3W2W | pdb_00003w2w

Crystal structure of the Cmr2dHD-Cmr3 subcomplex bound to ATP

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 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	d3w2wa2	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	d3w2wa4	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	d3w2wa1	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)
B	SCOP2 Family	Cas_Cmr3-like	8045410	4004460	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	CRISPR-associated proteins	8052172	3001554	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	CRISPR-associated proteins	8052173	3001554	SCOP2 (2022-06-29)
A	SCOP2 Family	Cas_Cmr2 nucleotide cyclase domain-like	8047595	4005707	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Nucleotide cyclase/DNA polymerase palm domain-like	8052174	3001272	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Nucleotide cyclase/DNA polymerase palm domain-like	8052175	3001272	SCOP2 (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
B	LSM	e3w2wB1	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: Phosphofructokinase N-terminal domain	F: LSM	ECOD (v294.1)
B	SapB_2,SapB_1	e3w2wB3	A: a/b three-layered sandwiches	X: Fusion glycoprotein F2	H: HTH	T: winged helix domain	F: SapB_2,SapB_1	ECOD (v294.1)
A	Fz	e3w2wA1	A: a/b three-layered sandwiches	X: Suppressor of Fused, C-terminal domain	H: HTH	T: winged helix domain	F: Fz	ECOD (v294.1)
A	SidM_Rab1-act	e3w2wA6	A: a/b three-layered sandwiches	X: DEATH domain	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F: SidM_Rab1-act	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	3.30.1040.70	Alpha Beta	2-Layer Sandwich	Carboxypeptidase Inhibitor	Chain A	CATH (4.3.0)
B	2.60.40.4350	Mainly Beta	Sandwich	Immunoglobulin-like		CATH (4.3.0)
A	3.30.70.2220	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	CRISPR-Cas system, Cmr2 subunit, D1 domain, cysteine cluster	CATH (4.3.0)
A	1.10.10.1720	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	CRISPR-Cas system, Cmr2 subunit, D2 domain, helical bundle	CATH (4.3.0)
A	3.30.70.270	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	Reverse transcriptase/Diguanylate cyclase domain	CATH (4.3.0)
A	1.20.120.1260	Mainly Alpha	Up-down Bundle	Four Helix Bundle (Hemerythrin (Met), subunit A)	CRISPR-Cas system, Cmr2 subunit, D4 domain, six-helix bundle	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B	PF09700	CRISPR-associated protein (Cas_Cmr3) (Cas_Cmr3)	CRISPR-associated protein (Cas_Cmr3)	-	Family
A	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	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	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	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	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
B	CRISPR system Cmr subunit Cmr3	RNA binding binding nucleic acid binding nucleoside phosphate binding nucleotide binding heterocyclic compound binding small molecule 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	cellular anatomical structure intracellular anatomical structure cytoplasm
A	CRISPR system Cmr subunit Cmr2	binding nucleoside phosphate 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 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	cellular anatomical structure intracellular anatomical structure cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B	IPR010165	Type III-B CRISPR module-associated protein Cmr3	Family
B	IPR019117	CRISPR-associated protein, Cmr3	Family
A	IPR024615	CRISPR-associated protein Cmr2, N-terminal	Domain
A	IPR000160	GGDEF domain	Domain
A	IPR048690	CRISPR RNA silencing complex Cmr2 subunit, Zn-binding domain	Domain
A	IPR048693	CRISPR RNA silencing complex Cmr2-like, C-terminal domain	Domain
A	IPR043128	Reverse transcriptase/Diguanylate cyclase domain	Homologous Superfamily
A	IPR038242	CRISPR-Cas system, Cmr2 subunit, D1 domain, cysteine cluster	Homologous Superfamily
A	IPR013407	CRISPR-associated protein Cmr2	Family
A	IPR048694	CRISPR RNA silencing complex Cmr2 subunit, first helical domain	Domain
A	IPR052117	CRISPR-associated Cas10/Csm1 subtype III-A protein	Family
A	IPR054767	Cas10/Cmr2, second palm 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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.