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: 5.5 Å
  • R-Value Free: 0.291 
  • R-Value Work: 0.281 

wwPDB Validation 3D Report Full Report


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: 10.1038/nature13453
  • Primary Citation of Related Structures:  

  • 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 ligh ...

    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

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Photosystem II protein D1 1
A, a
334Thermosynechococcus elongatus (strain BP-1)Mutation(s): 0 
Gene Names: psbA1 (psbA-1)
EC: 1.10.3.9
Find proteins for P0A444 (Thermosynechococcus elongatus (strain BP-1))
Go to UniProtKB:  P0A444
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Photosystem II CP47 reaction center protein
B, b
504Thermosynechococcus elongatus (strain BP-1)Mutation(s): 0 
Gene Names: psbB
Find proteins for Q8DIQ1 (Thermosynechococcus elongatus (strain BP-1))
Go to UniProtKB:  Q8DIQ1
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Photosystem II CP43 reaction center protein
C, c
461Thermosynechococcus elongatus (strain BP-1)Mutation(s): 0 
Gene Names: psbC
Find proteins for Q8DIF8 (Thermosynechococcus elongatus (strain BP-1))
Go to UniProtKB:  Q8DIF8
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Photosystem II D2 protein
D, d
342Thermosynechococcus elongatus (strain BP-1)Mutation(s): 0 
Gene Names: psbD1, psbD2
EC: 1.10.3.9
Find proteins for Q8CM25 (Thermosynechococcus elongatus (strain BP-1))
Go to UniProtKB:  Q8CM25
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Cytochrome b559 subunit alpha
E, e
81Thermosynechococcus elongatus (strain BP-1)Mutation(s): 0 
Gene Names: psbE
Find proteins for Q8DIP0 (Thermosynechococcus elongatus (strain BP-1))
Go to UniProtKB:  Q8DIP0
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
Cytochrome b559 subunit beta
F, f
34Thermosynechococcus elongatus (strain BP-1)Mutation(s): 0 
Gene Names: psbF
Find proteins for Q8DIN9 (Thermosynechococcus elongatus (strain BP-1))
Go to UniProtKB:  Q8DIN9
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
Photosystem II reaction center protein H
H, h
65Thermosynechococcus elongatus (strain BP-1)Mutation(s): 0 
Gene Names: psbH
Find proteins for Q8DJ43 (Thermosynechococcus elongatus (strain BP-1))
Go to UniProtKB:  Q8DJ43
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
Photosystem II reaction center protein I
I, i
38Thermosynechococcus elongatus (strain BP-1)Mutation(s): 0 
Gene Names: psbI
Find proteins for Q8DJZ6 (Thermosynechococcus elongatus (strain BP-1))
Go to UniProtKB:  Q8DJZ6
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
Photosystem II reaction center protein J
J, j
40Thermosynechococcus elongatus (strain BP-1)Mutation(s): 0 
Gene Names: psbJ
Find proteins for P59087 (Thermosynechococcus elongatus (strain BP-1))
Go to UniProtKB:  P59087
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
Photosystem II reaction center protein K
K, k
37Thermosynechococcus elongatus (strain BP-1)Mutation(s): 0 
Gene Names: psbK
Find proteins for Q9F1K9 (Thermosynechococcus elongatus (strain BP-1))
Go to UniProtKB:  Q9F1K9
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
Photosystem II reaction center protein L
L, l
37Thermosynechococcus elongatus (strain BP-1)Mutation(s): 0 
Gene Names: psbL
Find proteins for Q8DIN8 (Thermosynechococcus elongatus (strain BP-1))
Go to UniProtKB:  Q8DIN8
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
Photosystem II reaction center protein M
M, m
34Thermosynechococcus elongatus (strain BP-1)Mutation(s): 0 
Gene Names: psbM
Find proteins for Q8DHA7 (Thermosynechococcus elongatus (strain BP-1))
Go to UniProtKB:  Q8DHA7
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
Photosystem II manganese-stabilizing polypeptide
O, o
243Thermosynechococcus elongatus (strain BP-1)Mutation(s): 0 
Gene Names: psbO
Find proteins for P0A431 (Thermosynechococcus elongatus (strain BP-1))
Go to UniProtKB:  P0A431
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
Photosystem II reaction center protein T
T, t
30Thermosynechococcus elongatus (strain BP-1)Mutation(s): 0 
Gene Names: psbT
Find proteins for Q8DIQ0 (Thermosynechococcus elongatus (strain BP-1))
Go to UniProtKB:  Q8DIQ0
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
Photosystem II 12 kDa extrinsic protein
U, u
97Thermosynechococcus elongatus (strain BP-1)Mutation(s): 0 
Gene Names: psbU
Find proteins for Q9F1L5 (Thermosynechococcus elongatus (strain BP-1))
Go to UniProtKB:  Q9F1L5
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
Cytochrome c-550
V, v
137Thermosynechococcus elongatus (strain BP-1)Mutation(s): 0 
Gene Names: psbV
Find proteins for P0A386 (Thermosynechococcus elongatus (strain BP-1))
Go to UniProtKB:  P0A386
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
Photosystem II reaction center X protein
X, x
39Thermosynechococcus elongatus (strain BP-1)Mutation(s): 0 
Gene Names: psbX
Find proteins for Q9F1R6 (Thermosynechococcus elongatus (strain BP-1))
Go to UniProtKB:  Q9F1R6
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
Photosystem II reaction center protein Ycf12
Y, y
29Thermosynechococcus elongatus (strain BP-1)Mutation(s): 0 
Gene Names: ycf12
Find proteins for Q8DJI1 (Thermosynechococcus elongatus (strain BP-1))
Go to UniProtKB:  Q8DJI1
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
Photosystem II reaction center protein Z
Z, z
62Thermosynechococcus elongatus (strain BP-1)Mutation(s): 0 
Gene Names: psbZ
Find proteins for Q8DHJ2 (Thermosynechococcus elongatus (strain BP-1))
Go to UniProtKB:  Q8DHJ2
Small Molecules
Ligands 15 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SQD
Query on SQD

Download SDF File 
Download CCD File 
a, A, B, b, D, d, l, L
1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL
SULFOQUINOVOSYLDIACYLGLYCEROL
C41 H78 O12 S
RVUUQPKXGDTQPG-JUDHQOGESA-N
 Ligand Interaction
CLA
Query on CLA

Download SDF File 
Download CCD File 
a, A, b, B, C, c, D, d
CHLOROPHYLL A
C55 H72 Mg N4 O5
VIQFHHZSLDFWDU-AENOIHSZSA-M
 Ligand Interaction
PL9
Query on PL9

Download SDF File 
Download CCD File 
a, A, D, 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
PLASTOQUINONE 9
C53 H80 O2
FKUYMLZIRPABFK-UHFFFAOYSA-N
 Ligand Interaction
OEX
Query on OEX

Download SDF File 
Download CCD File 
A, a
CA-MN4-O5 CLUSTER
Ca Mn4 O5
SEXWDHMBWJEXOJ-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download SDF File 
Download CCD File 
A, a, u, U
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
CA
Query on CA

Download SDF File 
Download CCD File 
b, B, f, F, O, o
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
DGD
Query on DGD

Download SDF File 
Download CCD File 
C, c, D, d, h, H
DIGALACTOSYL DIACYL GLYCEROL (DGDG)
C51 H96 O15
LDQFLSUQYHBXSX-HXXRYREZSA-N
 Ligand Interaction
LMG
Query on LMG

Download SDF File 
Download CCD File 
a, A, b, B, C, c, D, d, z, Z
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
 Ligand Interaction
BCT
Query on BCT

Download SDF File 
Download CCD File 
a, A
BICARBONATE ION
C H O3
BVKZGUZCCUSVTD-UHFFFAOYSA-M
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
J, j
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
HEM
Query on HEM

Download SDF File 
Download CCD File 
F, f, V, v
PROTOPORPHYRIN IX CONTAINING FE
HEME
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
BCR
Query on BCR

Download SDF File 
Download CCD File 
A, a, b, B, C, c, D, d, h, H, K, k, t, T
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
 Ligand Interaction
PHO
Query on PHO

Download SDF File 
Download CCD File 
A, a
PHEOPHYTIN A
C55 H74 N4 O5
CQIKWXUXPNUNDV-RCBXBCQGSA-N
 Ligand Interaction
FE2
Query on FE2

Download SDF File 
Download CCD File 
A, a
FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
 Ligand Interaction
LHG
Query on LHG

Download SDF File 
Download CCD File 
d, D, E, e, l, L
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 5.5 Å
  • R-Value Free: 0.291 
  • R-Value Work: 0.281 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 136.610α = 90.00
b = 228.090β = 90.00
c = 308.680γ = 90.00
Software Package:
Software NamePurpose
CrystFELdata scaling
Cheetahdata collection
PHENIXrefinement
PHASERphasing
CrystFELdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History