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15  structures 54  species 0  interactions 67  sequences 2  architectures

Family: GCSF (PF16647)

Summary: Granulocyte colony-stimulating factor

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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.

Granulocyte colony-stimulating factor Provide feedback

GCSF is a family of higher eukaryotic granulocyte colony-stimulating factor proteins. Granulocyte colony-stimulating factors are cytokines that are involved in haematopoeisis. They control the production, differentiation and function of white blood cell granulocytes. GCSF binds to the extracellular Ig-like and CRH domain of its receptor GCSFR, thereby triggering the receptor to homodimerise. Homodimerisation result in activation of Janus tyrosine kinase-signal transducers and other activators of transcription (JAK-STAT)-type signalling cascades [2].

Literature references

  1. Tamada T, Honjo E, Maeda Y, Okamoto T, Ishibashi M, Tokunaga M, Kuroki R;, Proc Natl Acad Sci U S A. 2006;103:3135-3140.: Homodimeric cross-over structure of the human granulocyte colony-stimulating factor (GCSF) receptor signaling complex. PUBMED:16492764 EPMC:16492764


Internal database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR030474

Interleukin-6 (IL6), also refered to as B-cell stimulatory factor-2 (BSF-2) and interferon beta-2, is a cytokine involved in a wide variety of biological functions [PUBMED:3491322]. It plays an essential role in the final differentiation of B-cells into IG-secreting cells, as well as inducing myeloma/plasmacytoma growth, nerve cell differentiation and, in hepatocytes, acute phase reactants [PUBMED:3491322, PUBMED:2037043].

A number of other cytokines may be grouped with IL6 on the basis of sequence similarity [PUBMED:3491322, PUBMED:2037043, PUBMED:2472117]: these include granulocyte colony-stimulating factor (GCSF) and myelomonocytic growth factor (MGF). GCSF acts in hematopoiesis by affecting the production, differentiation and function of 2 related white cell groups in the blood [PUBMED:2472117]. MGF also acts in hematopoiesis, stimulating proliferation and colony formation of normal and transformed avian cells of the myeloid lineage.

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 4H_Cytokine (CL0053), which has the following description:

Cytokines are regulatory peptides that can be produced by various cells for communicating and orchestrating the large multicellular system. Cytokines are key mediators of hematopoiesis, immunity, allergy, inflammation, tissue remodeling, angiogenesis, and embryonic development [2]. This superfamily includes both the long and short chain helical cytokines.

The clan contains the following 29 members:

CNTF CSF-1 EPO_TPO Flt3_lig GCSF GM_CSF Hormone_1 IFN-gamma IL10 IL11 IL12 IL13 IL15 IL2 IL22 IL23 IL28A IL3 IL34 IL4 IL5 IL6 IL7 Interferon Leptin LIF_OSM PRF SCF TSLP

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, 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
(3)
Full
(67)
Representative proteomes UniProt
(81)
NCBI
(248)
Meta
(0)
RP15
(7)
RP35
(22)
RP55
(39)
RP75
(58)
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available

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

Format an alignment

  Seed
(3)
Full
(67)
Representative proteomes UniProt
(81)
NCBI
(248)
Meta
(0)
RP15
(7)
RP35
(22)
RP55
(39)
RP75
(58)
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
(3)
Full
(67)
Representative proteomes UniProt
(81)
NCBI
(248)
Meta
(0)
RP15
(7)
RP35
(22)
RP55
(39)
RP75
(58)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download    
Gzipped Download   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: PF00489
Previous IDs: none
Type: Domain
Author: Coggill P
Number in seed: 3
Number in full: 67
Average length of the domain: 140.30 aa
Average identity of full alignment: 53 %
Average coverage of the sequence by the domain: 73.45 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 26740544 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 30.4 30.4
Trusted cut-off 31.1 30.8
Noise cut-off 29.2 28.9
Model length: 149
Family (HMM) version: 4
Download: download the raw HMM for this family

Species distribution

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

Selections

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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 GCSF domain has been found. There are 15 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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