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 5.00 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.261 
  • R-Value Observed: 0.261 

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Ligand Structure Quality Assessment 


This is version 1.8 of the entry. See complete history


Literature

Serial time-resolved crystallography of photosystem II using a femtosecond X-ray laser.

Kupitz, C.Basu, S.Grotjohann, I.Fromme, R.Zatsepin, N.A.Rendek, K.N.Hunter, M.S.Shoeman, R.L.White, T.A.Wang, D.James, D.Yang, J.H.Cobb, D.E.Reeder, B.Sierra, R.G.Liu, H.Barty, A.Aquila, A.L.Deponte, D.Kirian, R.A.Bari, S.Bergkamp, J.J.Beyerlein, K.R.Bogan, M.J.Caleman, C.Chao, T.C.Conrad, C.E.Davis, K.M.Fleckenstein, H.Galli, L.Hau-Riege, S.P.Kassemeyer, S.Laksmono, H.Liang, M.Lomb, L.Marchesini, S.Martin, A.V.Messerschmidt, M.Milathianaki, D.Nass, K.Ros, A.Roy-Chowdhury, S.Schmidt, K.Seibert, M.Steinbrener, J.Stellato, F.Yan, L.Yoon, C.Moore, T.A.Moore, A.L.Pushkar, Y.Williams, G.J.Boutet, S.Doak, R.B.Weierstall, U.Frank, M.Chapman, H.N.Spence, J.C.Fromme, P.

(2014) Nature 513: 261-265

  • DOI: 10.1038/nature13453
  • Primary Citation of Related Structures:  
    4PBU, 4RVY

  • PubMed Abstract: 
  • Photosynthesis, a process catalysed by plants, algae and cyanobacteria converts sunlight to energy thus sustaining all higher life on Earth. Two large membrane protein complexes, photosystem I and II (PSI and PSII), act in series to catalyse the light-driven reactions in photosynthesis ...

    Photosynthesis, a process catalysed by plants, algae and cyanobacteria converts sunlight to energy thus sustaining all higher life on Earth. Two large membrane protein complexes, photosystem I and II (PSI and PSII), act in series to catalyse the light-driven reactions in photosynthesis. PSII catalyses the light-driven water splitting process, which maintains the Earth's oxygenic atmosphere. In this process, the oxygen-evolving complex (OEC) of PSII cycles through five states, S0 to S4, in which four electrons are sequentially extracted from the OEC in four light-driven charge-separation events. Here we describe time resolved experiments on PSII nano/microcrystals from Thermosynechococcus elongatus performed with the recently developed technique of serial femtosecond crystallography. Structures have been determined from PSII in the dark S1 state and after double laser excitation (putative S3 state) at 5 and 5.5 Å resolution, respectively. The results provide evidence that PSII undergoes significant conformational changes at the electron acceptor side and at the Mn4CaO5 core of the OEC. These include an elongation of the metal cluster, accompanied by changes in the protein environment, which could allow for binding of the second substrate water molecule between the more distant protruding Mn (referred to as the 'dangler' Mn) and the Mn3CaOx cubane in the S2 to S3 transition, as predicted by spectroscopic and computational studies. This work shows the great potential for time-resolved serial femtosecond crystallography for investigation of catalytic processes in biomolecules.


    Organizational Affiliation

    Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287-1604, USA.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem Q(B) protein 1A, T [auth a]334Thermosynechococcus vestitus BP-1Mutation(s): 0 
Gene Names: psbA1psbA-1tlr1843
EC: 1.10.3.9
Membrane Entity: Yes 
UniProt
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II core light harvesting proteinB, U [auth b]504Thermosynechococcus vestitus BP-1Mutation(s): 0 
Gene Names: psbBtlr1530
Membrane Entity: Yes 
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II CP43 proteinC, V [auth c]455Thermosynechococcus vestitus BP-1Mutation(s): 0 
Gene Names: psbCtlr1631
Membrane Entity: Yes 
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II D2 proteinD, W [auth d]342Thermosynechococcus vestitus BP-1Mutation(s): 0 
Gene Names: psbD1tlr0455psbD2tlr1630
EC: 1.10.3.9
Membrane Entity: Yes 
UniProt
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome b559 subunit alphaE, X [auth e]81Thermosynechococcus vestitus BP-1Mutation(s): 0 
Gene Names: psbEtsr1541
Membrane Entity: Yes 
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome b559 subunit betaF, Y [auth f]34Thermosynechococcus vestitus BP-1Mutation(s): 0 
Gene Names: psbFtsr1542
Membrane Entity: Yes 
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II reaction center protein HG [auth H], Z [auth h]65Thermosynechococcus vestitus BP-1Mutation(s): 0 
Gene Names: psbHtsl1386
Membrane Entity: Yes 
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II reaction center protein IH [auth I], AA [auth i]38Thermosynechococcus vestitus BP-1Mutation(s): 0 
Gene Names: psbItsr1074
Membrane Entity: Yes 
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II reaction center protein JI [auth J], BA [auth j]40Thermosynechococcus vestitus BP-1Mutation(s): 0 
Gene Names: psbJtsr1544
Membrane Entity: Yes 
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II reaction center protein KJ [auth K], CA [auth k]37Thermosynechococcus vestitus BP-1Mutation(s): 0 
Gene Names: psbKtsl0176
Membrane Entity: Yes 
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II reaction center protein LK [auth L], DA [auth l]37Thermosynechococcus vestitus BP-1Mutation(s): 0 
Gene Names: psbLtsr1543
Membrane Entity: Yes 
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II reaction center protein ML [auth M], EA [auth m]34Thermosynechococcus vestitus BP-1Mutation(s): 0 
Gene Names: psbMtsl2052
Membrane Entity: Yes 
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II manganese-stabilizing polypeptideM [auth O], FA [auth o]243Thermosynechococcus vestitus BP-1Mutation(s): 0 
Gene Names: psbOtll0444
Membrane Entity: Yes 
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II reaction center protein TN [auth T], GA [auth t]30Thermosynechococcus vestitus BP-1Mutation(s): 0 
Gene Names: psbTtsr1531
Membrane Entity: Yes 
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II 12 kDa extrinsic proteinO [auth U], HA [auth u]97Thermosynechococcus vestitus BP-1Mutation(s): 0 
Gene Names: psbUtll2409
Membrane Entity: Yes 
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome c-550P [auth V], IA [auth v]137Thermosynechococcus vestitus BP-1Mutation(s): 0 
Gene Names: psbVtll1285
Membrane Entity: Yes 
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II reaction center protein Ycf12Q [auth Y], JA [auth y]29Thermosynechococcus vestitus BP-1Mutation(s): 0 
Gene Names: ycf12tsr1242
Membrane Entity: Yes 
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II reaction center X proteinR [auth X], KA [auth x]39Thermosynechococcus vestitus BP-1Mutation(s): 0 
Gene Names: psbXtsr2013
Membrane Entity: Yes 
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II reaction center protein ZS [auth Z], LA [auth z]62Thermosynechococcus vestitus BP-1Mutation(s): 0 
Gene Names: psbZtsr1967
Membrane Entity: Yes 
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  • Reference Sequence
Small Molecules
Ligands 14 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DGD (Subject of Investigation/LOI)
Query on DGD

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AG [auth j] , CD [auth H] , IF [auth c] , JF [auth c] , MC [auth C] , NC [auth C] , OC [auth C] , QF [auth d] , 
AG [auth j], CD [auth H], IF [auth c], JF [auth c], MC [auth C], NC [auth C], OC [auth C], QF [auth d], UC [auth D], ZF [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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AC [auth C] , AE [auth b] , AF [auth c] , BC [auth C] , BE [auth b] , BF [auth c] , CB [auth B] , CC [auth C] , 
AC [auth C], AE [auth b], AF [auth c], BC [auth C], BE [auth b], BF [auth c], CB [auth B], CC [auth C], CE [auth b], CF [auth c], DB [auth B], DC [auth C], DE [auth b], DF [auth c], EB [auth B], EC [auth C], EE [auth b], EF [auth c], FB [auth B], FC [auth C], FE [auth b], FF [auth c], GB [auth B], GC [auth C], GE [auth b], GF [auth c], HB [auth B], HC [auth C], HE [auth b], IB [auth B], IC [auth C], IE [auth b], JB [auth B], JC [auth C], JE [auth b], KB [auth B], KE [auth b], LB [auth B], LE [auth b], LF [auth d], MB [auth B], ME [auth b], NB [auth B], NE [auth b], NF [auth d], OB [auth B], OE [auth b], OF [auth d], PB [auth B], PE [auth b], QB [auth B], QC [auth D], QD [auth a], RA [auth A], RB [auth B], RC [auth D], RD [auth a], SA [auth A], SD [auth a], UA [auth A], UE [auth c], VE [auth c], WE [auth c], XB [auth C], XE [auth c], YB [auth C], YE [auth c], ZA [auth A], ZB [auth C], ZE [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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MF [auth d], PC [auth D], TA [auth A], WD [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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ED [auth L], EG [auth l], MD [auth a], RF [auth d], VD [auth a], XA [auth A], YA [auth A], ZC [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
 Ligand Interaction
PL9 (Subject of Investigation/LOI)
Query on PL9

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PF [auth d], TC [auth D], UD [auth a], WA [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
 Ligand Interaction
LHG (Subject of Investigation/LOI)
Query on LHG

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AB [auth A] , SE [auth b] , SF [auth d] , TF [auth d] , UF [auth d] , VB [auth B] , VC [auth D] , WC [auth D] , 
AB [auth A], SE [auth b], SF [auth d], TF [auth d], UF [auth d], VB [auth B], VC [auth D], WC [auth D], XC [auth D], XD [auth a]
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
 Ligand Interaction
HEM (Subject of Investigation/LOI)
Query on HEM

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HG [auth v], JD [auth V], VF [auth e], YC [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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BD [auth H] , CG [auth k] , DD [auth K] , DG [auth k] , GD [auth T] , HD [auth T] , HF [auth c] , KC [auth C] , 
BD [auth H], CG [auth k], DD [auth K], DG [auth k], GD [auth T], HD [auth T], HF [auth c], KC [auth C], KD [auth Y], KF [auth c], LC [auth C], QE [auth b], RE [auth b], SB [auth B], SC [auth D], TB [auth B], TD [auth a], UB [auth B], VA [auth A], WB [auth B], WF [auth f], YF [auth h]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
 Ligand Interaction
OEX (Subject of Investigation/LOI)
Query on OEX

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LD [auth a], MA [auth A]CA-MN4-O5 CLUSTER
Ca Mn4 O5
SEXWDHMBWJEXOJ-UHFFFAOYSA-N
 Ligand Interaction
BCT
Query on BCT

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

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

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AD [auth F], BB [auth B], FD [auth O], FG [auth o], TE [auth c], XF [auth f], ZD [auth b]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

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GG [auth v], ID [auth V], OA [auth A], OD [auth a], PA [auth A], PD [auth a]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
MG
Query on MG

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BG [auth j]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 5.00 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.261 
  • R-Value Observed: 0.261 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 133.25α = 90
b = 226.26β = 90
c = 307.09γ = 90
Software Package:
Software NamePurpose
Cheetahdata collection
CrystFELdata reduction
PDB_EXTRACTdata extraction
PHASERphasing
PHENIXrefinement

Structure Validation

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Ligand Structure Quality Assessment  



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Department of Energy (DOE, United States)United StatesDE-SC0001016
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States1R01GM095583
National Science Foundation (NSF, United States)United StatesMCB-1021557
National Science Foundation (NSF, United States)United StatesMCB- 1120997
German Research Foundation (DFG)GermanyEXC 306
German Research Foundation (DFG)Germany?Center for Ultrafast Imaging?
Max Planck SocietyGermanyAtomic, Molecular and Optical Sciences Program
Department of Energy (DOE, United States)United StatesChemical Sciences Geosciences and Biosciences Division
SLACUnited StatesLDRD
Department of Energy (DOE, United States)United StatesDE-AC52- 07NA27344
UCOP Lab Fee ProgramUnited States118036
LLNL LDRDUnited States12-ERD-031
Hamburg Initiative for Excellence in ResearchGermanyHamburg Ministry of Science and Research and Joachim Herz Stiftung
National Science Foundation (NSF, United States)United StatesBioFEL Science Technology Center (award 1231306)

Revision History  (Full details and data files)

  • Version 1.0: 2014-07-16
    Type: Initial release
  • Version 1.1: 2014-07-30
    Changes: Database references
  • Version 1.2: 2014-08-06
    Changes: Structure summary
  • Version 1.3: 2014-10-01
    Changes: Database references
  • Version 1.4: 2015-09-23
    Changes: Data collection
  • Version 1.5: 2017-09-06
    Changes: Author supporting evidence, Derived calculations
  • Version 1.6: 2017-11-22
    Changes: Refinement description
  • Version 1.7: 2018-09-19
    Changes: Data collection
  • Version 1.8: 2019-11-27
    Changes: Author supporting evidence