4RVY

Serial Time resolved crystallography of Photosystem II using a femtosecond X-ray laser. The S state after two flashes (S3)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 5.50 Å
  • R-Value Free: 0.291 
  • R-Value Work: 0.281 
  • R-Value Observed: 0.281 

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Ligand Structure Quality Assessment 


This is version 1.2 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 ...

    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 II protein D1 1A,
B [auth a]
334Thermosynechococcus vestitus BP-1Mutation(s): 0 
Gene Names: psbA1psbA-1tlr1843
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
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II CP47 reaction center proteinC [auth B],
D [auth b]
504Thermosynechococcus vestitus BP-1Mutation(s): 0 
Gene Names: psbBtlr1530
Membrane Entity: Yes 
UniProt
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II CP43 reaction center proteinE [auth C],
F [auth c]
461Thermosynechococcus vestitus BP-1Mutation(s): 0 
Gene Names: psbCtlr1631
Membrane Entity: Yes 
UniProt
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II D2 proteinG [auth D],
H [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 alphaI [auth E],
J [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 betaK [auth F],
L [auth f]
34Thermosynechococcus vestitus BP-1Mutation(s): 0 
Gene Names: psbFtsr1542
Membrane Entity: Yes 
UniProt
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II reaction center protein HM [auth H],
N [auth h]
65Thermosynechococcus vestitus BP-1Mutation(s): 0 
Gene Names: psbHtsl1386
Membrane Entity: Yes 
UniProt
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II reaction center protein IO [auth I],
P [auth i]
38Thermosynechococcus vestitus BP-1Mutation(s): 0 
Gene Names: psbItsr1074
Membrane Entity: Yes 
UniProt
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II reaction center protein JQ [auth J],
R [auth j]
40Thermosynechococcus vestitus BP-1Mutation(s): 0 
Gene Names: psbJtsr1544
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
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II reaction center protein KS [auth K],
T [auth k]
37Thermosynechococcus vestitus BP-1Mutation(s): 0 
Gene Names: psbKtsl0176
Membrane Entity: Yes 
UniProt
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II reaction center protein LU [auth L],
V [auth l]
37Thermosynechococcus vestitus BP-1Mutation(s): 0 
Gene Names: psbLtsr1543
Membrane Entity: Yes 
UniProt
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II reaction center protein MW [auth M],
X [auth m]
34Thermosynechococcus vestitus BP-1Mutation(s): 0 
Gene Names: psbMtsl2052
Membrane Entity: Yes 
UniProt
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II manganese-stabilizing polypeptideY [auth O],
Z [auth o]
243Thermosynechococcus vestitus BP-1Mutation(s): 0 
Gene Names: psbOtll0444
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
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II reaction center protein TAA [auth T],
BA [auth t]
30Thermosynechococcus vestitus BP-1Mutation(s): 0 
Gene Names: psbTtsr1531
Membrane Entity: Yes 
UniProt
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II 12 kDa extrinsic proteinCA [auth U],
DA [auth u]
97Thermosynechococcus vestitus BP-1Mutation(s): 0 
Gene Names: psbUtll2409
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
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome c-550EA [auth V],
FA [auth v]
137Thermosynechococcus vestitus BP-1Mutation(s): 0 
Gene Names: psbVtll1285
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
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II reaction center X proteinGA [auth X],
HA [auth x]
39Thermosynechococcus vestitus BP-1Mutation(s): 0 
Gene Names: psbXtsr2013
Membrane Entity: Yes 
UniProt
Find proteins for Q9F1R6 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II reaction center protein Ycf12IA [auth Y],
JA [auth y]
29Thermosynechococcus vestitus BP-1Mutation(s): 0 
Gene Names: ycf12tsr1242
Membrane Entity: Yes 
UniProt
Find proteins for Q8DJI1 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II reaction center protein ZKA [auth Z],
LA [auth z]
62Thermosynechococcus vestitus BP-1Mutation(s): 0 
Gene Names: psbZtsr1967
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 15 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DGD
Query on DGD

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DF [auth D],
OF [auth d],
PE [auth c],
QE [auth c],
RE [auth c],
DF [auth D],
OF [auth d],
PE [auth c],
QE [auth c],
RE [auth c],
VD [auth C],
WD [auth C],
XD [auth C],
XF [auth H],
ZF [auth h]
DIGALACTOSYL DIACYL GLYCEROL (DGDG)
C51 H96 O15
LDQFLSUQYHBXSX-HXXRYREZSA-N
 Ligand Interaction
CLA
Query on CLA

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AC [auth B],
AD [auth b],
AE [auth c],
BC [auth B],
BE [auth c],
AC [auth B],
AD [auth b],
AE [auth c],
BC [auth B],
BE [auth c],
CB [auth a],
CC [auth B],
CE [auth c],
DB [auth a],
DC [auth B],
DE [auth c],
EC [auth B],
EE [auth c],
FE [auth c],
FF [auth d],
GB [auth a],
GD [auth C],
GE [auth c],
GF [auth d],
HD [auth C],
HE [auth c],
HF [auth d],
ID [auth C],
IE [auth c],
JD [auth C],
JE [auth c],
KD [auth C],
KE [auth c],
LC [auth b],
LD [auth C],
LE [auth c],
MC [auth b],
MD [auth C],
ME [auth c],
NC [auth b],
ND [auth C],
OA [auth A],
OC [auth b],
OD [auth C],
PA [auth A],
PB [auth B],
PC [auth b],
PD [auth C],
QB [auth B],
QC [auth b],
QD [auth C],
RB [auth B],
RC [auth b],
RD [auth C],
SA [auth A],
SB [auth B],
SC [auth b],
SD [auth C],
TB [auth B],
TC [auth b],
UB [auth B],
UC [auth b],
UE [auth D],
VB [auth B],
VC [auth b],
VE [auth D],
WB [auth B],
WC [auth b],
WE [auth D],
XB [auth B],
XC [auth b],
YB [auth B],
YC [auth b],
ZB [auth B],
ZC [auth b]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
 Ligand Interaction
PHO
Query on PHO

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EB [auth a],
FB [auth a],
QA [auth A],
RA [auth A]
PHEOPHYTIN A
C55 H74 N4 O5
CQIKWXUXPNUNDV-RCBXBCQGSA-N
 Ligand Interaction
SQD
Query on SQD

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ED [auth b],
EF [auth D],
GG [auth L],
IB [auth a],
IG [auth l],
ED [auth b],
EF [auth D],
GG [auth L],
IB [auth a],
IG [auth l],
JG [auth l],
KC [auth b],
OB [auth B],
PF [auth d],
UA [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
Query on LMG

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CD [auth b],
HC [auth B],
KF [auth d],
NB [auth a],
SE [auth c],
CD [auth b],
HC [auth B],
KF [auth d],
NB [auth a],
SE [auth c],
TE [auth c],
UG [auth Z],
VG [auth z],
YD [auth C],
ZA [auth A],
ZD [auth C],
ZE [auth D]
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
 Ligand Interaction
PL9
Query on PL9

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BF [auth D],
MB [auth a],
MF [auth d],
YA [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
Query on LHG

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AF [auth D],
CF [auth D],
HG [auth L],
JF [auth d],
KG [auth l],
AF [auth D],
CF [auth D],
HG [auth L],
JF [auth d],
KG [auth l],
LF [auth d],
NF [auth d],
QF [auth E],
RF [auth e],
YE [auth D]
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
 Ligand Interaction
HEM
Query on HEM

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SF [auth F],
SG [auth V],
TG [auth v],
UF [auth f]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
BCR
Query on BCR

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BD [auth b],
CG [auth K],
DG [auth K],
EG [auth k],
FC [auth B],
BD [auth b],
CG [auth K],
DG [auth K],
EG [auth k],
FC [auth B],
FD [auth b],
FG [auth k],
GC [auth B],
HB [auth a],
IF [auth d],
JC [auth B],
NE [auth c],
NG [auth T],
OE [auth c],
OG [auth T],
PG [auth t],
TA [auth A],
TD [auth C],
UD [auth C],
WF [auth H],
XE [auth D],
YF [auth h]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
 Ligand Interaction
OEX
Query on OEX

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

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

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DD [auth b],
IC [auth B],
LG [auth O],
MG [auth o],
TF [auth F],
DD [auth b],
IC [auth B],
LG [auth O],
MG [auth o],
TF [auth F],
VF [auth f]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

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JB [auth a],
KB [auth a],
QG [auth U],
RG [auth u],
VA [auth A],
JB [auth a],
KB [auth a],
QG [auth U],
RG [auth u],
VA [auth A],
WA [auth A]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
MG
Query on MG

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 5.50 Å
  • R-Value Free: 0.291 
  • R-Value Work: 0.281 
  • R-Value Observed: 0.281 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 136.61α = 90
b = 228.09β = 90
c = 308.68γ = 90
Software Package:
Software NamePurpose
Cheetahdata collection
PHASERphasing
PHENIXrefinement
CrystFELdata reduction
CrystFELdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History