Summary: Recombination-activating protein 1 zinc-finger domain
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Recombination-activating protein 1 zinc-finger domain Provide feedback
This is a C2-H2 zinc-finger domain closely resembling the classical TFIIIA-type zinc-finger, CX3FX5LX2-3H, despite having a valine and a tyrosine at the core instead of a phenylalanine and a leucine, hence CX3VX1LX2YX2H. The structure, nevertheless, contains the characteristic two-stranded beta-sheet and alpha-helix of a classical zinc-finger. The domain binds one zinc and, in complex with the zinc-RING-finger domain, helps to stabilise the whole of the dimerisation region of recombination activating protein 1 (RAG1) [1]. The function of the whole is to bind double-stranded DNA.
Literature references
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Bellon SF, Rodgers KK, Schatz DG, Coleman JE, Steitz TA; , Nat Struct Biol. 1997;4:586-591.: Crystal structure of the RAG1 dimerization domain reveals multiple zinc-binding motifs including a novel zinc binuclear cluster. PUBMED:9228952 EPMC:9228952
This tab holds annotation information from the InterPro database.
InterPro entry IPR019485
The development of B and T cells depends on the rearrangement of variable (V), diversity (D), and joining (J) gene segments to produce mature Ig and T cell receptor coding regions. This rearrangement process, known as V(D)J recombination is initiated by the complex, multi-domain proteins RAG1 and RAG2. The RAG proteins catalyze DNA cleavage in the first phase of the reaction using a recombination signal sequence (RSS) that flanks V, D and J segments [PUBMED:9228952, PUBMED:14671314, PUBMED:22796426].
RAG1 contains a zinc-binding dimerization domain immediately N-terminal to the catalytic core region, which in turn contains a putative DNA-binding domain at its N terminus. The dimerization domain consists of a zinc C3HC4 RING finger and a C2H2 zinc RAG1-type finger.
The C2H2 RAG1-type zinc finger contains the hallmarks of a classical zinc finger structure with a two stranded beta-sheet and an alpha-helix [PUBMED:9228952].
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 C2H2-zf (CL0361), which has the following description:
Superfamily of classical and closely related C2H2 or beta-beta-alpha zinc finger DNA-binding domains.
The clan contains the following 52 members:
ARS2 DUF3449 GAGA Hat1_N Integrase_H2C2 KN17_SH3 Nairovirus_M ROS_MUCR Sgf11 UBZ_FAAP20 Zap1_zf2 zf-AD zf-BED zf-C2H2 zf-C2H2_10 zf-C2H2_11 zf-C2H2_2 zf-C2H2_3 zf-C2H2_3rep zf-C2H2_4 zf-C2H2_6 zf-C2H2_7 zf-C2H2_8 zf-C2H2_9 zf-C2H2_aberr zf-C2H2_jaz zf-C2HC_2 zf-C2HE zf-CRD zf-DBF zf-Di19 zf-H2C2 zf-H2C2_2 zf-H2C2_5 zf-H3C2 zf-LYAR zf-met zf-met2 zf-MYST zf-RAG1 zf-U1 zf-U11-48K zf-WRNIP1_ubi zf_C2H2_10 zf_C2H2_13 zf_C2H2_6 zf_C2H2_ZHX zf_C2HC_14 zf_Hakai zf_UBZ zf_ZIC Zn-C2H2_12Alignments
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, the UniProtKB sequence database, the NCBI sequence database, and our metagenomics 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 (7) |
Full (104) |
Representative proteomes | UniProt (10822) |
NCBI (10786) |
Meta (0) |
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RP15 (6) |
RP35 (24) |
RP55 (58) |
RP75 (100) |
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PP/heatmap | 1 |
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key:
available,
not generated,
— not available.
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Seed (7) |
Full (104) |
Representative proteomes | UniProt (10822) |
NCBI (10786) |
Meta (0) |
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RP15 (6) |
RP35 (24) |
RP55 (58) |
RP75 (100) |
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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: | Gene3D, pdb_1rmd |
Previous IDs: | none |
Type: | Domain |
Sequence Ontology: | SO:0000417 |
Author: |
Finn RD |
Number in seed: | 7 |
Number in full: | 104 |
Average length of the domain: | 30.00 aa |
Average identity of full alignment: | 67 % |
Average coverage of the sequence by the domain: | 2.90 % |
HMM information
HMM build commands: |
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 47079205 -E 1000 --cpu 4 HMM pfamseq
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Model details: |
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Model length: | 30 | ||||||||||||
Family (HMM) version: | 10 | ||||||||||||
Download: | download the raw HMM for this family |
Species distribution
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Interactions
There is 1 interaction for this family. More...
zf-C3HC4Structures
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 zf-RAG1 domain has been found. There are 1 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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