3X1L | pdb_00003x1l

Crystal Structure of the CRISPR-Cas RNA Silencing Cmr Complex Bound to a Target Analog

External Resource: Annotation

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: 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	8052174	3001272	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	CRISPR-associated proteins	8052172	3001554	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	CRISPR-associated proteins	8052173	3001554	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	CRISPR-associated proteins	8052157	3001554	SCOP2B (2022-06-29)
D	SCOP2 Family	RAMP-like	8044858	4004180	SCOP2 (2022-06-29)
D	SCOP2 Superfamily	CRISPR-associated proteins	8052157	3001554	SCOP2 (2022-06-29)
E	SCOP2B Superfamily	CRISPR-associated proteins	8052157	3001554	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	AF1862-like	8035071	3001582	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	AF1862-like	8035071	3001582	SCOP2B (2022-06-29)
H	SCOP2 Family	RAMP-like	8044865	4004180	SCOP2 (2022-06-29)
H	SCOP2 Superfamily	CRISPR-associated proteins	8052158	3001554	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)
A	EUF08082	e3x1lA1	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: EUF08082	ECOD (1.6)
A	EUF08084	e3x1lA2	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: EUF08084	ECOD (1.6)
A	DUF3692	e3x1lA4	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: DUF3692	ECOD (1.6)
A	Cas10_III_2nd	e3x1lA3	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	cas_TM1794_Cmr2	e3x1lA5	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: cas_TM1794_Cmr2	ECOD (1.6)
B	Cas_Cmr3_C	e3x1lB2	A: a+b two layers	X: Alpha-beta plaits	H: CRISPR transcript (pre-crRNA) processing endoribonuclease-related (From Topology)	T: CRISPR transcript (pre-crRNA) processing endoribonuclease-related	F: Cas_Cmr3_C	ECOD (1.6)
B	Cas_Cmr3_N	e3x1lB1	A: a+b two layers	X: Alpha-beta plaits	H: CRISPR transcript (pre-crRNA) processing endoribonuclease-related (From Topology)	T: CRISPR transcript (pre-crRNA) processing endoribonuclease-related	F: Cas_Cmr3_N	ECOD (1.6)
C	RAMPs	e3x1lC1	A: a+b two layers	X: Alpha-beta plaits	H: Cas7-related	T: CRISPR-associated protein Cas7/Csa2-related	F: RAMPs	ECOD (1.6)
D	RAMPs	e3x1lD1	A: a+b two layers	X: Alpha-beta plaits	H: Cas7-related	T: CRISPR-associated protein Cas7/Csa2-related	F: RAMPs	ECOD (1.6)
E	RAMPs	e3x1lE1	A: a+b two layers	X: Alpha-beta plaits	H: Cas7-related	T: CRISPR-associated protein Cas7/Csa2-related	F: RAMPs	ECOD (1.6)
F	Cas_Cmr5	e3x1lF1	A: alpha bundles	X: ATPD N-terminal domain-like	H: Cas Cmr5-like (From Topology)	T: Cas Cmr5-like	F: Cas_Cmr5	ECOD (1.6)
G	Cas_Cmr5	e3x1lG1	A: alpha bundles	X: ATPD N-terminal domain-like	H: Cas Cmr5-like (From Topology)	T: Cas Cmr5-like	F: Cas_Cmr5	ECOD (1.6)
H	RAMPs_1	e3x1lH1	A: a+b two layers	X: Alpha-beta plaits	H: Cas7-related	T: CRISPR-associated protein Cas7/Csa2-related	F: RAMPs_1	ECOD (1.6)

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)
F	1.10.520.30	Mainly Alpha	Orthogonal Bundle	Peroxidase	domain 1	CATH (4.3.0)
G	1.10.520.30	Mainly Alpha	Orthogonal Bundle	Peroxidase	domain 1	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
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
B	PF09700	CRISPR-associated protein (Cas_Cmr3) (Cas_Cmr3)	CRISPR-associated protein (Cas_Cmr3)	-	Family
C, D, E	PF03787	RAMP superfamily (RAMPs)	RAMP superfamily	-	Family
F, G	PF09701	CRISPR-associated protein (Cas_Cmr5) (Cas_Cmr5)	CRISPR-associated protein (Cas_Cmr5)	-	Family
H	PF03787	RAMP superfamily (RAMPs)	RAMP superfamily	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
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 response to stimulus response to other organism defense response 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	cellular anatomical structure intracellular anatomical structure cytoplasm
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 response to stimulus response to other organism defense response 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	cellular anatomical structure intracellular anatomical structure cytoplasm
C, D, E	Cmr4	-	biological process involved in interspecies interaction between organisms response to stimulus response to other organism defense response 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	-
F, G	CRISPR system Cmr subunit Cmr5	-	biological process involved in interspecies interaction between organisms response to stimulus response to other organism defense response 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	cellular anatomical structure intracellular anatomical structure cytoplasm
H	Cmr6	-	biological process involved in interspecies interaction between organisms response to stimulus response to other organism defense response 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	-
I	RNA (32-MER)	-	-	-
J	DNA (5'-D(TPGPCPTPCPTPCPAPGPCPCPGPCPAPAPGPGPAPCPCPGPCPAPTPAPCPTPAPCPAP*A)-3')	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
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
B	IPR010165	Type III-B CRISPR module-associated protein Cmr3	Family
B	IPR019117	CRISPR-associated protein, Cmr3	Family
C, D, E	IPR013410	CRISPR-associated RAMP Cmr4	Family
C, D, E	IPR005537	CRISPR type III-associated protein	Domain
F, G	IPR010160	CRISPR-associated protein, Cmr5	Family
F, G	IPR023101	AF1862-like domain superfamily	Homologous Superfamily
H	IPR010172	CRISPR-associated protein, TM1791	Family
H	IPR005537	CRISPR type III-associated protein	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.