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60  structures 1259  species 0  interactions 1428  sequences 20  architectures

Family: NDUF_B7 (PF05676)

Summary: NADH-ubiquinone oxidoreductase B18 subunit (NDUFB7)

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This is the Wikipedia entry entitled "NADH dehydrogenase (ubiquinone)". More...

NADH dehydrogenase (ubiquinone) Edit Wikipedia article

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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.

NADH-ubiquinone oxidoreductase B18 subunit (NDUFB7) Provide feedback

This family consists of several NADH-ubiquinone oxidoreductase B18 subunit proteins from different eukaryotic organisms. Oxidative phosphorylation is the well-characterised process in which ATP, the principal carrier of chemical energy of individual cells, is produced due to a mitochondrial proton gradient formed by the transfer of electrons from NADH and FADH2 to molecular oxygen. The oxidative phosphorylation (OXPHOS) system is located in the mitochondrial inner membrane and consists of five multi-subunit enzyme complexes and two small electron carriers: coenzyme Q10 and cytochrome C. At least 70 structural proteins involved in the formation of the whole OXPHOS system are encoded by nuclear genes, whereas 13 structural proteins are encoded by the mitochondrial genome. Deficiency of NADH ubiquinone oxidoreductase, the first enzyme complex of the mitochondrial respiratory chain, is one of the most frequent causes of human mitochondrial encephalomyopathies [1].

Literature references

  1. Triepels R, Smeitink J, Loeffen J, Smeets R, Trijbels F, van den Heuvel L; , Hum Genet 2000;106:385-391.: Characterization of the human complex I NDUFB7 and 17.2-kDa cDNAs and mutational analysis of 19 genes of the HP fraction in complex I-deficient-patients. PUBMED:10830904 EPMC:10830904


Internal database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR008698

This family consists of the accessory subunit of complex I NADH-ubiquinone oxidoreductase NDUB7 (or NDUFB7, also known as B18), which is not involved in catalysis [ PUBMED:27626371 , PUBMED:31485716 ].

NADH:ubiquinone oxidoreductase (complex I) ( EC ) is a respiratory-chain enzyme that catalyses the transfer of two electrons from NADH to ubiquinone in a reaction that is associated with proton translocation across the membrane (NADH + ubiquinone = NAD+ + ubiquinol) [ PUBMED:1470679 ]. Complex I is a major source of reactive oxygen species (ROS) that are predominantly formed by electron transfer from FMNH(2). Complex I is found in bacteria, cyanobacteria (as a NADH-plastoquinone oxidoreductase), archaea [ PUBMED:10940377 ], mitochondria, and in the hydrogenosome, a mitochondria-derived organelle. In general, the bacterial complex consists of 14 different subunits, while the mitochondrial complex contains homologues to these subunits in addition to approximately 31 additional proteins [ PUBMED:18394423 ].

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:

CHCH Cmc1 COX17 COX6B CX9C MTCP1 NDUF_B7 Ndufs5

Alignments

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.

  Seed
(70)
Full
(1428)
Representative proteomes UniProt
(2123)
RP15
(304)
RP35
(695)
RP55
(1105)
RP75
(1464)
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PP/heatmap 1 View           

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

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

Format an alignment

  Seed
(70)
Full
(1428)
Representative proteomes UniProt
(2123)
RP15
(304)
RP35
(695)
RP55
(1105)
RP75
(1464)
Alignment:
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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.

  Seed
(70)
Full
(1428)
Representative proteomes UniProt
(2123)
RP15
(304)
RP35
(695)
RP55
(1105)
RP75
(1464)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   Download   Download   Download   Download   Download   Download  

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...

Trees

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_7077 (release 8.0)
Previous IDs: NDUFB7;
Type: Family
Sequence Ontology: SO:0100021
Author: Moxon SJ
Number in seed: 70
Number in full: 1428
Average length of the domain: 62.1 aa
Average identity of full alignment: 47 %
Average coverage of the sequence by the domain: 54.39 %

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 26.1 26.0
Noise cut-off 25.7 25.9
Model length: 63
Family (HMM) version: 16
Download: download the raw HMM for this family

Species distribution

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Archea Archea Eukaryota Eukaryota
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Viroids Viroids Unclassified sequence Unclassified sequence

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Structures

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 NDUF_B7 domain has been found. There are 60 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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