Summary: Cystine-knot domain
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Cystine knot Edit Wikipedia article
Structure of human chorionic gonadotropin.
A cystine knot is a protein structural motif containing three disulfide bridges (formed from pairs of cysteine molecules). The sections of polypeptide that occur between two of them form a loop through which a third disulfide bond passes, forming a rotaxane substructure. It occurs in many proteins across many species and provides considerable structural stability. There are three types of cystine knot, which differ in the topology of the disulfide bonds:
- The Growth Factor Cystine Knot (GFCK)
- Inhibitor Cystine Knot (ICK) common in spider and snail toxins
- Cyclic Cystine Knot, or cyclotide
The growth factor cystine knot (GFCK) was first observed in the structure of Nerve Growth Factor, solved by X-ray crystallography and published in 1991 by Tom Blundell in Nature. All GFCK structures that have been determined are dimeric, but their dimerization modes in different classes are different.
- Wu H, Lustbader JW, Liu Y, Canfield RE, Hendrickson WA (June 1994). "Structure of human chorionic gonadotropin at 2.6 A resolution from MAD analysis of the selenomethionyl protein". Structure 2 (6): 545–58. PMID 7922031.
- Daly, N. L.; Craik, D. J. (2011). "Bioactive cystine knot proteins". Current Opinion in Chemical Biology 15 (3): 362–368. doi:10.1016/j.cbpa.2011.02.008. PMID 21362584.
- PDB 1bet; McDonald NQ, Lapatto R, Murray-Rust J, Gunning J, Wlodawer A, Blundell TL (December 1991). "New protein fold revealed by a 2.3-A resolution crystal structure of nerve growth factor". Nature 354 (6352): 411–4. doi:10.1038/354411a0. PMID 1956407.
- Jiang X, Dias JA, He X (Aug 2013). "Structural biology of glycoprotein hormones and their receptors: Insights to signaling". Mol Cell Endocrinol. doi:10.1016/j.mce.2013.08.021. PMID 24001578.
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Cystine-knot domain Provide feedback
The family comprises glycoprotein hormones and the C-terminal domain of various extracellular proteins. It is believed to be involved in disulfide-linked dimerisation.
External database links
- the number of sequences which exhibit this architecture
a textual description of the architecture, e.g. Gla, EGF x 2, Trypsin.
This example describes an architecture with one
Gladomain, followed by two consecutive
EGFdomains, and finally a single
- the UniProt description of the protein sequence
- the number of residues in the sequence
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The cytokine families in this clan have the cystine-knot fold. In this 6 cysteines form three disulphide bridges that are interlinked.
The clan contains the following 9 members:Coagulin Cys_knot DAN Hormone_6 NGF Noggin PDGF Sclerostin TGF_beta
We make a range of alignments for each Pfam-A family:
- the curated alignment from which the HMM for the family is built
- the alignment generated by searching the sequence database using the HMM
- Representative Proteomes (RPs) at 15%, 35%, 55% and 75% co-membership thresholds
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Curation and family details
|Seed source:||Published_alignment enriched with PDOC00234 members.|
|Number in seed:||24|
|Number in full:||1416|
|Average length of the domain:||92.30 aa|
|Average identity of full alignment:||29 %|
|Average coverage of the sequence by the domain:||44.70 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||17|
|Download:||download the raw HMM for this family|
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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 Cys_knot domain has been found. There are 7 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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