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136  structures 1410  species 0  interactions 3590  sequences 57  architectures

Family: COX6B (PF02297)

Summary: Cytochrome oxidase c subunit VIb

Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.

This is the Wikipedia entry entitled "Cytochrome c oxidase". More...

Cytochrome c oxidase Edit Wikipedia article

The enzyme cytochrome c oxidase is a large transmembrane protein found in the mitochondrion and is the terminal electron acceptor in the electron transfer chain, taking four reducing equivalents from cytochrome c and converting molecular oxygen to water. In the process, it translocates protons, helping to establish a chemiosmotic potential that ATP synthase then uses to synthesize ATP.

Summary reaction:

4 Fe+2-cyochrome c + 4H+ + O2 → 4 Fe+3-cytochrome c + H20.

The complex is a large lipoprotein comprised of a number of metal prosthetic sites and 13 protein subunits, which in mammals, 10 are nuclear in origin and 3 are synthesized mitochondrially. The complex contains 2 cytochromes, the a and a3 cytochromes, and two copper centers, the CuA and CuB centers. In fact, the cytochrome a3 and CuB are a binuclear center and this is the site of oxygen reduction. The mechanism of action of this large complex is still an active research topic.

Further information

The Cytochrome Oxidase home page

This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.

Cytochrome oxidase c subunit VIb Provide feedback

Cytochrome c oxidase, a 13 sub-unit complex, EC: is the terminal oxidase in the mitochondrial electron transport chain. This family is composed of the potentially heme-binding subunit IVb of the oxidase.

Literature references

  1. Carrero-Valenzuela RD, Quan F, Lightowlers R, Kennaway NG, Litt M, Forte M; , Gene 1991;102:229-236.: Human cytochrome c oxidase subunit VIb: characterization and mapping of a multigene family. PUBMED:1651883 EPMC:1651883

Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR003213

Cytochrome c oxidase ( EC ) is an oligomeric enzymatic complex that is a component of the respiratory chain complex and is involved in the transfer of electrons from cytochrome c to oxygen [ PUBMED:6307356 ]. In eukaryotes this enzyme complex is located in the mitochondrial inner membrane; in aerobic prokaryotes it is found in the plasma membrane.

In eukaryotes, in addition to the three large subunits, I, II and III, that form the catalytic centre of the enzyme complex, there are a variable number of small polypeptide subunits. One of these subunits is the potentially haem-binding subunit, VIb, which is encoded in the nucleus [ PUBMED:11136449 ]. Subunit VIb is one of three mammalian subunits that lacks a transmembrane region. It is located on the cytosolic side of the membrane and helps form the dimer interface with the corresponding subunit on the other monomer complex [ PUBMED:12874793 , PUBMED:16364442 ].

Gene Ontology

The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

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Pfam Clan

This family is a member of clan CHCH (CL0351), which has the following description:

The conserved [coiled coil 1]-[helix 1]-[coiled coil 2]-[helix 2] domain (CHCH domain) superfamily members include NADH-ubiquinone oxidoreductases, some cytochrome oxidases and yeast mitochondrial ribosomal proteins. Within each helix of the CHCH domain there are two cysteines present in a C-X9-C motif.

The clan contains the following 8 members:



We store a range of different sequence alignments for families. As well as the seed alignment from which the family is built, we provide the full alignment, generated by searching the sequence database (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets and the UniProtKB sequence database. More...

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We make a range of alignments for each Pfam-A family. You can see a description of each above. You can view these alignments in various ways but please note that some types of alignment are never generated while others may not be available for all families, most commonly because the alignments are too large to handle.

Representative proteomes UniProt
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: ✓ available, x not generated, not available.

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Representative proteomes UniProt

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We make all of our alignments available in Stockholm format. You can download them here as raw, plain text files or as gzip-compressed files.

Representative proteomes UniProt
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You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

HMM logo

HMM logos is one way of visualising profile HMMs. Logos provide a quick overview of the properties of an HMM in a graphical form. You can see a more detailed description of HMM logos and find out how you can interpret them here. More...


This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.

Note: You can also download the data file for the tree.

Curation and family details

This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.

Curation View help on the curation process

Seed source: Pfam-B_9188 (release 5.2)
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Mian N , Bateman A
Number in seed: 57
Number in full: 3590
Average length of the domain: 66.6 aa
Average identity of full alignment: 31 %
Average coverage of the sequence by the domain: 54.45 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 26.0 26.0
Trusted cut-off 26.0 26.0
Noise cut-off 25.6 25.9
Model length: 76
Family (HMM) version: 20
Download: download the raw HMM for this family

Species distribution

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Colour assignments

Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
Viruses Viruses Unclassified Unclassified
Viroids Viroids Unclassified sequence Unclassified sequence


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This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the adjacent tab. More...

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The tree shows the occurrence of this domain across different species. More...


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For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the COX6B domain has been found. There are 136 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein sequence.

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AlphaFold Structure Predictions

The list of proteins below match this family and have AlphaFold predicted structures. Click on the protein accession to view the predicted structure.

Protein Predicted structure External Information
A0A044SPK9 View 3D Structure Click here
A0A044UVL4 View 3D Structure Click here
A0A077Z1M5 View 3D Structure Click here
A0A077Z344 View 3D Structure Click here
A0A0D2G7J7 View 3D Structure Click here
A0A0D2GFF9 View 3D Structure Click here
A0A0G2JUM8 View 3D Structure Click here
A0A0K0E7S7 View 3D Structure Click here
A0A0K0E8X4 View 3D Structure Click here
A0A0N4U1G5 View 3D Structure Click here
A0A0N4UGB7 View 3D Structure Click here
A0A0R0FKK9 View 3D Structure Click here
A0A0R0FKP0 View 3D Structure Click here
A0A175VXR2 View 3D Structure Click here
A0A175W1Q3 View 3D Structure Click here
A0A1C1CFV7 View 3D Structure Click here
A0A1C1D0J9 View 3D Structure Click here
A0A1D6P7V7 View 3D Structure Click here
A0A1D6Q4N8 View 3D Structure Click here
A0A1D8PQD5 View 3D Structure Click here
A0A1D8PU62 View 3D Structure Click here
A0A2K6W300 View 3D Structure Click here
A0A3P7GK67 View 3D Structure Click here
A0A3Q0KLZ7 View 3D Structure Click here
B4FCQ4 View 3D Structure Click here
B6T8C0 View 3D Structure Click here
B7Z107 View 3D Structure Click here
B8A5J2 View 3D Structure Click here
C0NCW2 View 3D Structure Click here
C0NGN0 View 3D Structure Click here
C1H5Q7 View 3D Structure Click here
C1HAU2 View 3D Structure Click here
C4Q820 View 3D Structure Click here
D3ZD09 View 3D Structure Click here
G2TRP6 View 3D Structure Click here
I1JGN2 View 3D Structure Click here
I1JGV5 View 3D Structure Click here
I1LGX3 View 3D Structure Click here
I1LVX2 View 3D Structure Click here
I1MAW4 View 3D Structure Click here