9MK3 | pdb_00009mk3

Engineered AsCas12a (M537R, F870L)

PDB DOI: https://doi.org/10.2210/pdb9MK3/pdb

Classification: SPLICING/DNA/RNA
Organism(s): Acidaminococcus
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2024-12-16 Released: 2025-12-24
Deposition Author(s): Dementiev, A., White, A., Olland, A.M., Suto, R.K.
Funding Organization(s): Other private

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free:
0.240 (Depositor), 0.239 (DCC)
R-Value Work:
0.196 (Depositor), 0.198 (DCC)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Mechanistic basis for improved activity of Engineered AsCas12a

Jansson-Fritzberg, L., Chica, B., Latrick, C., Olland, A., Dementiev, A., White, A., Lemercier, J., Wolk, S.K.

To be published.

Macromolecule Content

Total Structure Weight: 358.62 kDa
Atom Count: 24,407
Modeled Residue Count: 2,750
Deposited Residue Count: 2,790
Unique protein chains: 1
Unique nucleic acid chains: 3

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CRISPR-associated endonuclease Cas12a	A, E	1,307	Acidaminococcus	Mutation(s): 2 Gene Names: cas12a, cpf1, HMPREF1246_0236 EC: 3.1.21.1 (PDB Primary Data), 4.6.1.22 (PDB Primary Data)
UniProt
Find proteins for U2UMQ6 (Acidaminococcus sp. (strain BV3L6)) Explore U2UMQ6 Go to UniProtKB: U2UMQ6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	U2UMQ6
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Length	Organism	Image
gRNA (41-MER)	B, F	44	Acidaminococcus
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Length	Organism	Image
TS DNA (31-MER)	C, G	34	Acidaminococcus
Sequence Annotations Expand
Reference Sequence

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Entity ID: 4
Molecule	Chains	Length	Organism	Image
NTS DNA (5'-D(CPAPGPTPCPCPTPTPTPT)-3')	D, H	10	Acidaminococcus
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain Q [auth A] SDF format, chain T [auth E] SDF format, chain U [auth E] SDF format, chain V [auth E] SDF format, chain W [auth G] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain T [auth E] MOL2 format, chain U [auth E] MOL2 format, chain V [auth E] MOL2 format, chain W [auth G] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain O [auth A] mmCIF format, chain P [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain T [auth E] mmCIF format, chain U [auth E] mmCIF format, chain V [auth E] mmCIF format, chain W [auth G]	K [auth A] L [auth A] M [auth A] N [auth A] O [auth A] K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], P [auth A], Q [auth A], T [auth E], U [auth E], V [auth E], W [auth G]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain T [auth E] Focus chain U [auth E] Focus chain V [auth E] Focus chain W [auth G] Interactions & Density Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain T [auth E] Focus chain U [auth E] Focus chain V [auth E] Focus chain W [auth G]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain S [auth E] MOL2 format, chain J [auth A] MOL2 format, chain S [auth E] mmCIF format, chain J [auth A] mmCIF format, chain S [auth E]	J [auth A], S [auth E]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain J [auth A] Focus chain S [auth E] Interactions & Density Focus chain J [auth A] Focus chain S [auth E]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain R [auth E] MOL2 format, chain I [auth A] MOL2 format, chain R [auth E] mmCIF format, chain I [auth A] mmCIF format, chain R [auth E]	I [auth A], R [auth E]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain R [auth E] Interactions & Density Focus chain I [auth A] Focus chain R [auth E]