6KL9 | pdb_00006kl9

Structure of LbCas12a-crRNA complex bound to AcrVA4 (form A complex)

External Resource: Annotation

Domain Annotation: ECOD Classification
Protein Family Annotation
InterPro: Protein Family Classification

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	cas_Cpf1_4th	e6kl9A5	A: beta barrels	X: OB-fold	H: Small protein B (SmpB) (From Topology)	T: Small protein B (SmpB)	F: cas_Cpf1_4th	ECOD (1.6)
A	cas_Cpf1_3rd	e6kl9A3	A: alpha arrays	X: CRISPR-associated endonuclease Cpf1 PI (PAM-interacting) domain (From Topology)	H: CRISPR-associated endonuclease Cpf1 PI (PAM-interacting) domain (From Topology)	T: CRISPR-associated endonuclease Cpf1 PI (PAM-interacting) domain	F: cas_Cpf1_3rd	ECOD (1.6)
A	cas_Cpf1_1st	e6kl9A4	A: alpha complex topology	X: CRISPR-associated endonuclease first helical domain	H: CRISPR-associated endonuclease Cpf1 first helical domain (From Topology)	T: CRISPR-associated endonuclease Cpf1 first helical domain	F: cas_Cpf1_1st	ECOD (1.6)
A	cas_Cpf1_2nd	e6kl9A2	A: alpha complex topology	X: CRISPR-associated endonuclease Cpf1 second helical domain (From Topology)	H: CRISPR-associated endonuclease Cpf1 second helical domain (From Topology)	T: CRISPR-associated endonuclease Cpf1 second helical domain	F: cas_Cpf1_2nd	ECOD (1.6)
A	cas_Cpf1_5th	e6kl9A6	A: mixed a+b and a/b	X: Ribonuclease H-like	H: Ribonuclease H-like (From Topology)	T: Ribonuclease H-like	F: cas_Cpf1_5th	ECOD (1.6)
A	cas_Cpf1_6th	e6kl9A1	A: few secondary structure elements	X: CRISPR-associated endonuclease Cpf1 nuclease domain (From Topology)	H: CRISPR-associated endonuclease Cpf1 nuclease domain (From Topology)	T: CRISPR-associated endonuclease Cpf1 nuclease domain	F: cas_Cpf1_6th	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF22222	CRISPR-associated endonuclease Cpf1 PI domain (Cpf1_PI-like)	CRISPR-associated endonuclease Cpf1 PI domain	The CRISPR-Cpf1 system is a class 2 CRISPR-Cas system that mediates robust DNA interference. Cpf1 differ from Cas9 in many aspects including the guide RNAs and substrate specificity. The Cpf1-crRNA complex cleaves a target double-stranded DNA contain ...	The CRISPR-Cpf1 system is a class 2 CRISPR-Cas system that mediates robust DNA interference. Cpf1 differ from Cas9 in many aspects including the guide RNAs and substrate specificity. The Cpf1-crRNA complex cleaves a target double-stranded DNA containing a short T-rich PAM motif on the 5' end of the non-target strand. This PAM motif is recognized by the Cpf1 PI (PAM-interacting) domain. This domain folds into array of four helices and along with the helix-loop-helix motif in the REC1 domain, channel the PAM strand into a cavity leading to the nuclease site [1-2].	Domain
A	PF18510	Nuclease domain (NUC)	Nuclease domain	This is a nuclease (NUC) domain found in Cpf1, an RNA-guided endonuclease of a type V CRISPR-Cas system. Structural and functional analysis indicate that this domain is involved in DNA cleavage [1].	Domain
A	PF21918	CRISPR-associated endonuclease Cpf1 REC2 domain (cas_Cpf1_2nd)	CRISPR-associated endonuclease Cpf1 REC2 domain	This Pfam entry represents the REC2 domain from the Cpf1 protein, an RNA-guided endonuclease of a type V CRISPR-Cas system that has been harnessed for genome editing. The REC2 domain is a part of the REC lobe of the bilobed architecture of Cpf1, whic ...	This Pfam entry represents the REC2 domain from the Cpf1 protein, an RNA-guided endonuclease of a type V CRISPR-Cas system that has been harnessed for genome editing. The REC2 domain is a part of the REC lobe of the bilobed architecture of Cpf1, which consists of both REC1 and REC2 domains. The REC2 domain comprises 10 alpha helices and 2 beta strands that form a small antiparallel sheet. The crRNA-target DNA heteroduplex is accommodated within the positively charged, central channel formed by the REC1, REC2, and RuvC domains, and is recognized by the protein in a sequence-independent manner.	Domain
A	PF18501	Alpha helical recognition lobe domain (REC1)	Alpha helical recognition lobe domain	Cpf1 is an RNA-guided endonuclease of a type V CRISPR-Cas system. Cpf1 adopts a bilobed architecture consisting of an alpha-helical recognition (REC) lobe and a nuclease (NUC) lobe, with the small CRISPR RNAs (crRNAs)-target DNA heteroduplex bound to ...	Cpf1 is an RNA-guided endonuclease of a type V CRISPR-Cas system. Cpf1 adopts a bilobed architecture consisting of an alpha-helical recognition (REC) lobe and a nuclease (NUC) lobe, with the small CRISPR RNAs (crRNAs)-target DNA heteroduplex bound to the positively charged, central channel between the two lobes. The REC lobe consists of the REC1 and REC2 domains where REC1 comprises 13 alpha helices, and REC2 comprises ten alpha helices and two beta strands that form a small antiparallel sheet [1]. This entry represents REC1 domain.	Domain
A	PF18516	RuvC nuclease domain (RuvC_1)	RuvC nuclease domain	This is a RuvC nuclease domain found in type V CRISPR-associated protein Cas12a (Cpf1), used for genome editing applications. These proteins carry out endoribonuclease activity for processing its own guide RNAs and RNA-guided DNase activity for targe ...	This is a RuvC nuclease domain found in type V CRISPR-associated protein Cas12a (Cpf1), used for genome editing applications. These proteins carry out endoribonuclease activity for processing its own guide RNAs and RNA-guided DNase activity for target DNA cleavage. The C-terminal region of Cas12a carries the RUVC domain, NUC domain Pfam:PF18510 and the arginine-rich bridge helix (BH). Both the NUC and BH domains are nested in the RuvC domain. Mutations in the RuvC domain impair cleavage of both strands in a target DNA duplex, while a mutation in the Nuc domain impaired target strand cleavage only. This indicates that the DNA nuclease active sites are located at the interface of the RuvC and Nuc domains and that cleavage of the non-target DNA strand by the RuvC domain is a prerequisite for target strand cleavage by the Nuc domain [1].	Domain

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR054116	Cas12a, REC2 domain	Domain
A	IPR040852	Cas12a, RuvC nuclease domain	Domain
A	IPR040787	Cas12a, REC1 domain	Domain
A	IPR027620	CRISPR-associated endonuclease Cas12a	Family
A	IPR040882	Cas12a, nuclease domain	Domain
A	IPR053993	Cas12a, PI 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.