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 2.0 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: https://doi.org/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. 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

    1] Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287-1604, USA [2].


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem Q(B) protein 1A,
T [auth a]
334Thermosynechococcus vestitus BP-1Mutation(s): 0 
EC: 1.10.3.9
Membrane Entity: Yes 
UniProt
Find proteins for P0A444 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II core light harvesting proteinB,
U [auth b]
504Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q8DIQ1 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II CP43 proteinC,
V [auth c]
455Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q8DIF8 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II D2 proteinD,
W [auth d]
342Thermosynechococcus vestitus BP-1Mutation(s): 0 
EC: 1.10.3.9
Membrane Entity: Yes 
UniProt
Find proteins for Q8CM25 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b559 subunit alphaE,
X [auth e]
81Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q8DIP0 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b559 subunit betaF,
Y [auth f]
34Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q8DIN9 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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UniProt GroupQ8DIN9
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein HG [auth H],
Z [auth h]
65Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q8DJ43 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein IAA [auth i],
H [auth I]
38Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q8DJZ6 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein JBA [auth j],
I [auth J]
40Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P59087 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein KCA [auth k],
J [auth K]
37Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q9F1K9 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein LDA [auth l],
K [auth L]
37Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q8DIN8 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein MEA [auth m],
L [auth M]
34Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q8DHA7 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II manganese-stabilizing polypeptideFA [auth o],
M [auth O]
243Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P0A431 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein TGA [auth t],
N [auth T]
30Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q8DIQ0 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II 12 kDa extrinsic proteinHA [auth u],
O [auth U]
97Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q9F1L5 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c-550IA [auth v],
P [auth V]
137Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P0A386 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein Ycf12JA [auth y],
Q [auth Y]
29Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q8DJI1 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center X proteinKA [auth x],
R [auth X]
39Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q9F1R6 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein ZLA [auth z],
S [auth Z]
62Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q8DHJ2 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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Small Molecules
Ligands 14 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DGD
Query on DGD

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AG [auth j]
CD [auth H]
IF [auth c]
JF [auth c]
MC [auth C]
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
CLA
Query on CLA

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AC [auth C]
AE [auth b]
AF [auth c]
BC [auth C]
BE [auth b]
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
PHO
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
SQD
Query on SQD

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ED [auth L]
EG [auth l]
MD [auth a]
RF [auth d]
VD [auth a]
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
PL9
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
LHG
Query on LHG

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AB [auth A]
SE [auth b]
SF [auth d]
TF [auth d]
UF [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
HEM
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
BCR
Query on BCR

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BD [auth H]
CG [auth k]
DD [auth K]
DG [auth k]
GD [auth T]
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
OEX
Query on OEX

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

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

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

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AD [auth F]
BB [auth B]
FD [auth O]
FG [auth o]
TE [auth c]
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
CL
Query on CL

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

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BG [auth j]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
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
  • Version 2.0: 2023-09-27
    Changes: Data collection, Database references, Derived calculations, Non-polymer description, Refinement description