6SH8 | pdb_00006sh8

Cryo-EM structure of the Type III-B Cmr-beta bound to cognate target RNA and AMPPnP, state 2, in the presence of ssDNA

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)
G	SCOP2B Superfamily	CRISPR-associated proteins	8097728	3001554	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	CRISPR-associated proteins	8097728	3001554	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	CRISPR-associated proteins	8097728	3001554	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	CRISPR-associated proteins	8097728	3001554	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)
Z [auth o]	EUF08448	e6sh8o1	A: a+b two layers	X: BtrG-like (Pfam 03674) (From Topology)	H: BtrG-like (Pfam 03674) (From Topology)	T: BtrG-like (Pfam 03674)	F: EUF08448	ECOD (1.6)
Y [auth n]	EUF08448	e6sh8n1	A: a+b two layers	X: BtrG-like (Pfam 03674) (From Topology)	H: BtrG-like (Pfam 03674) (From Topology)	T: BtrG-like (Pfam 03674)	F: EUF08448	ECOD (1.6)
X [auth m]	EUF08448	e6sh8m1	A: a+b two layers	X: BtrG-like (Pfam 03674) (From Topology)	H: BtrG-like (Pfam 03674) (From Topology)	T: BtrG-like (Pfam 03674)	F: EUF08448	ECOD (1.6)
W [auth l]	EUF08448	e6sh8l1	A: a+b two layers	X: BtrG-like (Pfam 03674) (From Topology)	H: BtrG-like (Pfam 03674) (From Topology)	T: BtrG-like (Pfam 03674)	F: EUF08448	ECOD (1.6)
V [auth X]	EUF08448	e6sh8X1	A: a+b two layers	X: BtrG-like (Pfam 03674) (From Topology)	H: BtrG-like (Pfam 03674) (From Topology)	T: BtrG-like (Pfam 03674)	F: EUF08448	ECOD (1.6)
U [auth W]	EUF08448	e6sh8W1	A: a+b two layers	X: BtrG-like (Pfam 03674) (From Topology)	H: BtrG-like (Pfam 03674) (From Topology)	T: BtrG-like (Pfam 03674)	F: EUF08448	ECOD (1.6)
T	EUF08448	e6sh8T1	A: a+b two layers	X: BtrG-like (Pfam 03674) (From Topology)	H: BtrG-like (Pfam 03674) (From Topology)	T: BtrG-like (Pfam 03674)	F: EUF08448	ECOD (1.6)
S	EUF08448	e6sh8S1	A: a+b two layers	X: BtrG-like (Pfam 03674) (From Topology)	H: BtrG-like (Pfam 03674) (From Topology)	T: BtrG-like (Pfam 03674)	F: EUF08448	ECOD (1.6)
R	EUF08448	e6sh8R1	A: a+b two layers	X: BtrG-like (Pfam 03674) (From Topology)	H: BtrG-like (Pfam 03674) (From Topology)	T: BtrG-like (Pfam 03674)	F: EUF08448	ECOD (1.6)
Q	EUF08448	e6sh8Q1	A: a+b two layers	X: BtrG-like (Pfam 03674) (From Topology)	H: BtrG-like (Pfam 03674) (From Topology)	T: BtrG-like (Pfam 03674)	F: EUF08448	ECOD (1.6)
P	EUF08448	e6sh8P1	A: a+b two layers	X: BtrG-like (Pfam 03674) (From Topology)	H: BtrG-like (Pfam 03674) (From Topology)	T: BtrG-like (Pfam 03674)	F: EUF08448	ECOD (1.6)
O	EUF08448	e6sh8O1	A: a+b two layers	X: BtrG-like (Pfam 03674) (From Topology)	H: BtrG-like (Pfam 03674) (From Topology)	T: BtrG-like (Pfam 03674)	F: EUF08448	ECOD (1.6)
N	EUF08448	e6sh8N1	A: a+b two layers	X: BtrG-like (Pfam 03674) (From Topology)	H: BtrG-like (Pfam 03674) (From Topology)	T: BtrG-like (Pfam 03674)	F: EUF08448	ECOD (1.6)
MA [auth y]	EUF08448	e6sh8y1	A: a+b two layers	X: BtrG-like (Pfam 03674) (From Topology)	H: BtrG-like (Pfam 03674) (From Topology)	T: BtrG-like (Pfam 03674)	F: EUF08448	ECOD (1.6)
M	EUF08448	e6sh8M1	A: a+b two layers	X: BtrG-like (Pfam 03674) (From Topology)	H: BtrG-like (Pfam 03674) (From Topology)	T: BtrG-like (Pfam 03674)	F: EUF08448	ECOD (1.6)
LA [auth Y]	EUF08448	e6sh8Y1	A: a+b two layers	X: BtrG-like (Pfam 03674) (From Topology)	H: BtrG-like (Pfam 03674) (From Topology)	T: BtrG-like (Pfam 03674)	F: EUF08448	ECOD (1.6)
L	EUF08448	e6sh8L1	A: a+b two layers	X: BtrG-like (Pfam 03674) (From Topology)	H: BtrG-like (Pfam 03674) (From Topology)	T: BtrG-like (Pfam 03674)	F: EUF08448	ECOD (1.6)
KA [auth z]	EUF08448	e6sh8z1	A: a+b two layers	X: BtrG-like (Pfam 03674) (From Topology)	H: BtrG-like (Pfam 03674) (From Topology)	T: BtrG-like (Pfam 03674)	F: EUF08448	ECOD (1.6)
JA [auth Z]	EUF08448	e6sh8Z1	A: a+b two layers	X: BtrG-like (Pfam 03674) (From Topology)	H: BtrG-like (Pfam 03674) (From Topology)	T: BtrG-like (Pfam 03674)	F: EUF08448	ECOD (1.6)
GA [auth x]	EUF08448	e6sh8x1	A: a+b two layers	X: BtrG-like (Pfam 03674) (From Topology)	H: BtrG-like (Pfam 03674) (From Topology)	T: BtrG-like (Pfam 03674)	F: EUF08448	ECOD (1.6)
FA [auth w]	EUF08448	e6sh8w1	A: a+b two layers	X: BtrG-like (Pfam 03674) (From Topology)	H: BtrG-like (Pfam 03674) (From Topology)	T: BtrG-like (Pfam 03674)	F: EUF08448	ECOD (1.6)
EA [auth t]	EUF08448	e6sh8t1	A: a+b two layers	X: BtrG-like (Pfam 03674) (From Topology)	H: BtrG-like (Pfam 03674) (From Topology)	T: BtrG-like (Pfam 03674)	F: EUF08448	ECOD (1.6)
DA [auth s]	EUF08448	e6sh8s1	A: a+b two layers	X: BtrG-like (Pfam 03674) (From Topology)	H: BtrG-like (Pfam 03674) (From Topology)	T: BtrG-like (Pfam 03674)	F: EUF08448	ECOD (1.6)
CA [auth r]	EUF08448	e6sh8r1	A: a+b two layers	X: BtrG-like (Pfam 03674) (From Topology)	H: BtrG-like (Pfam 03674) (From Topology)	T: BtrG-like (Pfam 03674)	F: EUF08448	ECOD (1.6)
BA [auth q]	EUF08448	e6sh8q1	A: a+b two layers	X: BtrG-like (Pfam 03674) (From Topology)	H: BtrG-like (Pfam 03674) (From Topology)	T: BtrG-like (Pfam 03674)	F: EUF08448	ECOD (1.6)
AA [auth p]	EUF08448	e6sh8p1	A: a+b two layers	X: BtrG-like (Pfam 03674) (From Topology)	H: BtrG-like (Pfam 03674) (From Topology)	T: BtrG-like (Pfam 03674)	F: EUF08448	ECOD (1.6)
H	Cas_Cmr3_N	e6sh8H1	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)
H	UNK_F_TYPE	e6sh8H2	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: UNK_F_TYPE	ECOD (1.6)
G	RAMPs	e6sh8G1	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	RAMPs	e6sh8F1	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	e6sh8E1	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	e6sh8D1	A: a+b two layers	X: Alpha-beta plaits	H: Cas7-related	T: CRISPR-associated protein Cas7/Csa2-related	F: RAMPs	ECOD (1.6)
C	UNK_F_TYPE	e6sh8C1	A: alpha bundles	X: ATPD N-terminal domain-like	H: Cas Cmr5-like (From Topology)	T: Cas Cmr5-like	F: UNK_F_TYPE	ECOD (1.6)
B	UNK_F_TYPE	e6sh8B1	A: alpha bundles	X: ATPD N-terminal domain-like	H: Cas Cmr5-like (From Topology)	T: Cas Cmr5-like	F: UNK_F_TYPE	ECOD (1.6)
A	UNK_F_TYPE	e6sh8A1	A: alpha bundles	X: ATPD N-terminal domain-like	H: Cas Cmr5-like (From Topology)	T: Cas Cmr5-like	F: UNK_F_TYPE	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
C	1.10.520.30	Mainly Alpha	Orthogonal Bundle	Peroxidase	domain 1	CATH (utative)
A	1.10.520.30	Mainly Alpha	Orthogonal Bundle	Peroxidase	domain 1	CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
AA [auth p], BA [auth q], CA [auth r], DA [auth s], EA [auth t], AA [auth p], BA [auth q], CA [auth r], DA [auth s], EA [auth t], FA [auth w], GA [auth x], JA [auth Z], KA [auth z], L, LA [auth Y], M, MA [auth y], N, O, P, Q, R, S, T, U [auth W], V [auth X], W [auth l], X [auth m], Y [auth n], Z [auth o]	PF19021	CRISPR system CMR subunit Cmr7 1 (Cmr7A)	CRISPR system CMR subunit Cmr7 1	-	Family
K	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
K	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
J	PF03787	RAMP superfamily (RAMPs)	RAMP superfamily	-	Family
I	PF03787	RAMP superfamily (RAMPs)	RAMP superfamily	-	Family
H	PF09700	CRISPR-associated protein (Cas_Cmr3) (Cas_Cmr3)	CRISPR-associated protein (Cas_Cmr3)	-	Family
D, E, F, G	PF03787	RAMP superfamily (RAMPs)	RAMP superfamily	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
IA [auth V]	crRNA	-	-	-
HA [auth U]	Cognate target RNA	-	-	-
AA [auth p], BA [auth q], CA [auth r], DA [auth s], EA [auth t], AA [auth p], BA [auth q], CA [auth r], DA [auth s], EA [auth t], FA [auth w], GA [auth x], JA [auth Z], KA [auth z], L, LA [auth Y], M, MA [auth y], N, O, P, Q, R, S, T, U [auth W], V [auth X], W [auth l], X [auth m], Y [auth n], Z [auth o]	CRISPR-associated protein Cmrx	-	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 clearance of foreign intracellular nucleic acids response to biotic stimulus defense response to other organism response to stress CRISPR-cas system response to external biotic stimulus defense response to virus response to virus	-
K	CRISPR-associated protein, Cmr2 family	-	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 membrane
J	Cmr1,CRISPR-associated RAMP protein, Cmr1 family	-	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	-
I	CRISPR-associated RAMP protein, Cmr6 family	-	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	-
H	CRISPR-associated protein, Cmr3 family	-	-	-
D, E, F, G	CRISPR-associated RAMP protein, Cmr4 family	-	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	-
A, B, C	CRISPR-associated protein, Cmr5 family	-	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
AA [auth p], BA [auth q], CA [auth r], DA [auth s], EA [auth t], AA [auth p], BA [auth q], CA [auth r], DA [auth s], EA [auth t], FA [auth w], GA [auth x], JA [auth Z], KA [auth z], L, LA [auth Y], M, MA [auth y], N, O, P, Q, R, S, T, U [auth W], V [auth X], W [auth l], X [auth m], Y [auth n], Z [auth o]	IPR053743	CRISPR system Cmr7 complex component	Homologous Superfamily
AA [auth p], BA [auth q], CA [auth r], DA [auth s], EA [auth t], AA [auth p], BA [auth q], CA [auth r], DA [auth s], EA [auth t], FA [auth w], GA [auth x], JA [auth Z], KA [auth z], L, LA [auth Y], M, MA [auth y], N, O, P, Q, R, S, T, U [auth W], V [auth X], W [auth l], X [auth m], Y [auth n], Z [auth o]	IPR043959	CRISPR system CMR subunit Cmr7 1	Family
K	IPR024615	CRISPR-associated protein Cmr2, N-terminal	Domain
K	IPR038242	CRISPR-Cas system, Cmr2 subunit, D1 domain, cysteine cluster	Homologous Superfamily
K	IPR013407	CRISPR-associated protein Cmr2	Family
K	IPR054767	Cas10/Cmr2, second palm domain	Domain
K	IPR043128	Reverse transcriptase/Diguanylate cyclase domain	Homologous Superfamily
J	IPR007522	CRISPR-associated protein TM1795	Family
J	IPR005537	CRISPR type III-associated protein	Domain
I	IPR010172	CRISPR-associated protein, TM1791	Family
I	IPR005537	CRISPR type III-associated protein	Domain
H	IPR010165	Type III-B CRISPR module-associated protein Cmr3	Family
H	IPR052875	CRISPR-associated endoribonuclease	Family
H	IPR019117	CRISPR-associated protein, Cmr3	Family
D, E, F, G	IPR013410	CRISPR-associated RAMP Cmr4	Family
D, E, F, G	IPR005537	CRISPR type III-associated protein	Domain
A, B, C	IPR010160	CRISPR-associated protein, Cmr5	Family
A, B, C	IPR023101	AF1862-like domain superfamily	Homologous Superfamily