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PDBsum entry 3cxh

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protein ligands Protein-protein interface(s) links
Oxidoreductase PDB id
3cxh
Jmol
Contents
Protein chains
431 a.a. *
352 a.a. *
385 a.a. *
246 a.a. *
185 a.a. *
74 a.a. *
125 a.a. *
93 a.a. *
55 a.a. *
127 a.a. *
107 a.a. *
112 a.a. *
Ligands
UMQ ×2
HEM ×7
SMA ×2
8PE ×2
CN6 ×2
9PE ×2
7PH ×2
FES ×2
6PH ×2
SUC
Waters ×548
* Residue conservation analysis
PDB id:
3cxh
Name: Oxidoreductase
Title: Structure of yeast complex iii with isoform-2 cytochromE C b definition of a minimal core interface for electron transfe
Structure: Cytochrome b-c1 complex subunit 1, mitochondrial. Chain: a, l. Synonym: ubiquinol- cytochromE-C reductase complex core pro core protein i, complex iii subunit 1. Cytochrome b-c1 complex subunit 2, mitochondrial. Chain: b, m. Synonym: ubiquinol- cytochromE-C reductase complex core pro core protein ii, complex iii subunit 2. Cytochrome b.
Source: Saccharomyces cerevisiae. Yeast. Mus musculus. House mouse. Organism_taxid: 10090. Expressed in: escherichia coli. Expression_system_taxid: 562. Yeast
Resolution:
2.50Å     R-factor:   0.225     R-free:   0.256
Authors: S.R.N.Solmaz,C.Hunte
Key ref:
S.R.Solmaz and C.Hunte (2008). Structure of complex III with bound cytochrome c in reduced state and definition of a minimal core interface for electron transfer. J Biol Chem, 283, 17542-17549. PubMed id: 18390544 DOI: 10.1074/jbc.M710126200
Date:
24-Apr-08     Release date:   13-May-08    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P07256  (QCR1_YEAST) -  Cytochrome b-c1 complex subunit 1, mitochondrial
Seq:
Struc:
457 a.a.
431 a.a.*
Protein chains
Pfam   ArchSchema ?
P07257  (QCR2_YEAST) -  Cytochrome b-c1 complex subunit 2, mitochondrial
Seq:
Struc:
368 a.a.
352 a.a.
Protein chains
Pfam   ArchSchema ?
P00163  (CYB_YEAST) -  Cytochrome b
Seq:
Struc:
385 a.a.
385 a.a.
Protein chains
Pfam   ArchSchema ?
P07143  (CY1_YEAST) -  Cytochrome c1, heme protein, mitochondrial
Seq:
Struc:
309 a.a.
246 a.a.
Protein chains
Pfam   ArchSchema ?
P08067  (UCRI_YEAST) -  Cytochrome b-c1 complex subunit Rieske, mitochondrial
Seq:
Struc:
215 a.a.
185 a.a.
Protein chains
Pfam   ArchSchema ?
P00127  (QCR6_YEAST) -  Cytochrome b-c1 complex subunit 6
Seq:
Struc:
147 a.a.
74 a.a.
Protein chains
Pfam   ArchSchema ?
P00128  (QCR7_YEAST) -  Cytochrome b-c1 complex subunit 7
Seq:
Struc:
127 a.a.
125 a.a.
Protein chains
Pfam   ArchSchema ?
P08525  (QCR8_YEAST) -  Cytochrome b-c1 complex subunit 8
Seq:
Struc:
94 a.a.
93 a.a.
Protein chains
Pfam   ArchSchema ?
P22289  (QCR9_YEAST) -  Cytochrome b-c1 complex subunit 9
Seq:
Struc:
66 a.a.
55 a.a.
Protein chains
No UniProt id for this chain
Struc: 127 a.a.
Protein chains
No UniProt id for this chain
Struc: 107 a.a.
Protein chain
Pfam   ArchSchema ?
P00045  (CYC7_YEAST) -  Cytochrome c iso-2
Seq:
Struc:
113 a.a.
112 a.a.*
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 2 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: Chains E, P: E.C.1.10.2.2  - Quinol--cytochrome-c reductase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Quinol + 2 ferricytochrome c = quinone + 2 ferrocytochrome c + 2 H+
Quinol
Bound ligand (Het Group name = SMA)
matches with 46.34% similarity
+
2 × ferricytochrome c
Bound ligand (Het Group name = HEM)
matches with 63.64% similarity
= quinone
+ 2 × ferrocytochrome c
+ 2 × H(+)
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     membrane   9 terms 
  Biological process     oxidation-reduction process   9 terms 
  Biochemical function     catalytic activity     12 terms  

 

 
    reference    
 
 
DOI no: 10.1074/jbc.M710126200 J Biol Chem 283:17542-17549 (2008)
PubMed id: 18390544  
 
 
Structure of complex III with bound cytochrome c in reduced state and definition of a minimal core interface for electron transfer.
S.R.Solmaz, C.Hunte.
 
  ABSTRACT  
 
In cellular respiration, cytochrome c transfers electrons from cytochrome bc(1) complex (complex III) to cytochrome c oxidase by transiently binding to the membrane proteins. Here, we report the structure of isoform-1 cytochrome c bound to cytochrome bc(1) complex at 1.9 A resolution in reduced state. The dimer structure is asymmetric. Monovalent cytochrome c binding is correlated with conformational changes of the Rieske head domain and subunit QCR6p and with a higher number of interfacial water molecules bound to cytochrome c(1). Pronounced hydration and a "mobility mismatch" at the interface with disordered charged residues on the cytochrome c side are favorable for transient binding. Within the hydrophobic interface, a minimal core was identified by comparison with the novel structure of the complex with bound isoform-2 cytochrome c. Four core interactions encircle the heme cofactors surrounded by variable interactions. The core interface may be a feature to gain specificity for formation of the reactive complex.
 
  Selected figure(s)  
 
Figure 2.
FIGURE 2. The interface of cyt c (green) and cyt c[1] (pink) at high resolution. Hemes, black; water molecules, cyan. A, 2F[o] - F[c] electron density map at the interface, contoured at 1 and drawn as a blue mesh. B, stereo view of the core interface. The minimal core interface (dashed lines) is defined by four residue pairs (labeled) that were identified in three structures of the electron transfer complex. The contact of the heme CBC atoms is shown as a dotted line.
Figure 3.
FIGURE 3. The building blocks of the interface. The cyt c[1] (A)-cyt c (B) interface is shown in open book view. The heme groups (black) are encircled by the core interface (orange area, interacting atoms as orange spheres). The variable interface (yellow) surrounds the latter. Residues mediating long-range electrostatic interactions (pink and blue for negative and positive charges, respectively) form a semicircle around the central hydrophobic contact site. C, the semitransparent surface representation of cyt c[1] (gray) and cyt c (green) shows the position of these long-range electrostatic interactions in the high resolution structure (Table 1) as highlighted in blue-green and pink (positive and negative charges, respectively). Heme groups are shown in black. A high number of water molecules (cyan spheres) are bound at the interface of cyt c[1] (D) but not of cyt c (E). Only two of these water molecules form hydrogen bonds to both cyt c[1] and cyt c (green spheres). F, interface water molecules bound to cyt c[1] colored in cyan and green (as in D) are superimposed with all surface water molecules that are present at the other cyt c[1] with the non-occupied cyt c binding site (dark blue spheres). Surface water molecules up to a distance of 3.5 Å are included.
 
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2008, 283, 17542-17549) copyright 2008.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21359406 I.Bertini, G.Cavallaro, and A.Rosato (2011).
Principles and patterns in the interaction between mono-heme cytochrome c and its partners in electron transfer processes.
  Metallomics, 3, 354-362.  
20352475 L.Macchioni, T.Corazzi, M.Davidescu, E.Francescangeli, R.Roberti, and L.Corazzi (2010).
Cytochrome c redox state influences the binding and release of cytochrome c in model membranes and in brain mitochondria.
  Mol Cell Biochem, 341, 149-157.  
20624914 M.Bestwick, M.Y.Jeong, O.Khalimonchuk, H.Kim, and D.R.Winge (2010).
Analysis of Leigh syndrome mutations in the yeast SURF1 homolog reveals a new member of the cytochrome oxidase assembly factor family.
  Mol Cell Biol, 30, 4480-4491.  
19892700 M.Castellani, R.Covian, T.Kleinschroth, O.Anderka, B.Ludwig, and B.L.Trumpower (2010).
Direct demonstration of half-of-the-sites reactivity in the dimeric cytochrome bc1 complex: enzyme with one inactive monomer is fully active but unable to activate the second ubiquinol oxidation site in response to ligand binding at the ubiquinone reduction site.
  J Biol Chem, 285, 502-510.  
19189962 D.Baniulis, E.Yamashita, J.P.Whitelegge, A.I.Zatsman, M.P.Hendrich, S.S.Hasan, C.M.Ryan, and W.A.Cramer (2009).
Structure-Function, Stability, and Chemical Modification of the Cyanobacterial Cytochrome b6f Complex from Nostoc sp. PCC 7120.
  J Biol Chem, 284, 9861-9869.
PDB code: 2zt9
19254042 J.W.Cooley, D.W.Lee, and F.Daldal (2009).
Across membrane communication between the Q(o) and Q(i) active sites of cytochrome bc(1).
  Biochemistry, 48, 1888-1899.  
19890332 M.Nojiri, H.Koteishi, T.Nakagami, K.Kobayashi, T.Inoue, K.Yamaguchi, and S.Suzuki (2009).
Structural basis of inter-protein electron transfer for nitrite reduction in denitrification.
  Nature, 462, 117-120.
PDB code: 2zon
19236481 V.Zara, L.Conte, and B.L.Trumpower (2009).
Evidence that the assembly of the yeast cytochrome bc1 complex involves the formation of a large core structure in the inner mitochondrial membrane.
  FEBS J, 276, 1900-1914.  
19006325 J.Janzon, Q.Yuan, F.Malatesta, P.Hellwig, B.Ludwig, B.Durham, and F.Millett (2008).
Probing the Paracoccus denitrificans cytochrome c(1)-cytochrome c(552) interaction by mutagenesis and fast kinetics.
  Biochemistry, 47, 12974-12984.  
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 code is shown on the right.