4W8Y

Structure of full length Cmr2 from Pyrococcus furiosus (Manganese bound form)

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
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	d4w8ya4	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-B interference complex protein Cmr2, D2	(Pyrococcus furiosus DSM 3638 ) [TaxId: 186497 ],	SCOPe (2.08)
A	d4w8ya5	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-B interference complex protein Cmr2, D4	(Pyrococcus furiosus DSM 3638 ) [TaxId: 186497 ],	SCOPe (2.08)
A	d4w8ya1	All alpha proteins	HD-domain/PDEase-like	HD-domain/PDEase-like	HD domain from Cmr2-like	CRISPR-Cas type III-B interference complex protein Cmr2	(Pyrococcus furiosus DSM 3638 ) [TaxId: 186497 ],	SCOPe (2.08)
A	d4w8ya2	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-B interference complex protein Cmr2	(Pyrococcus furiosus DSM 3638 ) [TaxId: 186497 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Nucleotide cyclase/DNA polymerase palm domain-like	8052175	3001272	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Nucleotide cyclase/DNA polymerase palm domain-like	8052174	3001272	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Nucleotide cyclase/DNA polymerase palm domain-like	8052175	3001272	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Nucleotide cyclase/DNA polymerase palm domain-like	8052174	3001272	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	PF20824	e4w8yA3	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: PF20824	ECOD (1.6)
A	PF20822	e4w8yA4	A: alpha bundles	X: CRISPR RNA silencing complex Cmr2 subunit first helical domain (From Topology)	H: CRISPR RNA silencing complex Cmr2 subunit first helical domain (From Topology)	T: CRISPR RNA silencing complex Cmr2 subunit first helical domain	F: PF20822	ECOD (1.6)
A	PF12469	e4w8yA1	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: PF12469	ECOD (1.6)
A	PF22335	e4w8yA2	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: PF22335	ECOD (1.6)
A	PF20823	e4w8yA5	A: few secondary structure elements	X: CRISPR RNA silencing complex Cmr2 subunit Zn-binding domain (From Topology)	H: CRISPR RNA silencing complex Cmr2 subunit Zn-binding domain (From Topology)	T: CRISPR RNA silencing complex Cmr2 subunit Zn-binding domain	F: PF20823	ECOD (1.6)
B	PF20824	e4w8yB3	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: PF20824	ECOD (1.6)
B	PF20822	e4w8yB4	A: alpha bundles	X: CRISPR RNA silencing complex Cmr2 subunit first helical domain (From Topology)	H: CRISPR RNA silencing complex Cmr2 subunit first helical domain (From Topology)	T: CRISPR RNA silencing complex Cmr2 subunit first helical domain	F: PF20822	ECOD (1.6)
B	PF12469	e4w8yB1	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: PF12469	ECOD (1.6)
B	PF22335	e4w8yB2	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: PF22335	ECOD (1.6)
B	PF20823	e4w8yB5	A: few secondary structure elements	X: CRISPR RNA silencing complex Cmr2 subunit Zn-binding domain (From Topology)	H: CRISPR RNA silencing complex Cmr2 subunit Zn-binding domain (From Topology)	T: CRISPR RNA silencing complex Cmr2 subunit Zn-binding domain	F: PF20823	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF20823	CRISPR RNA silencing complex Cmr2 subunit, Zn-binding domain (Cmr2_Zn-bd)	CRISPR RNA silencing complex Cmr2 subunit, Zn-binding domain	The prokaryotic CRISPR RNA-Cas protein (Cmr) complex provides protection against mobile genetic elements by cleaving foreign RNA. Its largest subunit is Cmr2. This protein shows a N-terminal HD (histidine-aspartate) domain, two RRM domains resembling ...	The prokaryotic CRISPR RNA-Cas protein (Cmr) complex provides protection against mobile genetic elements by cleaving foreign RNA. Its largest subunit is Cmr2. This protein shows a N-terminal HD (histidine-aspartate) domain, two RRM domains resembling adenylate cyclase and two alpha-helical domains. This entry represents the conserved Zn binding subdomain included in the first RMM domain (D1 domain) of Cmr2 [1-5]. This region shows two alpha-helices.	Domain
A, B	PF20822	CRISPR RNA silencing complex Cmr2 subunit, first helical domain (Cmr2_hel_dom1)	CRISPR RNA silencing complex Cmr2 subunit, first helical domain	The prokaryotic CRISPR RNA-Cas protein (Cmr) complex provides protection against mobile genetic elements by cleaving foreign RNA. Its largest subunit is Cmr2. This protein shows a N-terminal HD (histidine-aspartate) domain, two RRM domains resembling ...	The prokaryotic CRISPR RNA-Cas protein (Cmr) complex provides protection against mobile genetic elements by cleaving foreign RNA. Its largest subunit is Cmr2. This protein shows a N-terminal HD (histidine-aspartate) domain, two RRM domains resembling adenylate cyclase and two alpha-helical domains. This entry represents the first alpha-helical domain, which is similar to the thumb of DNA polymerases [1-5].	Domain
A, B	PF20824	CRISPR RNA silencing complex Cmr2 subunit, second helical domain (Cmr2_hel_dom2)	CRISPR RNA silencing complex Cmr2 subunit, second helical domain	The prokaryotic CRISPR RNA-Cas protein (Cmr) complex provides protection against mobile genetic elements by cleaving foreign RNA. Its largest subunit is Cmr2. This protein shows a N-terminal HD (histidine-aspartate) domain, two RRM domains resembling ...	The prokaryotic CRISPR RNA-Cas protein (Cmr) complex provides protection against mobile genetic elements by cleaving foreign RNA. Its largest subunit is Cmr2. This protein shows a N-terminal HD (histidine-aspartate) domain, two RRM domains resembling adenylate cyclase and two alpha-helical domains. This entry represents the second alpha-helical domain. It is similar to the small subunit Cmr5, which contains six alpha-helices and two helical insertions that fold into a single globular structure [1-5]. This domain is also found in Cas10 proteins from bacteria [6].	Domain
A, B	PF12469	CRISPR-associated protein Cmr2, N-terminal (Cmr2_N)	CRISPR-associated protein Cmr2, N-terminal	This domain family is typically between 101 and 138 amino acids in length and it is found in subunit Crm2 of the CRISPR RNA-Cas protein complex (Cmr complex) [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	CRISPR system Cmr subunit Cmr2	binding nucleoside phosphate binding organic cyclic compound binding nucleotide binding heterocyclic compound binding small molecule binding RNA binding nucleic acid binding cation binding ion binding metal ion binding	biological process involved in interspecies interaction between organisms response to stimulus response to other organism defense response defense response to symbiont response to external stimulus response to biotic stimulus defense response to virus defense response to other organism response to stress response to external biotic stimulus response to virus	intracellular anatomical structure cytoplasm cellular anatomical entity

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR024615	CRISPR-associated protein Cmr2, N-terminal	Domain
A, B	IPR000160	GGDEF domain	Domain
A, B	IPR048690	CRISPR RNA silencing complex Cmr2 subunit, Zn-binding domain	Domain
A, B	IPR048693	CRISPR RNA silencing complex Cmr2-like, C-terminal domain	Domain
A, B	IPR043128	Reverse transcriptase/Diguanylate cyclase domain	Homologous Superfamily
A, B	IPR038242	CRISPR-Cas system, Cmr2 subunit, D1 domain, cysteine cluster	Homologous Superfamily
A, B	IPR013407	CRISPR-associated protein Cmr2	Family
A, B	IPR048694	CRISPR RNA silencing complex Cmr2 subunit, first helical domain	Domain

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.