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209  structures 2978  species 0  interactions 4827  sequences 14  architectures

Family: Cas_Cas1 (PF01867)

Summary: CRISPR associated protein Cas1

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This is the Wikipedia entry entitled "Cas1". More...

Cas1 Edit Wikipedia article

CRISPR-associated protein 1

CRISPR-associated protein 1 (cas1) is one of the two universally conserved proteins found in the CRISPR prokaryotic immune defense system. Cas1 is a metal-dependent DNA-specific endonuclease that produces double-stranded DNA fragments.[1] Cas1 forms a stable complex with the other universally conserved CRISPR-associated protein, cas2, which is essential to spacer acquisition for CRISPR systems.[2]

In July 2017, researchers led by Jennifer Doudna from the University of California at Berkeley, in Berkeley, California, using electron microscopy and X-ray crystallography, at the Advanced Light Source at Lawrence Berkeley National Laboratory, the Stanford Linear Accelerator Center, and the HHMI electron microscope facility at UC Berkeley, discovered how Cas1-Cas2, the proteins responsible for the ability of the CRISPR immune system (CRISPR means: clustered regularly interspaced short palindromic repeats) in bacteria to adapt to new viral infections, identify the site in the genome where they insert viral DNA so they can recognize it later and mount an attack. A protein called IHF plays a crucial role in this process.[3] Scientists also discovered that Cas-1 inhibits Cas-2/3 enzymatic activity as a nuclease and in the same discussion postulated that Cas1-Cas2 had an evolutionary origin as a toxin-antitoxin complex. This could result in a change in the evolutionary model of the Cas1-Cas2 complex.[4]


  1. ^ Wiedenheft B, Zhou K, Jinek M, Coyle SM, Ma W, Doudna JA (2009). "Structural basis for DNase activity of a conserved protein implicated in CRISPR-mediated genome defense". Structure. 17 (6): 904–12. doi:10.1016/j.str.2009.03.019. PMID 19523907.
  2. ^ Nuñez JK, Kranzusch PJ, Noeske J, Wright AV, Davies CW, Doudna JA (2014). "Cas1-Cas2 complex formation mediates spacer acquisition during CRISPR-Cas adaptive immunity". Nat. Struct. Mol. Biol. 21 (6): 528–34. doi:10.1038/nsmb.2820. PMC 4075942. PMID 24793649.
  3. ^ "Researchers discover how CRISPR proteins find their target". 20 July 2017.
  4. ^ Rollins, MaryClare F.; Chowdhury, Saikat; Carter, Joshua; Golden, Sarah M.; Wilkinson, Royce A.; Bondy-Denomy, Joseph; Lander, Gabriel C.; Wiedenheft, Blake (24 April 2017). "Cas1 and the Csy complex are opposing regulators of Cas2/3 nuclease activity". Proceedings of the National Academy of Sciences. 114 (26): E5113–E5121. doi:10.1073/pnas.1616395114. PMC 5495223. PMID 28438998.

This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

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 associated protein Cas1 Provide feedback

Clustered regularly interspaced short palindromic repeats (CRISPRs) are a family of DNA direct repeats found in many prokaryotic genomes. This family of proteins corresponds to Cas1, a CRISPR-associated protein. Cas1 may be involved in linking DNA segments to CRISPR [2].

Literature references

  1. Haft DH, Selengut J, Mongodin EF, Nelson KE; , PLoS Comput Biol. 2005;1:e60.: A guild of 45 CRISPR-associated (Cas) protein families and multiple CRISPR/Cas subtypes exist in prokaryotic genomes. PUBMED:16292354 EPMC:16292354

  2. Bolotin A, Quinquis B, Sorokin A, Ehrlich SD; , Microbiology. 2005;151:2551-2561.: Clustered regularly interspaced short palindrome repeats (CRISPRs) have spacers of extrachromosomal origin. PUBMED:16079334 EPMC:16079334

This tab holds annotation information from the InterPro database.

InterPro entry IPR002729

The CRISPR-Cas system is a prokaryotic defense mechanism against foreign genetic elements. The key elements of this defense system are the Cas proteins and the CRISPR RNA.

Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) are a family of DNA direct repeats separated by regularly sized non-repetitive spacer sequences that are found in most bacterial and archaeal genomes [ PUBMED:17442114 ]. CRISPRs appear to provide acquired resistance against mobile genetic elements (viruses, transposable elements and conjugative plasmids). CRISPR clusters contain sequences complementary to antecedent mobile elements and target invading nucleic acids. CRISPR clusters are transcribed and processed into CRISPR RNA (crRNA).

The defense reaction is divided into three stages. In the adaptation stage, the invader DNA is cleaved, and a piece of it is selected to be integrated as a new spacer into the CRISPR locus, where it is stored as an identity tag for future attacks by this invader. During the second stage (the expression stage), the CRISPR RNA (pre-crRNA) is transcribed and subsequently processed into the mature crRNAs. In the third stage (the interference stage), Cas proteins, together with crRNAs, identify and degrade the invader [ PUBMED:17379808 , PUBMED:16545108 , PUBMED:21699496 ].

The CRISPR-Cas systems have been sorted into three major classes. In CRISPR-Cas types I and III, the mature crRNA is generally generated by a member of the Cas6 protein family. Whereas in system III the Cas6 protein acts alone, in some class I systems it is part of a complex of Cas proteins known as Cascade (CRISPR-associated complex for antiviral defense). The Cas6 protein is an endoribonuclease necessary for crRNA production whereas the additional Cas proteins that form the Cascade complex are needed for crRNA stability [ PUBMED:24459147 ].

This entry represents Cas1, which is a metal-dependent DNA-specific endonuclease [ PUBMED:19523907 ]. Cas1 may play a role in the recognition, cleavage, and/or integration of foreign nucleic acids into CRISPRs.

Gene Ontology

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Domain organisation

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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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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: Enright A
Previous IDs: DUF48;
Type: Family
Sequence Ontology: SO:0100021
Author: Enright A , Ouzounis C , Bateman A
Number in seed: 339
Number in full: 4827
Average length of the domain: 234.00 aa
Average identity of full alignment: 21 %
Average coverage of the sequence by the domain: 73.78 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 22.3 22.3
Trusted cut-off 22.6 22.3
Noise cut-off 22.2 22.2
Model length: 283
Family (HMM) version: 19
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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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 Cas_Cas1 domain has been found. There are 209 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
A1RZT8 View 3D Structure Click here
A2BKJ8 View 3D Structure Click here
B1L400 View 3D Structure Click here
B5YIU9 View 3D Structure Click here
B5YJS2 View 3D Structure Click here
B5YL10 View 3D Structure Click here
D3E288 View 3D Structure Click here
D3E3B3 View 3D Structure Click here
D3E4V4 View 3D Structure Click here
D4GQP0 View 3D Structure Click here
F7V5D5 View 3D Structure Click here
G4RJY6 View 3D Structure Click here
O27156 View 3D Structure Click here
O28401 View 3D Structure Click here
O30236 View 3D Structure Click here
O66692 View 3D Structure Click here
P9WPJ5 View 3D Structure Click here
Q1CW50 View 3D Structure Click here
Q2FL78 View 3D Structure Click here
Q2FNT7 View 3D Structure Click here
Q2FPW6 View 3D Structure Click here
Q2FQQ2 View 3D Structure Click here
Q2RHR1 View 3D Structure Click here
Q2RL66 View 3D Structure Click here
Q2RV90 View 3D Structure Click here
Q2RW61 View 3D Structure Click here
Q2RY11 View 3D Structure Click here
Q2RY21 View 3D Structure Click here
Q46896 View 3D Structure Click here
Q53VV5 View 3D Structure Click here
Q53W21 View 3D Structure Click here
Q53WG8 View 3D Structure Click here
Q57823 View 3D Structure Click here
Q5JGA9 View 3D Structure Click here
Q6D0X0 View 3D Structure Click here
Q74DC4 View 3D Structure Click here
Q74H36 View 3D Structure Click here
Q74N45 View 3D Structure Click here
Q8F1F5 View 3D Structure Click here
Q8F874 View 3D Structure Click here