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13  structures 5723  species 0  interactions 6358  sequences 9  architectures

Family: SMC_ScpA (PF02616)

Summary: Segregation and condensation protein ScpA

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Segregation and condensation protein ScpA Provide feedback

This is a family of proteins that from part of the condensin complex that regulates chromosome segregation. This is the A subunit, which binds to the ScpB subunit, PF04079 and SMC, PF02463 to participate in chromosomal partition during cell division [2,3]. The condensin complex pulls DNA away from the mid-cell into both cell halves [1]. These proteins are part of the Kleisin superfamily.

Literature references

  1. Schleiffer A, Kaitna S, Maurer-Stroh S, Glotzer M, Nasmyth K, Eisenhaber F; , Mol Cell 2003;11:571-575.: Kleisins: a superfamily of bacterial and eukaryotic SMC protein partners. PUBMED:12667442 EPMC:12667442

  2. Burmann F, Shin HC, Basquin J, Soh YM, Gimenez-Oya V, Kim YG, Oh BH, Gruber S;, Nat Struct Mol Biol. 2013;20:371-379.: An asymmetric SMC-kleisin bridge in prokaryotic condensin. PUBMED:23353789 EPMC:23353789

  3. Kamada K, Miyata M, Hirano T;, Structure. 2013;21:581-594.: Molecular basis of SMC ATPase activation: role of internal structural changes of the regulatory subcomplex ScpAB. PUBMED:23541893 EPMC:23541893

Internal database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR003768

This family represents ScpA, which along with ScpB ( INTERPRO ) interacts with SMC in vivo forming a complex that is required for chromosome condensation and segregation [ PUBMED:12065423 , PUBMED:12897137 ]. The SMC-Scp complex appears to be similar to the MukB-MukE-Muk-F complex in Escherichia coli [ PUBMED:10545099 ], where MukB ( INTERPRO ) is the homologue of SMC. ScpA and ScpB have little sequence similarity to MukE ( INTERPRO ) or MukF ( INTERPRO ), they are predicted to be structurally similar, being predominantly alpha-helical with coiled coil regions.

In general scpA and scpB form an operon in most bacterial genomes. Flanking genes are highly variable suggesting that the operon has moved throughout evolution. Bacteria containing an smc gene also contain scpA or scpB but not necessarily both. An exception is found in Deinococcus radiodurans, which contains scpB but neither smc nor scpA. In the archaea the gene order SMC-ScpA is conserved in nearly all species, as is the very short distance between the two genes, indicating co-transcription of the both in different archaeal genera and arguing that interaction of the gene products is not confined to the homologues in Bacillus subtilis. It would seem probable that, in light of all the studies, SMC, ScpA and ScpB proteins or homologues act together in chromosome condensation and segregation in all prokaryotes [ PUBMED:12100548 ].

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 Kleisin (CL0157), which has the following description:

The kleisin superfamily includes ScpA, Scc1, Rec8, and Barren [1]. Scc1 interacts with SMC proteins through N- and C-terminal domains to form a ring-like structure [1].

The clan contains the following 2 members:

Rad21_Rec8 SMC_ScpA


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 and the UniProtKB 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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Representative proteomes UniProt

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You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

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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...


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

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: COG1354
Previous IDs: DUF173; ScpA_ScpB;
Type: Family
Sequence Ontology: SO:0100021
Author: Mian N , Bateman A
Number in seed: 5
Number in full: 6358
Average length of the domain: 206.50 aa
Average identity of full alignment: 26 %
Average coverage of the sequence by the domain: 75.38 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 24.6 24.6
Trusted cut-off 24.6 24.7
Noise cut-off 24.5 24.5
Model length: 241
Family (HMM) version: 16
Download: download the raw HMM for this family

Species distribution

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Colour assignments

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


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This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the adjacent tab. More...

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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 SMC_ScpA 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 sequence.

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AlphaFold Structure Predictions

The list of proteins below match this family and have AlphaFold predicted structures. Click on the protein accession to view the predicted structure.

Protein Predicted structure External Information
O33208 View 3D Structure Click here
Q2FY76 View 3D Structure Click here
Q58534 View 3D Structure Click here