1QLE

CRYO-STRUCTURE OF THE PARACOCCUS DENITRIFICANS FOUR-SUBUNIT CYTOCHROME C OXIDASE IN THE COMPLETELY OXIDIZED STATE COMPLEXED WITH AN ANTIBODY FV FRAGMENT


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.309 
  • R-Value Work: 0.235 
  • R-Value Observed: 0.235 

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This is version 1.3 of the entry. See complete history


Literature

The Cytochrome C Oxidase from Paracoccus Denitrificans Does not Change the Metal Center Ligation Upon Reduction

Harrenga, A.Michel, H.

(1999) J Biol Chem 274: 33296

  • DOI: 10.1074/jbc.274.47.33296
  • Primary Citation of Related Structures:  
    1QLE

  • PubMed Abstract: 
  • Cytochrome c oxidase catalyzes the reduction of oxygen to water. This process is accompanied by the vectorial transport of protons across the mitochondrial or bacterial membrane ("proton pumping"). The mechanism of proton pumping is still a matter of ...

    Cytochrome c oxidase catalyzes the reduction of oxygen to water. This process is accompanied by the vectorial transport of protons across the mitochondrial or bacterial membrane ("proton pumping"). The mechanism of proton pumping is still a matter of debate. Many proposed mechanisms require structural changes during the reaction cycle of cytochrome c oxidase. Therefore, the structure of the cytochrome c oxidase was determined in the completely oxidized and in the completely reduced states at a temperature of 100 K. No ligand exchanges or other major structural changes upon reduction of the cytochrome c oxidase from Paracoccus denitrificans were observed. The three histidine Cu(B) ligands are well defined in the oxidized and in the reduced states. These results are hardly compatible with the "histidine cycle" mechanisms formulated previously.


    Organizational Affiliation

    Max-Planck-Institut für Biophysik, Abteilung für molekulare Membranbiologie, Heinrich-Hoffmann-Strasse 7, 60528 Frankfurt am Main, Germany.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
CYTOCHROME C OXIDASE POLYPEPTIDE I-BETAA538Paracoccus denitrificansMutation(s): 0 
Gene Names: ctaDII
EC: 1.9.3.1 (PDB Primary Data), 7.1.1.9 (UniProt)
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Complexes: Complex IV (Cytochrome C Oxidase)
Protein: 
Cytochrome C Oxidase, aa3, Fully Oxidized
Find proteins for P98002 (Paracoccus denitrificans)
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Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
CYTOCHROME C OXIDASE POLYPEPTIDE IIB252Paracoccus denitrificansMutation(s): 0 
Gene Names: ctaCcoiIctaB
EC: 1.9.3.1 (PDB Primary Data), 7.1.1.9 (UniProt)
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Complexes: Complex IV (Cytochrome C Oxidase)
Protein: 
Cytochrome C Oxidase, aa3, Fully Oxidized
Find proteins for P08306 (Paracoccus denitrificans)
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
CYTOCHROME C OXIDASE POLYPEPTIDE IIIC273Paracoccus denitrificansMutation(s): 0 
Gene Names: ctaEcoiII
EC: 1.9.3.1 (PDB Primary Data), 7.1.1.9 (UniProt)
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Complexes: Complex IV (Cytochrome C Oxidase)
Protein: 
Cytochrome C Oxidase, aa3, Fully Oxidized
Find proteins for P06030 (Paracoccus denitrificans)
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
CCYTOCHROME C OXIDASED43Paracoccus denitrificansMutation(s): 0 
Gene Names: ctaH
EC: 1.9.3.1 (PDB Primary Data), 7.1.1.9 (UniProt)
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Complexes: Complex IV (Cytochrome C Oxidase)
Protein: 
Cytochrome C Oxidase, aa3, Fully Oxidized
Find proteins for P77921 (Paracoccus denitrificans)
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
HEAVY CHAIN ANTIBODY FV FRAGMENTH119Mus musculusMutation(s): 0 
Protein Feature View
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
LIGHT CHAIN ANTIBODY FV FRAGMENTL108Mus musculusMutation(s): 0 
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  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEA
Query on HEA

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A
HEME-A
C49 H56 Fe N4 O6
ZGGYGTCPXNDTRV-PRYGPKJJSA-L
 Ligand Interaction
PC1
Query on PC1

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C
1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
C44 H88 N O8 P
NRJAVPSFFCBXDT-HUESYALOSA-N
 Ligand Interaction
CUA
Query on CUA

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B
DINUCLEAR COPPER ION
Cu2
ALKZAGKDWUSJED-UHFFFAOYSA-N
 Ligand Interaction
CU
Query on CU

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A
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
 Ligand Interaction
MN
Query on MN

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B
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

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A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.309 
  • R-Value Work: 0.235 
  • R-Value Observed: 0.235 
  • Space Group: P 4
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 205.2α = 90
b = 205.2β = 90
c = 81.1γ = 90
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-12-02
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-07-12
    Changes: Derived calculations