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- EMDB-0449: Structure of LbCas12a-crRNA -

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Basic information

Database: EMDB / ID: EMD-0449
TitleStructure of LbCas12a-crRNA
Map data
Sampleprotein complex 1:
Cpf1 / nucleic-acidNucleic acid / (ligand) x 2
Function / homologyCRISPR-associated endonuclease Cas12a / Cas12a, REC1 domain / Cas12a, RuvC nuclease domain / Cas12a, nuclease domain / Alpha helical recognition lobe domain / Nuclease domain / RuvC nuclease domain / Cpf1
Function and homology information
Biological speciesLachnospiraceae bacterium ND2006 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.67 Å
AuthorsChang L / Li Z / Zhang H
CitationJournal: Cell Host Microbe / Year: 2019
Title: Structural Basis for the Inhibition of CRISPR-Cas12a by Anti-CRISPR Proteins.
Authors: Heng Zhang / Zhuang Li / Courtney M Daczkowski / Clinton Gabel / Andrew D Mesecar / Leifu Chang /
Abstract: CRISPR-Cas12a (Cpf1), a type V CRISPR-associated nuclease, provides bacterial immunity against bacteriophages and plasmids but also serves as a tool for genome editing. Foreign nucleic acids are ...CRISPR-Cas12a (Cpf1), a type V CRISPR-associated nuclease, provides bacterial immunity against bacteriophages and plasmids but also serves as a tool for genome editing. Foreign nucleic acids are integrated into the CRISPR locus, prompting transcription of CRISPR RNAs (crRNAs) that guide Cas12a cleavage of foreign complementary DNA. However, mobile genetic elements counteract Cas12a with inhibitors, notably type V-A anti-CRISPRs (AcrVAs). We present cryoelectron microscopy structures of Cas12a-crRNA bound to AcrVA1 and AcrVA4 at 3.5 and 3.3 Å resolutions, respectively. AcrVA1 is sandwiched between the recognition (REC) and nuclease (NUC) lobes of Cas12a and inserts into the binding pocket for the protospacer-adjacent motif (PAM), a short DNA sequence guiding Cas12a targeting. AcrVA1 cleaves crRNA in a Cas12a-dependent manner, inactivating Cas12a-crRNA complexes. The AcrVA4 dimer is anchored around the crRNA pseudoknot of Cas12a-crRNA, preventing required conformational changes for crRNA-DNA heteroduplex formation. These results uncover molecular mechanisms for CRISPR-Cas12a inhibition, providing insights into bacteria-phage dynamics.
Validation ReportPDB-ID: 6nme

SummaryFull reportAbout validation report
DateDeposition: Jan 10, 2019 / Header (metadata) release: Jun 12, 2019 / Map release: Jun 12, 2019 / Update: Jun 12, 2019

Structure visualization

  • Surface view with section colored by density value
  • Surface level: 0.0229
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.0229
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
Supplemental images

Downloads & links


FileDownload / File: emd_0449.map.gz / Format: CCP4 / Size: 6.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

AxesZ (Sec.)Y (Row.)X (Col.)
1.35 Å/pix.
x 120 pix.
= 162. Å
1.35 Å/pix.
x 120 pix.
= 162. Å
1.35 Å/pix.
x 120 pix.
= 162. Å



Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.35 Å
Contour LevelBy AUTHOR: 0.0229 / Movie #1: 0.0229
Minimum - Maximum-0.08509276 - 0.1525452
Average (Standard dev.)0.0010884809 (±0.0072791507)
SymmetrySpace group: 1


Map geometry
Axis orderXYZ
CellA=B=C: 162.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.351.351.35
M x/y/z120120120
origin x/y/z0.0000.0000.000
length x/y/z162.000162.000162.000
MAP C/R/S123
start NC/NR/NS000
D min/max/mean-0.0850.1530.001

Supplemental data

Sample components

Entire protein complex 1

EntireName: protein complex 1 / Number of components: 5

Component #1: protein, protein complex 1

ProteinName: protein complex 1 / Recombinant expression: No
SourceSpecies: Lachnospiraceae bacterium ND2006 (bacteria)

Component #2: protein, Cpf1

ProteinName: Cpf1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 143.750219 kDa
SourceSpecies: Lachnospiraceae bacterium ND2006 (bacteria)
Source (engineered)Expression System: Escherichia coli (E. coli)

Component #3: nucleic-acid, crRNA

nucleic acidName: crRNA / Class: RNA / Structure: OTHER / Synthetic: No
MassTheoretical: 12.879634 kDa
SourceSpecies: Lachnospiraceae bacterium ND2006 (bacteria)

Component #4: ligand, MAGNESIUM ION

LigandName: MAGNESIUM ION / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 2.430505 MDa

Component #5: ligand, water

LigandName: water / Number of Copies: 6 / Recombinant expression: No
MassTheoretical: 1.801505 MDa

Experimental details

Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionSpecimen conc.: 1 mg/mL / pH: 7.5
Support filmunspecified
VitrificationCryogen name: ETHANE

Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 35 e/Å2 / Illumination mode: SPOT SCAN
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 78756
3D reconstructionSoftware: RELION / Resolution: 5.67 Å / Resolution method: FSC 0.143 CUT-OFF

Atomic model buiding

Output model

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