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- PDB-8ja0: Cryo-EM structure of the NmeCas9-sgRNA-AcrIIC4 ternary complex -

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Basic information

Entry
Database: PDB / ID: 8ja0
TitleCryo-EM structure of the NmeCas9-sgRNA-AcrIIC4 ternary complex
Components
  • CRISPR-associated endonuclease Cas9
  • RNA (117-MER)
  • Uncharacterized protein
KeywordsRNA BINDING PROTEIN/RNA / a protein complex / VIRAL PROTEIN / RNA BINDING PROTEIN-RNA complex
Function / homology
Function and homology information


maintenance of CRISPR repeat elements / endonuclease activity / defense response to virus / Hydrolases; Acting on ester bonds / DNA binding / RNA binding / metal ion binding
Similarity search - Function
RuvC endonuclease subdomain 3 / RuvC endonuclease subdomain 3 / CRISPR-associated endonuclease Cas9 / HNH endonuclease / Cas9-type HNH domain / Cas9-type HNH domain profile. / HNH nuclease / Ribonuclease H superfamily
Similarity search - Domain/homology
RNA / RNA (> 10) / RNA (> 100) / Uncharacterized protein / CRISPR-associated endonuclease Cas9
Similarity search - Component
Biological speciesNeisseria meningitidis (bacteria)
Haemophilus parainfluenzae (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.52 Å
AuthorsYin, H. / Li, Z. / Yu, G.M. / Li, X.Z.
CitationJournal: To Be Published
Title: Cryo-EM structure of the NmeCas9-sgRNA-AcrIIC4 ternary complex
Authors: Yin, H. / Li, Z. / Yu, G.M. / Li, X.Z.
History
DepositionMay 5, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 9, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CRISPR-associated endonuclease Cas9
D: Uncharacterized protein
B: RNA (117-MER)


Theoretical massNumber of molelcules
Total (without water)171,9663
Polymers171,9663
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein CRISPR-associated endonuclease Cas9


Mass: 124613.883 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria meningitidis (bacteria) / Gene: cas9, NMV_1993 / Production host: Escherichia coli (E. coli)
References: UniProt: C9X1G5, Hydrolases; Acting on ester bonds
#2: Protein Uncharacterized protein


Mass: 9985.316 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus parainfluenzae (bacteria) / Gene: NCTC10672_00033, NCTC10672_02354 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A377JKY9
#3: RNA chain RNA (117-MER)


Mass: 37367.059 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria meningitidis (bacteria) / Production host: Escherichia coli (E. coli)

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: a protein complex / Type: COMPLEX / Entity ID: all / Source: MULTIPLE SOURCES
Source (natural)Organism: Neisseria meningitidis (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2500 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.20.1_4487: / Classification: refinement
CTF correctionType: PHASE FLIPPING ONLY
3D reconstructionResolution: 3.52 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 251996 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00211739
ELECTRON MICROSCOPYf_angle_d0.5616380
ELECTRON MICROSCOPYf_dihedral_angle_d12.9262600
ELECTRON MICROSCOPYf_chiral_restr0.0351901
ELECTRON MICROSCOPYf_plane_restr0.0041707

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