1QLE

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

• PDB DOI: https://doi.org/10.2210/pdb1QLE/pdb

• Classification: OXIDOREDUCTASE/IMMUNE SYSTEM
• Organism(s): Paracoccus denitrificans, Mus musculus
• Expression System: Escherichia coli
• Mutation(s): No 
• Membrane Protein: Yes  OPMPDBTMMemProtMDmpstruc


• Deposited: 1999-08-30 Released: 1999-12-02 
• Deposition Author(s): Harrenga, A., Michel, H.

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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 

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

• PubMed: 10559205 
• DOI: https://doi.org/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 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 6-mer - A1B1C1D1E1F1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 6-mer - A2B1C1D1E1 

Biological assembly 1 generated by PQS (software)

Macromolecule Content

• Total Structure Weight: 152.42 kDa 
• Atom Count: 10,762 
• Modelled Residue Count: 1,333 
• Deposited Residue Count: 1,333 
• Unique protein chains: 6

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CYTOCHROME C OXIDASE POLYPEPTIDE I-BETA	A	538	Paracoccus denitrificans	Mutation(s): 0  EC: 1.9.3.1 (PDB Primary Data), 7.1.1.9 (UniProt) Membrane Entity: Yes
UniProt
Find proteins for P98002 (Paracoccus denitrificans) Explore P98002  Go to UniProtKB:  P98002

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
CYTOCHROME C OXIDASE POLYPEPTIDE II	B	252	Paracoccus denitrificans	Mutation(s): 0  EC: 1.9.3.1 (PDB Primary Data), 7.1.1.9 (UniProt) Membrane Entity: Yes
UniProt
Find proteins for P08306 (Paracoccus denitrificans) Explore P08306  Go to UniProtKB:  P08306

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
CYTOCHROME C OXIDASE POLYPEPTIDE III	C	273	Paracoccus denitrificans	Mutation(s): 0  EC: 1.9.3.1 (PDB Primary Data), 7.1.1.9 (UniProt) Membrane Entity: Yes
UniProt
Find proteins for P06030 (Paracoccus denitrificans) Explore P06030  Go to UniProtKB:  P06030

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
CCYTOCHROME C OXIDASE	D	43	Paracoccus denitrificans	Mutation(s): 0  EC: 1.9.3.1 (PDB Primary Data), 7.1.1.9 (UniProt) Membrane Entity: Yes
UniProt
Find proteins for P77921 (Paracoccus denitrificans) Explore P77921  Go to UniProtKB:  P77921

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
HEAVY CHAIN ANTIBODY FV FRAGMENT	E [auth H]	119	Mus musculus	Mutation(s): 0

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
LIGHT CHAIN ANTIBODY FV FRAGMENT	F [auth L]	108	Mus musculus	Mutation(s): 0

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEA	G [auth A], H [auth A]	HEME-A C49 H56 Fe N4 O6 ZGGYGTCPXNDTRV-PRYGPKJJSA-L
PC1	M [auth C], N [auth C]	1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE C44 H88 N O8 P NRJAVPSFFCBXDT-HUESYALOSA-N
CUA	L [auth B]	DINUCLEAR COPPER ION Cu2 ALKZAGKDWUSJED-UHFFFAOYSA-N
CU	I [auth A]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N
MN	K [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N
CA	J [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

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 = 205.2	α = 90
b = 205.2	β = 90
c = 81.1	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1999-12-02 
Deposition Author(s): Harrenga, A., Michel, H.

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
• Version 2.0: 2022-05-04
  Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary
• Version 2.1: 2024-10-23
  Changes: Data collection, Structure summary