Summary: Integrase Zinc binding domain
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This is the Wikipedia entry entitled "Integrase". More...
Integrase Edit Wikipedia article
HIV integrase is an 31 kd protein produced from the the C-terminal portion of the Pol gene product. The integrase protein contains three domains: an N-terminal HH-CC zinc finger domain believed to be partially responsible for multimerization, a central catalytic domain and an C-terminal DNA binding domain. Integrase is responsible for the integration of proviral DNA into the host genome, which is essential for HIV replication. Integrase, therefore, remains a promising potential target for new anti-HIV therapeutics
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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.
Integrase Zinc binding domain Provide feedback
Integrase mediates integration of a DNA copy of the viral genome into the host chromosome. Integrase is composed of three domains. This domain is the amino-terminal domain zinc binding domain. The central domain is the catalytic domain PF00665. The carboxyl terminal domain is a DNA binding domain PF00552.
Literature references
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Cai M, Zheng R, Caffrey M, Craigie R, Clore GM, Gronenborn AM; , Nat Struct Biol 1997;4:567-577.: Solution structure of the N-terminal zinc binding domain of HIV-1 integrase. PUBMED:9228950 EPMC:9228950
External database links
SCOP: | 1wjb |
This tab holds annotation information from the InterPro database.
InterPro entry IPR003308
Retroviral integrase mediates integration of a DNA copy of the viral genome into the host chromosome. Integrase is composed of three domains: an N-terminal zinc binding domain, a central catalytic core and a C-terminal DNA-binding domain [ PUBMED:11743009 , PUBMED:11101216 ]. Often found as part of the POL polyprotein.
Gene Ontology
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
Molecular function | zinc ion binding (GO:0008270) |
Domain organisation
Below is a listing of the unique domain organisations or architectures in which this domain is found. More...
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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 (17) |
Full (1393) |
Representative proteomes | UniProt (57667) |
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RP15 (1018) |
RP35 (1081) |
RP55 (1344) |
RP75 (1416) |
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PP/heatmap | 1 |
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key:
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not generated,
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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 (17) |
Full (1393) |
Representative proteomes | UniProt (57667) |
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RP15 (1018) |
RP35 (1081) |
RP55 (1344) |
RP75 (1416) |
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Raw Stockholm | |||||||
Gzipped |
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
Seed source: | PSI-BLAST 1wjb |
Previous IDs: | none |
Type: | Domain |
Sequence Ontology: | SO:0000417 |
Author: |
Bateman A |
Number in seed: | 17 |
Number in full: | 1393 |
Average length of the domain: | 37.5 aa |
Average identity of full alignment: | 49 % |
Average coverage of the sequence by the domain: | 5.1 % |
HMM information
HMM build commands: |
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
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Model details: |
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Model length: | 38 | ||||||||||||
Family (HMM) version: | 22 | ||||||||||||
Download: | download the raw HMM for this family |
Species distribution
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Selections
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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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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 Integrase_Zn domain has been found. There are 177 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 |
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P10266 | View 3D Structure | Click here |
P63132 | View 3D Structure | Click here |
P63133 | View 3D Structure | Click here |
P63135 | View 3D Structure | Click here |
P63136 | View 3D Structure | Click here |
Q9BXR3 | View 3D Structure | Click here |
Q9QC07 | View 3D Structure | Click here |
Q9UQG0 | View 3D Structure | Click here |
Q9WJR5 | View 3D Structure | Click here |