5MGA | pdb_00005mga

Structure of the Cpf1 endonuclease R-loop complex after DNA cleavage

PDB DOI: https://doi.org/10.2210/pdb5MGA/pdb
NAKB: 5MGA

Classification: HYDROLASE
Organism(s): Francisella tularensis subsp. novicida U112
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2016-11-21 Released: 2017-06-21
Deposition Author(s): Montoya, G., Stella, S.
Funding Organization(s): Novo Nordisk Foundation

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å
R-Value Free:
0.265 (Depositor), 0.260 (DCC)
R-Value Work:
0.242 (Depositor), 0.241 (DCC)
R-Value Observed:
0.243 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Structure of the Cpf1 endonuclease R-loop complex after target DNA cleavage.

Stella, S., Alcon, P., Montoya, G.

(2017) Nature 546: 559-563

PubMed: 28562584 Search on PubMed
DOI: https://doi.org/10.1038/nature22398
Primary Citation Related Structures:
5MGA

PubMed Abstract:
Cpf1 is an RNA-guided endonuclease that is emerging as a powerful genome-editing tool. Here we provide insight into its DNA-targeting mechanism by determining the structure of Francisella novicida Cpf1 with the triple-stranded R-loop generated after DNA cleavage. The structure reveals the machinery involved in DNA unwinding to form a CRISPR RNA (crRNA)-DNA hybrid and a displaced DNA strand. The protospacer adjacent motif (PAM) is recognized by the PAM-interacting domain. The loop-lysine helix-loop motif in this domain contains three conserved lysine residues that are inserted in a dentate manner into the double-stranded DNA. Unzipping of the double-stranded DNA occurs in a cleft arranged by acidic and hydrophobic residues facilitating the crRNA-DNA hybrid formation. The PAM single-stranded DNA is funnelled towards the nuclease site through a mixed hydrophobic and basic cavity. In this catalytic conformation, the PAM-interacting domain and the helix-loop-helix motif in the REC1 domain adopt a 'rail' shape and 'flap-on' conformations, respectively, channelling the PAM strand into the cavity. A steric barrier between the RuvC-II and REC1 domains forms the 'septum', separating the displaced PAM strand and the crRNA-DNA hybrid, avoiding DNA re-annealing. Mutations in key residues reveal a mechanism linking the PAM and DNA nuclease sites. Analysis of the Cpf1 structures proposes a singular working model of RNA-guided DNA cleavage, suggesting new avenues for redesign of Cpf1.

Organizational Affiliation

Protein Structure &Function Programme, Macromolecular Crystallography Group, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, Copenhagen 2200, Denmark.

Macromolecule Content

Total Structure Weight: 179.33 kDa
Atom Count: 11,351
Modeled Residue Count: 1,260
Deposited Residue Count: 1,401
Unique protein chains: 1
Unique nucleic acid chains: 3

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CRISPR-associated endonuclease Cpf1	A	1,323	Francisella tularensis subsp. novicida U112	Mutation(s): 0 Gene Names: cpf1, FTN_1397 EC: 3.1 (PDB Primary Data), 4.6.1.22 (UniProt), 3.1.21.1 (UniProt)
UniProt
Find proteins for A0Q7Q2 (Francisella tularensis subsp. novicida (strain ATCC 15482 / CCUG 33449 / U112)) Explore A0Q7Q2 Go to UniProtKB: A0Q7Q2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0Q7Q2
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff)

Molecule	Chains	Length	Organism
Entity ID: 2
RNA (40-MER)	B	40	Francisella tularensis subsp. novicida U112
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff)

Molecule	Chains	Length	Organism
Entity ID: 3
DNA (26-MER)	C	26	Francisella tularensis subsp. novicida U112
Sequence Annotations Expand
Reference Sequence

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Molecule	Chains	Length	Organism
Entity ID: 4
DNA (5'-D(PCPGPTPTPAPGPAPGPAPAPGPT)-3')	D	12	Francisella tularensis subsp. novicida U112
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain F [auth B] SDF format, chain E [auth B] MOL2 format, chain F [auth B] MOL2 format, chain E [auth B] mmCIF format, chain F [auth B] mmCIF format, chain E [auth B]	E [auth B], F [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain E [auth B] Focus chain F [auth B] Interactions & Density Focus chain E [auth B] Focus chain F [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å
R-Value Free: 0.265 (Depositor), 0.260 (DCC)
R-Value Work: 0.242 (Depositor), 0.241 (DCC)
R-Value Observed: 0.243 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.223	α = 90
b = 137.652	β = 90
c = 320.513	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2017-06-21

Deposition Author(s):

Montoya, G.

Stella, S.

Funding Organization	Location	Grant Number
Novo Nordisk Foundation	Denmark	NNF14CC0001

Revision History (Full details and data files)

Version 1.0: 2017-06-21
Type: Initial release
Version 1.1: 2017-06-28
Changes: Database references
Version 1.2: 2018-10-24
Changes: Advisory, Data collection, Derived calculations
Version 1.3: 2024-05-08
Changes: Data collection, Database references