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2  structures 165  species 0  interactions 190  sequences 10  architectures

Family: CENP-C_C (PF11699)

Summary: Mif2/CENP-C like

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Mif2/CENP-C like Provide feedback

CENP-C_C is a C-terminal family of fungal and eukaryote proteins necessary for centromere formation. CENP-C is the inner-kinetochore centromere (CEN) binding protein. In the budding-yeast, Mif2, the yeast homologue, binds in the CDEIII region of the centromere, and has been shown to recruit a substantial subset of all inner and outer kinetochore proteins [1]. Mif2 adopts a cupin fold and is extremely similar both in polypeptide chain conformation and in dimer geometry to the dimerisation domain of a bacterial transcription factor [1]. The Mif2 dimer appears to be part of an enhanceosome-like structure that nucleates kinetochore assembly in budding yeast [1]. This C-terminal domain is the region via which CENP-C localises to centromeres throughout the cell cycle 2,3].

Literature references

  1. Cohen RL, Espelin CW, De Wulf P, Sorger PK, Harrison SC, Simons KT; , Mol Biol Cell. 2008; [Epub ahead of print]: Structural and Functional Dissection of Mif2p, a Conserved DNA-binding Kinetochore Protein. PUBMED:18701705 EPMC:18701705

  2. Trazzi S, Perini G, Bernardoni R, Zoli M, Reese JC, Musacchio A, Della Valle G;, PLoS One. 2009;4:e5832.: The C-terminal domain of CENP-C displays multiple and critical functions for mammalian centromere formation. PUBMED:19503796 EPMC:19503796

  3. Przewloka MR, Venkei Z, Bolanos-Garcia VM, Debski J, Dadlez M, Glover DM;, Curr Biol. 2011;21:399-405.: CENP-C is a structural platform for kinetochore assembly. PUBMED:21353555 EPMC:21353555


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR025974

This entry represents a cupin domain found in Mif2 and CENP-C.

Mif2 is a yeast DNA-binding kinetochore protein which is orthologous to mammalian CENP-C, the inner-kinetochore centromere (CEN) binding protein [PUBMED:1339310]. Mif2 binds in the CDEIII region of the budding-yeast centromere, and has been shown to recruit a substantial subset of all inner and outer kinetochore proteins [PUBMED:18701705]. Mif2 adopts a cupin fold and is extremely similar both in polypeptide chain conformation and in dimer geometry to the dimerisation domain of a bacterial transcription factor [PUBMED:18701705]. The Mif2 dimer appears to be part of an enhanceosome-like structure that nucleates kinetochore assembly in budding yeast [PUBMED:18701705].

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 Cupin (CL0029), which has the following description:

This clan represents the conserved barrel domain of the 'cupin' superfamily [1] ('cupa' is the Latin term for a small barrel). The cupin fold is found in a wide variety of enzymes, but notably contains the non-enzymatic seed storage proteins also.

The clan contains the following 53 members:

2OG-Fe_Oxy_2 2OG-FeII_Oxy 2OG-FeII_Oxy_2 2OG-FeII_Oxy_3 2OG-FeII_Oxy_4 2OG-FeII_Oxy_5 3-HAO AraC_binding AraC_binding_2 AraC_N ARD Asp_Arg_Hydrox Auxin_BP CDO_I CENP-C_C CsiD Cupin_1 Cupin_2 Cupin_3 Cupin_4 Cupin_5 Cupin_6 Cupin_7 Cupin_8 dTDP_sugar_isom DUF1255 DUF1479 DUF1498 DUF1637 DUF1971 DUF386 DUF4437 Ectoine_synth EutQ FdtA FTO_NTD GPI HgmA HutD JmjC KduI MannoseP_isomer Ofd1_CTDD Oxygenase-NA PhyH Pirin Pirin_C PMI_typeI Pox_C4_C10 TauD Tet_JBP VIT VIT_2

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.

  Seed
(11)
Full
(190)
Representative proteomes NCBI
(209)
Meta
(11)
RP15
(37)
RP35
(73)
RP55
(106)
RP75
(133)
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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
(11)
Full
(190)
Representative proteomes NCBI
(209)
Meta
(11)
RP15
(37)
RP35
(73)
RP55
(106)
RP75
(133)
Alignment:
Format:
Order:
Sequence:
Gaps:
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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
(11)
Full
(190)
Representative proteomes NCBI
(209)
Meta
(11)
RP15
(37)
RP35
(73)
RP55
(106)
RP75
(133)
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.

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.

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: Manual
Previous IDs: Mif2;
Type: Domain
Author: Mistry J, Wood V
Number in seed: 11
Number in full: 190
Average length of the domain: 84.50 aa
Average identity of full alignment: 36 %
Average coverage of the sequence by the domain: 12.58 %

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 29.0 29.0
Trusted cut-off 29.0 29.0
Noise cut-off 28.9 28.9
Model length: 85
Family (HMM) version: 3
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 CENP-C_C domain has been found. There are 2 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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