1QLE | pdb_00001qle

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 OPM PDBTM MemProtMD mpstruc

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

Experimental Data Snapshot

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

wwPDB Validation 3D Report Full Report

This is version 2.1 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 Biological Chem 274: 33296

PubMed: 10559205 Search on PubMed
DOI: https://doi.org/10.1074/jbc.274.47.33296
Primary Citation 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.

Organizational Affiliation

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

Macromolecule Content

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

Macromolecules

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| 3D Structure

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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P98002
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P08306
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P06030
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P77921
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

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

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| 3D Structure

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	3D Interactions
HEA Query on HEA Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A]	G [auth A], H [auth A]	HEME-A C₄₉ H₅₆ Fe N₄ O₆ ZGGYGTCPXNDTRV-PRYGPKJJSA-L		Interactions Focus chain G [auth A] Focus chain H [auth A]
PC1 Query on PC1 Download:Ideal Coordinates CCD File SDF format, chain M [auth C] SDF format, chain N [auth C] MOL2 format, chain M [auth C] MOL2 format, chain N [auth C] mmCIF format, chain M [auth C] mmCIF format, chain N [auth C]	M [auth C], N [auth C]	1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE C₄₄ H₈₈ N O₈ P NRJAVPSFFCBXDT-HUESYALOSA-N		Interactions Focus chain M [auth C] Focus chain N [auth C]
CUA Query on CUA Download:Ideal Coordinates CCD File SDF format, chain L [auth B] MOL2 format, chain L [auth B] mmCIF format, chain L [auth B]	L [auth B]	DINUCLEAR COPPER ION Cu₂ ALKZAGKDWUSJED-UHFFFAOYSA-N		Interactions Focus chain L [auth B]
CU Query on CU Download:Ideal Coordinates CCD File SDF format, chain I [auth A] MOL2 format, chain I [auth A] mmCIF format, chain I [auth A]	I [auth A]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N		Interactions Focus chain I [auth A]
MN Query on MN Download:Ideal Coordinates CCD File SDF format, chain K [auth A] MOL2 format, chain K [auth A] mmCIF format, chain K [auth A]	K [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain K [auth A]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain J [auth A] MOL2 format, chain J [auth A] mmCIF format, chain J [auth A]	J [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain J [auth A]

Experimental Data & Validation

Experimental Data

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

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

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 1999-12-02

Deposition Author(s):

Harrenga, A.

Michel, H.

Revision History (Full details and data files)

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