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13  structures 27  species 0  interactions 39  sequences 1  architecture

Family: IL34 (PF15036)

Summary: Interleukin 34

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This is the Wikipedia entry entitled "Interleukin 34". More...

Interleukin 34 Edit Wikipedia article

Interleukin 34

Crystal Structure of Human Interleukin-34 dimer. PDB 4dkc
Available structures
PDB Ortholog search: PDBe, RCSB
Identifiers
Symbols IL34; C16orf77; IL-34
External IDs OMIM612081 MGI1923777 HomoloGene12648 GeneCards: IL34 Gene
Orthologs
Species Human Mouse
Entrez 146433 76527
Ensembl ENSG00000157368 ENSMUSG00000031750
UniProt Q6ZMJ4 Q8R1R4
RefSeq (mRNA) NM_001172771 NM_001135100
RefSeq (protein) NP_001166242 NP_001128572
Location (UCSC) Chr 16:
70.61 – 70.69 Mb
Chr 8:
110.74 – 110.81 Mb
PubMed search [1] [2]

Interleukin-34, or IL-34 is a protein belonging to a group of cytokines called interleukins. It was originally identified in humans, by large scale screening of secreted proteins; chimpanzee, murine, rat and chicken IL-34 orthologs have also been found. The protein is composed of 241 amino acids, 39 kilodaltons in mass, and forms homodimers. IL-34 increases growth or survival of immune cells known as monocytes; it elicits its activity by binding the Colony stimulating factor 1 receptor.

Messenger RNA (mRNA) expression of human IL-34 is most abundant in spleen but occurs in several other tissues: thymus, liver, small intestine, colon, prostate gland, lung, heart, brain, kidney, testes, and ovary. The discovery of IL-34 protein in the red pulp of the spleen suggests involvement in growth and development of myeloid cells, consistent with its activity on monocytes. [1]

References[edit]

  1. ^ Lin H, Lee E, Hestir K, et al. (May 2008). "Discovery of a cytokine and its receptor by functional screening of the extracellular proteome". Science 320 (5877): 807–11. doi:10.1126/science.1154370. PMID 18467591. 

External links[edit]

Interleukin-34 at the US National Library of Medicine Medical Subject Headings (MeSH)

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This tab holds annotation information from the InterPro database.

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Domain organisation

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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 using the family HMM. We also generate alignments using four representative proteomes (RP) sets, 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.

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(5)
Full
(39)
Representative proteomes NCBI
(42)
Meta
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(1)
RP35
(2)
RP55
(4)
RP75
(17)
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  Seed
(5)
Full
(39)
Representative proteomes NCBI
(42)
Meta
(0)
RP15
(1)
RP35
(2)
RP55
(4)
RP75
(17)
Alignment:
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  Seed
(5)
Full
(39)
Representative proteomes NCBI
(42)
Meta
(0)
RP15
(1)
RP35
(2)
RP55
(4)
RP75
(17)
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You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

External links

MyHits provides a collection of tools to handle multiple sequence alignments. For example, one can refine a seed alignment (sequence addition or removal, re-alignment or manual edition) and then search databases for remote homologs using HMMER3.

Pfam alignments:

HMM logo

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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.

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Curation and family details

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This family is new in this Pfam release.

Seed source: Jackhmmer:Q6ZMJ4
Previous IDs: none
Type: Domain
Author: Bateman A
Number in seed: 5
Number in full: 39
Average length of the domain: 160.20 aa
Average identity of full alignment: 69 %
Average coverage of the sequence by the domain: 72.21 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 27.0 27.0
Trusted cut-off 161.0 160.7
Noise cut-off 18.6 18.0
Model length: 169
Family (HMM) version: 1
Download: download the raw HMM for this family

Species distribution

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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 IL34 domain has been found. There are 13 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 seqence.

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