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12  structures 166  species 0  interactions 170  sequences 2  architectures

Family: Csm4_C (PF17953)

Summary: CRISPR Csm4 C-terminal domain

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This is the Wikipedia entry entitled "CRISPR". More...

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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.

CRISPR Csm4 C-terminal domain Provide feedback

Clustered, regularly interspaced, short palindromic repeat (CRISPR) loci play a pivotal role in the prokaryotic host defense system against invading genetic materials. The CRISPR loci are transcribed to produce CRISPR RNAs (crRNAs), which form interference complexes with CRISPR-associated (Cas) proteins to target the invading nucleic acid for degradation. The interference complex of the type III-A CRISPR-Cas system is composed of five Cas proteins (Csm1-Csm5) and a crRNA, and targets invading DNA. This entry represents the C-terminal domain found in Csm4. Csm4 structurally resembles Cmr3, a component of the type III-B CRISPR-Cas interference complex. Studies indicate that Csm3-Csm4 complex binds single-stranded RNA in a non-sequence-specific manner. Structural analysis show , Csm3 and Csm4 have one and two ferredoxin-like folds (also known as an RRM-like fold), respectively. The long beta-hairpin inserted into the C-terminal ferredoxin-like fold of Csm4, is well-conserved in the Cmr3 structure. The corresponding beta-hairpin of Cmr3 binds the D1 domain of Cmr2, as observed in the Cmr2-Cmr3 complex structure. Furthermore, it is suggested that the hairpin of Csm4 is responsible for the interaction with Csm1 (ortholog of Cmr2) [1].

Literature references

  1. Numata T, Inanaga H, Sato C, Osawa T;, J Mol Biol. 2015;427:259-273.: Crystal structure of the Csm3-Csm4 subcomplex in the type III-A CRISPR-Cas interference complex. PUBMED:25451598 EPMC:25451598


This tab holds annotation information from the InterPro database.

InterPro entry IPR040932

Clustered, regularly interspaced, short palindromic repeat (CRISPR) loci play a pivotal role in the prokaryotic host defense system against invading genetic materials. The CRISPR loci are transcribed to produce CRISPR RNAs (crRNAs), which form interference complexes with CRISPR-associated (Cas) proteins to target the invading nucleic acid for degradation. The interference complex of the type III-A CRISPR-Cas system is composed of five Cas proteins (Csm1-Csm5) and a crRNA, and targets invading DNA.

This entry represents the C-terminal domain found in Csm4. Csm4 structurally resembles Cmr3, a component of the type III-B CRISPR-Cas interference complex. Studies indicate that Csm3-Csm4 complex binds single-stranded RNA in a non-sequence-specific manner. Structural analysis show , Csm3 and Csm4 have one and two ferredoxin-like folds (also known as an RRM-like fold), respectively. The long beta-hairpin inserted into the C-terminal ferredoxin-like fold of Csm4, is well-conserved in the Cmr3 structure. The corresponding beta-hairpin of Cmr3 binds the D1 domain of Cmr2, as observed in the Cmr2-Cmr3 complex structure. Furthermore, it is suggested that the hairpin of Csm4 is responsible for the interaction with Csm1 (ortholog of Cmr2) [PUBMED:25451598].

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 RAMPS-Cas5-like (CL0362), which has the following description:

This group of families is one of several protein families that are always found associated with prokaryotic CRISPRs, themselves a family of clustered regularly interspaced short palindromic repeats, DNA repeats found in nearly half of all bacterial and archaeal genomes. These DNA repeat regions have a remarkably regular structure: unique sequences of constant size, called spacers, sit between each pair of repeats [1]. It has been shown that the CRISPRs are virus-derived sequences acquired by the host to enable them to resist viral infection. The Cas proteins from the host use the CRISPRs to mediate an antiviral response. After transcription of the CRISPR, a complex of Cas proteins termed Cascade cleaves a CRISPR RNA precursor in each repeat and retains the cleavage products containing the virus-derived sequence. Assisted by the helicase Cas3, these mature CRISPR RNAs then serve as small guide RNAs that enable Cascade to interfere with virus proliferation [2]. Cas5 contains an endonuclease motif, whose inactivation leads to loss of resistance, even in the presence of phage-derived spacers [3].

The clan contains the following 15 members:

Cas6 Cas6_N Cas6b_C Cas6b_N Cas_Cas5d Cas_Cas6 Cas_Cmr3 Cas_Csy4 Cas_CT1975 CRISPR_assoc CRISPR_Cas6 Csc2 Csm4_C DevR RAMPs

Alignments

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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
(46)
Full
(170)
Representative proteomes UniProt
(702)
NCBI
(932)
Meta
(1)
RP15
(45)
RP35
(111)
RP55
(163)
RP75
(262)
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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
(46)
Full
(170)
Representative proteomes UniProt
(702)
NCBI
(932)
Meta
(1)
RP15
(45)
RP35
(111)
RP55
(163)
RP75
(262)
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
(46)
Full
(170)
Representative proteomes UniProt
(702)
NCBI
(932)
Meta
(1)
RP15
(45)
RP35
(111)
RP55
(163)
RP75
(262)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   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: ECOD:EUF02722
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: El-Gebali S
Number in seed: 46
Number in full: 170
Average length of the domain: 91.40 aa
Average identity of full alignment: 27 %
Average coverage of the sequence by the domain: 27.48 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 47079205 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 25.9 25.9
Trusted cut-off 26.3 26.1
Noise cut-off 25.6 25.5
Model length: 91
Family (HMM) version: 2
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

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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 Csm4_C domain has been found. There are 12 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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