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PDBsum entry 1r2c
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protein ligands metals Protein-protein interface(s) links
Photosynthesis PDB id
1r2c

 

 

 

 

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JSmol PyMol  
Contents
Protein chains
332 a.a. *
273 a.a. *
323 a.a. *
258 a.a. *
Ligands
HEM ×4
BCB ×4
BPB ×2
UQ2
LDA ×6
SO4 ×4
MQ7
NS5
Metals
FE2
* Residue conservation analysis
PDB id:
1r2c
Name: Photosynthesis
Title: Photosynthetic reaction center blastochloris viridis (atcc)
Structure: Photosynthetic reaction center cytochromE C subunit precursor. Chain: c. Synonym: c558/c559. Reaction center protein l chain. Chain: l. Synonym: photosynthetic reaction center l subunit. Reaction center protein m chain. Chain: m.
Source: Blastochloris viridis. Organism_taxid: 1079. Organism_taxid: 1079
Biol. unit: Tetramer (from PQS)
Resolution:
2.86Å     R-factor:   0.202     R-free:   0.228
Authors: R.H.Baxter,N.Ponomarenko,R.Pahl,V.Srajer,K.Moffat,J.R.Norris
Key ref:
R.H.Baxter et al. (2004). Time-resolved crystallographic studies of light-induced structural changes in the photosynthetic reaction center. Proc Natl Acad Sci U S A, 101, 5982-5987. PubMed id: 15073325 DOI: 10.1073/pnas.0306840101
Date:
26-Sep-03     Release date:   27-Apr-04    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P07173  (CYCR_BLAVI) -  Photosynthetic reaction center cytochrome c subunit from Blastochloris viridis
Seq:
Struc: 		356 a.a.
332 a.a.
Protein chain
Pfam   ArchSchema ?
P06009  (RCEL_BLAVI) -  Reaction center protein L chain from Blastochloris viridis
Seq:
Struc: 		274 a.a.
273 a.a.
Protein chain
Pfam   ArchSchema ?
P06010  (RCEM_BLAVI) -  Reaction center protein M chain from Blastochloris viridis
Seq:
Struc: 		324 a.a.
323 a.a.
Protein chain
Pfam   ArchSchema ?
P06008  (RCEH_BLAVI) -  Reaction center protein H chain from Blastochloris viridis
Seq:
Struc: 		258 a.a.
258 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 

 
DOI no: 10.1073/pnas.0306840101 Proc Natl Acad Sci U S A 101:5982-5987 (2004)
PubMed id: 15073325  
 
 
Time-resolved crystallographic studies of light-induced structural changes in the photosynthetic reaction center.
R.H.Baxter, N.Ponomarenko, V.Srajer, R.Pahl, K.Moffat, J.R.Norris.
 
  ABSTRACT  
 
Light-induced structural changes in the bacterial reaction center were studied by a time-resolved crystallographic experiment. Crystals of protein from Blastochloris viridis (formerly Rhodopseudomonas viridis) were reconstituted with ubiquinone and analyzed by monochromatic and Laue diffraction, in the dark and 3 ms after illuminating the crystal with a pulsed laser (630 nm, 3 mJ/pulse, 7 ns duration). Refinement of monochromatic data shows that ubiquinone binds only in the "proximal" Q(B) binding site. No significant structural difference was observed between the light and dark datasets; in particular, no quinone motion was detected. This result may be reconciled with previous studies by postulating equilibration of the "distal" and "proximal" binding sites upon extended dark adaption, and in which movement of ubiquinone is not the conformational gate for the first electron transfer between Q(A) and Q(B).
 
  Selected figure(s)  
 
Figure 1.
Fig. 1. The Q[B] binding site and its immediate environment, showing the two positions observed for ubiquinone binding. The distal position is shown in purple, the proximal in orange. Shown are coordinates from 1AIG [PDB] and 1AIJ [PDB] (16). Figs. 1, 3 and 4 were prepared with PYMOL. 		Figure 3.
Fig. 3. Electron density for the Q[B] binding pocket. 2F[o] - F[c] maps show density from a simulated-annealing omit map omitting Q[B] (green) and density for the refined model (cyan). (A) Monochromatic dataset, 2.9-Å resolution, contour level 0.5 .(B) Dark Laue dataset, 3.3-Å resolution, contoured at 0.3 .
 
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20431017 A.B.Wöhri, G.Katona, L.C.Johansson, E.Fritz, E.Malmerberg, M.Andersson, J.Vincent, M.Eklund, M.Cammarata, M.Wulff, J.Davidsson, G.Groenhof, and R.Neutze (2010).
Light-induced structural changes in a photosynthetic reaction center caught by Laue diffraction.
  Science, 328, 630-633.
PDB codes: 2x5u 2x5v
20164644 S.Westenhoff, E.Nazarenko, E.Malmerberg, J.Davidsson, G.Katona, and R.Neutze (2010).
Time-resolved structural studies of protein reaction dynamics: a smorgasbord of X-ray approaches.
  Acta Crystallogr A, 66, 207-219.  
20119482 A.Specht, F.Bolze, Z.Omran, J.F.Nicoud, and M.Goeldner (2009).
Photochemical tools to study dynamic biological processes.
  HFSP J, 3, 255-264.  
18330555 H.Ohmori, L.Nagy, M.Dorogi, and M.Terazima (2008).
Charge stabilization in reaction center protein investigated by optical heterodyne detected transient grating spectroscopy.
  Eur Biophys J, 37, 1167-1174.  
18351332 J.Pieper, T.Hauss, A.Buchsteiner, and G.Renger (2008).
The effect of hydration on protein flexibility in photosystem II of green plants studied by quasielastic neutron scattering.
  Eur Biophys J, 37, 657-663.  
17914477 D.Bourgeois, F.Schotte, M.Brunori, and B.Vallone (2007).
Time-resolved methods in biophysics. 6. Time-resolved Laue crystallography as a tool to investigate photo-activated protein dynamics.
  Photochem Photobiol Sci, 6, 1047-1056.  
17159147 L.Li, D.Mustafi, Q.Fu, V.Tereshko, D.L.Chen, J.D.Tice, and R.F.Ismagilov (2006).
Nanoliter microfluidic hybrid method for simultaneous screening and optimization validated with crystallization of membrane proteins.
  Proc Natl Acad Sci U S A, 103, 19243-19248.
PDB code: 2i5n
16129597 D.Bourgeois, and A.Royant (2005).
Advances in kinetic protein crystallography.
  Curr Opin Struct Biol, 15, 538-547.  
15870207 H.Ihee, S.Rajagopal, V.Srajer, R.Pahl, S.Anderson, M.Schmidt, F.Schotte, P.A.Anfinrud, M.Wulff, and K.Moffat (2005).
Visualizing reaction pathways in photoactive yellow protein from nanoseconds to seconds.
  Proc Natl Acad Sci U S A, 102, 7145-7150.
PDB codes: 1ts0 1ts6 1ts7 1ts8
16254054 H.Ishikita, and E.W.Knapp (2005).
Induced conformational changes upon Cd2+ binding at photosynthetic reaction centers.
  Proc Natl Acad Sci U S A, 102, 16215-16220.  
15613631 L.Giachini, F.Francia, A.Mallardi, G.Palazzo, E.Carpenè, F.Boscherini, and G.Venturoli (2005).
Multiple scattering x-ray absorption studies of Zn2+ binding sites in bacterial photosynthetic reaction centers.
  Biophys J, 88, 2038-2046.  
15858271 R.H.Baxter, B.L.Seagle, N.Ponomarenko, and J.R.Norris (2005).
Cryogenic structure of the photosynthetic reaction center of Blastochloris viridis in the light and dark.
  Acta Crystallogr D Biol Crystallogr, 61, 605-612.
PDB code: 1vrn
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.

 

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