4UW2 | pdb_00004uw2

Crystal structure of Csm1 in T.onnurineus

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d4uw2a4	All alpha proteins	Four-helical up-and-down bundle	Helical bundle domains from Csm1/Cmr1-like	Helical bundle domains from Csm1/Cmr1	CRISPR-Cas type III-A interference complex protein Csm1, Domain D	(Thermococcus onnurineus NA1 ) [TaxId: 523850 ],	SCOPe (2.08)
A	d4uw2a1	All alpha proteins	HD-domain/PDEase-like	HD-domain/PDEase-like	HD domain	CRISPR-Cas type III-A interference complex protein Csm1	(Thermococcus onnurineus NA1 ) [TaxId: 523850 ],	SCOPe (2.08)
A	d4uw2a2	Alpha and beta proteins (a+b)	Ferredoxin-like	Ferredoxin-like domains from CRISPR-associated proteins	Nucleotide cyclase domains from Cmr2-like	CRISPR-Cas type III-A interference complex protein Csm1	(Thermococcus onnurineus NA1 ) [TaxId: 523850 ],	SCOPe (2.08)
A	d4uw2a5	Alpha and beta proteins (a+b)	B domain from Cmr1-like	B domain from Cmr1-like	B domain from Cmr1	CRISPR-Cas type III-A interference complex protein Csm1	(Thermococcus onnurineus NA1 ) [TaxId: 523850 ],	SCOPe (2.08)
A	d4uw2a6	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Thermococcus onnurineus NA1 ) [TaxId: 523850 ],	SCOPe (2.08)
B	d4uw2b5	All alpha proteins	Four-helical up-and-down bundle	Helical bundle domains from Csm1/Cmr1-like	Helical bundle domains from Csm1/Cmr1	CRISPR-Cas type III-A interference complex protein Csm1, Domain D	(Thermococcus onnurineus NA1 ) [TaxId: 523850 ],	SCOPe (2.08)
B	d4uw2b1	All alpha proteins	HD-domain/PDEase-like	HD-domain/PDEase-like	HD domain	CRISPR-Cas type III-A interference complex protein Csm1	(Thermococcus onnurineus NA1 ) [TaxId: 523850 ],	SCOPe (2.08)
B	d4uw2b2	Alpha and beta proteins (a+b)	Ferredoxin-like	Ferredoxin-like domains from CRISPR-associated proteins	Nucleotide cyclase domains from Cmr2-like	CRISPR-Cas type III-A interference complex protein Csm1	(Thermococcus onnurineus NA1 ) [TaxId: 523850 ],	SCOPe (2.08)
B	d4uw2b3	Alpha and beta proteins (a+b)	B domain from Cmr1-like	B domain from Cmr1-like	B domain from Cmr1	CRISPR-Cas type III-A interference complex protein Csm1	(Thermococcus onnurineus NA1 ) [TaxId: 523850 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	EUF08083	e4uw2A1	A: alpha bundles	X: CRISPR RNA silencing complex Cmr2 subunit second helical domain (From Topology)	H: CRISPR RNA silencing complex Cmr2 subunit second helical domain (From Topology)	T: CRISPR RNA silencing complex Cmr2 subunit second helical domain	F: EUF08083	ECOD (1.6)
A	HD	e4uw2A5	A: alpha complex topology	X: PDEase-like	H: HD-domain/PDEase-like (From Topology)	T: HD-domain/PDEase-like	F: HD	ECOD (1.6)
A	Cas10_III_2nd	e4uw2A3	A: a+b two layers	X: Alpha-beta plaits	H: Adenylyl and guanylyl cyclase catalytic domain-like	T: Adenylyl and guanylyl cyclase catalytic domain-like	F: Cas10_III_2nd	ECOD (1.6)
A	Cas10_III_1st	e4uw2A2	A: a+b two layers	X: Alpha-beta plaits	H: Adenylyl and guanylyl cyclase catalytic domain-like	T: Adenylyl and guanylyl cyclase catalytic domain-like	F: Cas10_III_1st	ECOD (1.6)
A	EUF08476	e4uw2A4	A: a+b two layers	X: Csm1 ferredoxin-like domain (From Topology)	H: Csm1 ferredoxin-like domain (From Topology)	T: Csm1 ferredoxin-like domain	F: EUF08476	ECOD (1.6)
B	EUF08083	e4uw2B5	A: alpha bundles	X: CRISPR RNA silencing complex Cmr2 subunit second helical domain (From Topology)	H: CRISPR RNA silencing complex Cmr2 subunit second helical domain (From Topology)	T: CRISPR RNA silencing complex Cmr2 subunit second helical domain	F: EUF08083	ECOD (1.6)
B	HD	e4uw2B1	A: alpha complex topology	X: PDEase-like	H: HD-domain/PDEase-like (From Topology)	T: HD-domain/PDEase-like	F: HD	ECOD (1.6)
B	Cas10_III_2nd	e4uw2B4	A: a+b two layers	X: Alpha-beta plaits	H: Adenylyl and guanylyl cyclase catalytic domain-like	T: Adenylyl and guanylyl cyclase catalytic domain-like	F: Cas10_III_2nd	ECOD (1.6)
B	Cas10_III_1st	e4uw2B2	A: a+b two layers	X: Alpha-beta plaits	H: Adenylyl and guanylyl cyclase catalytic domain-like	T: Adenylyl and guanylyl cyclase catalytic domain-like	F: Cas10_III_1st	ECOD (1.6)
B	EUF08476	e4uw2B3	A: a+b two layers	X: Csm1 ferredoxin-like domain (From Topology)	H: Csm1 ferredoxin-like domain (From Topology)	T: Csm1 ferredoxin-like domain	F: EUF08476	ECOD (1.6)
C	EUF08083	e4uw2C2	A: alpha bundles	X: CRISPR RNA silencing complex Cmr2 subunit second helical domain (From Topology)	H: CRISPR RNA silencing complex Cmr2 subunit second helical domain (From Topology)	T: CRISPR RNA silencing complex Cmr2 subunit second helical domain	F: EUF08083	ECOD (1.6)
C	Cas10_III_2nd	e4uw2C1	A: a+b two layers	X: Alpha-beta plaits	H: Adenylyl and guanylyl cyclase catalytic domain-like	T: Adenylyl and guanylyl cyclase catalytic domain-like	F: Cas10_III_2nd	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.30.70.270	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	Reverse transcriptase/Diguanylate cyclase domain	CATH (4.3.0)
B	3.30.70.270	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	Reverse transcriptase/Diguanylate cyclase domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF22335	Cas10/Cmr2, second palm domain (Cas10-Cmr2_palm2)	Cas10/Cmr2, second palm domain	This entry represents the second palm domain of Cas10 subunit (named Csm1 in Type III-A and Cmr2 in III-B systems) from type III CRISPR-Cas systems [6]. This domain contains a conserved GGDD motif that is important for DNA polymerase activity [1-5]. ...	This entry represents the second palm domain of Cas10 subunit (named Csm1 in Type III-A and Cmr2 in III-B systems) from type III CRISPR-Cas systems [6]. This domain contains a conserved GGDD motif that is important for DNA polymerase activity [1-5].	Domain
A, B, C, D	PF01966	HD domain (HD)	HD domain	-	Family
A, B, C, D	PF18211	Csm1 subunit domain B (Csm1_B)	Csm1 subunit domain B	This domain is found in the Csm1 subunit of the Csm complex found in Thermococcus onnurineus. Csm is a type III-A CRISPR-Cas system, which is an RNA-guided immune defense mechanism that detects and destroys foreign DNA or RNA. This domain is known as ...	This domain is found in the Csm1 subunit of the Csm complex found in Thermococcus onnurineus. Csm is a type III-A CRISPR-Cas system, which is an RNA-guided immune defense mechanism that detects and destroys foreign DNA or RNA. This domain is known as domain A and is positioned side by side with domain C. Both domain A and domain C adopt the BABBA topology. Domain A interacts primarily with domain B [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	CSM1	hydrolase activity, acting on ester bonds nuclease activity catalytic activity, acting on a nucleic acid hydrolase activity exonuclease activity catalytic activity binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding hydrolase activity, acting on ester bonds nuclease activity catalytic activity, acting on a nucleic acid hydrolase activity exonuclease activity catalytic activity binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding endonuclease activity transferase activity identical protein binding protein binding	biological process involved in interspecies interaction between organisms defense response to virus response to stimulus defense response response to other organism response to stress response to external stimulus response to external biotic stimulus response to virus response to biotic stimulus	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR000160	GGDEF domain	Domain
A, B, C, D	IPR041062	Csm1, subunit domain B	Domain
A, B, C, D	IPR043128	Reverse transcriptase/Diguanylate cyclase domain	Homologous Superfamily
A, B, C, D	IPR013408	CRISPR system single-strand-specific deoxyribonuclease Cas10/Csm1	Family
A, B, C, D	IPR052117	CRISPR-associated Cas10/Csm1 subtype III-A protein	Family
A, B, C, D	IPR054767	Cas10/Cmr2, second palm domain	Domain
A, B, C, D	IPR006674	HD domain	Domain

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.