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PDBsum entry 2ybb

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protein ligands metals Protein-protein interface(s) links
Oxidoreductase PDB id
2ybb
Jmol
Contents
Protein chains
437 a.a.
179 a.a.
754 a.a.
378 a.a.
196 a.a.
144 a.a.
127 a.a.
154 a.a.
443 a.a.
424 a.a.
365 a.a.
241 a.a.
196 a.a.
99 a.a.
75 a.a.
66 a.a.
42 a.a.
62 a.a.
22 a.a.
514 a.a.
227 a.a.
261 a.a.
144 a.a.
109 a.a.
98 a.a.
84 a.a.
75 a.a.
73 a.a.
57 a.a.
49 a.a.
47 a.a.
43 a.a.
104 a.a.
474 a.a.
391 a.a.
281 a.a.
Ligands
SF4 ×7
FMN
NAI
FES ×4
HEM ×5
SMA ×2
UQ1 ×2
HEC ×2
CDL ×4
HEA ×2
Metals
_MG ×7
_CA
_CU ×3
_ZN
Waters ×1598
PDB id:
2ybb
Name: Oxidoreductase
Title: Fitted model for bovine mitochondrial supercomplex i1iii2iv single particle cryo-em (emd-1876)
Structure: Nadh-quinone oxidoreductase subunit 1. Chain: 1. Synonym: nadh dehydrogenase i chain 1, ndh-1 subunit 1. Other_details: nqo1 (51kda). Nadh-quinone oxidoreductase subunit 2. Chain: 2. Synonym: nadh dehydrogenase i chain 2, ndh-1 subunit 2. Other_details: nqo2 (24kda). Nadh-quinone oxidoreductase subunit 3.
Source: Thermus thermophilus. Organism_taxid: 300852. Strain: hb8. Atcc: 27624. Bos taurus. Cattle. Organism_taxid: 9913. Organ: heart. Tissue: muscle.
Authors: T.Althoff,D.J.Mills,J.-L.Popot,W.Kuehlbrandt
Key ref: T.Althoff et al. (2011). Arrangement of electron transport chain components in bovine mitochondrial supercomplex I1III2IV1. EMBO J, 30, 4652-4664. PubMed id: 21909073 DOI: 10.1038/emboj.2011.324
Date:
02-Mar-11     Release date:   19-Oct-11    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q56222  (NQO1_THET8) -  NADH-quinone oxidoreductase subunit 1
Seq:
Struc:
438 a.a.
437 a.a.
Protein chain
Pfam   ArchSchema ?
Q56221  (NQO2_THET8) -  NADH-quinone oxidoreductase subunit 2
Seq:
Struc:
181 a.a.
179 a.a.
Protein chain
Pfam   ArchSchema ?
Q56223  (NQO3_THET8) -  NADH-quinone oxidoreductase subunit 3
Seq:
Struc:
 
Seq:
Struc:
783 a.a.
754 a.a.
Protein chain
Pfam   ArchSchema ?
Q56220  (NQO4_THET8) -  NADH-quinone oxidoreductase subunit 4
Seq:
Struc:
409 a.a.
378 a.a.
Protein chain
Pfam   ArchSchema ?
P13272  (UCRI_BOVIN) -  Cytochrome b-c1 complex subunit Rieske, mitochondrial
Seq:
Struc:
274 a.a.
196 a.a.*
Protein chain
Pfam   ArchSchema ?
Q56218  (NQO6_THET8) -  NADH-quinone oxidoreductase subunit 6
Seq:
Struc:
181 a.a.
144 a.a.
Protein chain
Pfam   ArchSchema ?
Q5SKZ7  (NQO15_THET8) -  NADH-quinone oxidoreductase subunit 15
Seq:
Struc:
129 a.a.
127 a.a.
Protein chain
Pfam   ArchSchema ?
Q56224  (NQO9_THET8) -  NADH-quinone oxidoreductase subunit 9
Seq:
Struc:
182 a.a.
154 a.a.
Protein chains
Pfam   ArchSchema ?
P13272  (UCRI_BOVIN) -  Cytochrome b-c1 complex subunit Rieske, mitochondrial
Seq:
Struc:
274 a.a.
443 a.a.*
Protein chains
Pfam   ArchSchema ?
P31800  (QCR1_BOVIN) -  Cytochrome b-c1 complex subunit 1, mitochondrial
Seq:
Struc:
480 a.a.
443 a.a.
Protein chains
Pfam   ArchSchema ?
P23004  (QCR2_BOVIN) -  Cytochrome b-c1 complex subunit 2, mitochondrial
Seq:
Struc:
453 a.a.
424 a.a.*
Protein chains
Pfam   ArchSchema ?
P00157  (CYB_BOVIN) -  Cytochrome b
Seq:
Struc:
379 a.a.
365 a.a.
Protein chains
Pfam   ArchSchema ?
P00125  (CY1_BOVIN) -  Cytochrome c1, heme protein, mitochondrial
Seq:
Struc:
325 a.a.
241 a.a.
Protein chains
Pfam   ArchSchema ?
P00396  (COX1_BOVIN) -  Cytochrome c oxidase subunit 1
Seq:
Struc:
514 a.a.
241 a.a.*
Protein chains
Pfam   ArchSchema ?
P13272  (UCRI_BOVIN) -  Cytochrome b-c1 complex subunit Rieske, mitochondrial
Seq:
Struc:
274 a.a.
196 a.a.
Protein chains
Pfam   ArchSchema ?
P00129  (QCR7_BOVIN) -  Cytochrome b-c1 complex subunit 7
Seq:
Struc:
111 a.a.
99 a.a.*
Protein chains
Pfam   ArchSchema ?
P13271  (QCR8_BOVIN) -  Cytochrome b-c1 complex subunit 8
Seq:
Struc:
82 a.a.
75 a.a.
Protein chains
Pfam   ArchSchema ?
P00126  (QCR6_BOVIN) -  Cytochrome b-c1 complex subunit 6, mitochondrial
Seq:
Struc:
91 a.a.
66 a.a.
Protein chains
Pfam   ArchSchema ?
P13272  (UCRI_BOVIN) -  Cytochrome b-c1 complex subunit Rieske, mitochondrial
Seq:
Struc:
274 a.a.
42 a.a.
Protein chains
Pfam   ArchSchema ?
P00130  (QCR9_BOVIN) -  Cytochrome b-c1 complex subunit 9
Seq:
Struc:
64 a.a.
62 a.a.
Protein chains
Pfam   ArchSchema ?
P07552  (QCR10_BOVIN) -  Cytochrome b-c1 complex subunit 10
Seq:
Struc:
56 a.a.
22 a.a.*
Protein chain
Pfam   ArchSchema ?
P00396  (COX1_BOVIN) -  Cytochrome c oxidase subunit 1
Seq:
Struc:
514 a.a.
514 a.a.
Protein chain
Pfam   ArchSchema ?
P68530  (COX2_BOVIN) -  Cytochrome c oxidase subunit 2
Seq:
Struc:
227 a.a.
227 a.a.
Protein chain
Pfam   ArchSchema ?
P00415  (COX3_BOVIN) -  Cytochrome c oxidase subunit 3
Seq:
Struc:
261 a.a.
261 a.a.
Protein chain
Pfam   ArchSchema ?
P00423  (COX41_BOVIN) -  Cytochrome c oxidase subunit 4 isoform 1, mitochondrial
Seq:
Struc:
169 a.a.
144 a.a.
Protein chain
Pfam   ArchSchema ?
P00426  (COX5A_BOVIN) -  Cytochrome c oxidase subunit 5A, mitochondrial
Seq:
Struc:
152 a.a.
109 a.a.
Protein chain
Pfam   ArchSchema ?
P00428  (COX5B_BOVIN) -  Cytochrome c oxidase subunit 5B, mitochondrial
Seq:
Struc:
129 a.a.
98 a.a.
Protein chain
Pfam   ArchSchema ?
P07471  (CX6A2_BOVIN) -  Cytochrome c oxidase subunit 6A2, mitochondrial
Seq:
Struc:
97 a.a.
84 a.a.
Protein chain
Pfam   ArchSchema ?
P00429  (CX6B1_BOVIN) -  Cytochrome c oxidase subunit 6B1
Seq:
Struc:
86 a.a.
75 a.a.
Protein chain
Pfam   ArchSchema ?
P04038  (COX6C_BOVIN) -  Cytochrome c oxidase subunit 6C
Seq:
Struc:
74 a.a.
73 a.a.
Protein chain
Pfam   ArchSchema ?
P07470  (CX7A1_BOVIN) -  Cytochrome c oxidase subunit 7A1, mitochondrial
Seq:
Struc:
80 a.a.
57 a.a.
Protein chain
Pfam   ArchSchema ?
P13183  (COX7B_BOVIN) -  Cytochrome c oxidase subunit 7B, mitochondrial
Seq:
Struc:
80 a.a.
49 a.a.
Protein chain
Pfam   ArchSchema ?
P00430  (COX7C_BOVIN) -  Cytochrome c oxidase subunit 7C, mitochondrial
Seq:
Struc:
63 a.a.
47 a.a.
Protein chain
Pfam   ArchSchema ?
P10175  (COX8B_BOVIN) -  Cytochrome c oxidase subunit 8B, mitochondrial
Seq:
Struc:
70 a.a.
43 a.a.
Protein chain
Pfam   ArchSchema ?
P62894  (CYC_BOVIN) -  Cytochrome c
Seq:
Struc:
105 a.a.
104 a.a.
Protein chain
No UniProt id for this chain
Struc: 474 a.a.
Protein chains
No UniProt id for this chain
Struc: 391 a.a.
Protein chain
No UniProt id for this chain
Struc: 281 a.a.
Key:    PfamA domain  Secondary structure
* PDB and UniProt seqs differ at 512 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class 1: Chains 5, A: 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 = NAI)
corresponds exactly
+ 2 × ferricytochrome c
= quinone
+ 2 × ferrocytochrome c
+ 2 × H(+)
   Enzyme class 2: Chain D: E.C.1.9.3.1  - Cytochrome-c oxidase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: 4 ferrocytochrome c + O2 + 4 H+ = 4 ferricytochrome c + 2 H2O
4 × ferrocytochrome c
Bound ligand (Het Group name = SMA)
matches with 46.34% similarity
+
2 × O(2)
Bound ligand (Het Group name = HEM)
matches with 63.64% similarity
+ 4 × H(+)
= 4 × ferricytochrome c
+ 2 × H(2)O
      Cofactor: Cu cation
Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     membrane   14 terms 
  Biological process     oxidation-reduction process   23 terms 
  Biochemical function     electron carrier activity     22 terms  

 

 
    reference    
 
 
DOI no: 10.1038/emboj.2011.324 EMBO J 30:4652-4664 (2011)
PubMed id: 21909073  
 
 
Arrangement of electron transport chain components in bovine mitochondrial supercomplex I1III2IV1.
T.Althoff, D.J.Mills, J.L.Popot, W.Kühlbrandt.
 
  ABSTRACT  
 
No abstract given.

 

Literature references that cite this PDB file's key reference

  PubMed id Reference
23417064 R.Baradaran, J.M.Berrisford, G.S.Minhas, and L.A.Sazanov (2013).
Crystal structure of the entire respiratory complex I.
  Nature, 494, 443-448.
PDB codes: 4he8 4hea
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.