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- PDB-8zdr: Cryo-EM structure of the Cas9d-sgRNA-target DNA complex -

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Basic information

Entry
Database: PDB / ID: 8zdr
TitleCryo-EM structure of the Cas9d-sgRNA-target DNA complex
Components
  • DNA (32-MER)
  • DNA (5'-D(P*CP*GP*GP*GP*TP*CP*AP*AP*AP*TP*G)-3')
  • RNA (144-MER)
  • a protein
KeywordsANTIVIRAL PROTEIN / a protein complex
Function / homologyDNA / DNA (> 10) / RNA / RNA (> 10) / RNA (> 100)
Function and homology information
Biological speciesmetagenome (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.65 Å
AuthorsZhang, H. / Li, X. / Liu, Z.
Funding support China, 1items
OrganizationGrant numberCountry
Other government China
CitationJournal: To Be Published
Title: Cryo-EM structure of the Cas9d-sgRNA-target DNA complex
Authors: Li, X. / Zhang, H. / Liu, Z.
History
DepositionMay 3, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 19, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA (144-MER)
B: DNA (32-MER)
C: a protein
D: DNA (5'-D(P*CP*GP*GP*GP*TP*CP*AP*AP*AP*TP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)160,5525
Polymers160,4874
Non-polymers651
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: RNA chain RNA (144-MER)


Mass: 51127.133 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) metagenome (others) / Production host: Escherichia coli (E. coli)
#2: DNA chain DNA (32-MER)


Mass: 11271.250 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) metagenome (others) / Production host: Escherichia coli (E. coli)
#3: Protein a protein


Mass: 86585.766 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) metagenome (others) / Production host: Escherichia coli (E. coli)
#4: DNA chain DNA (5'-D(P*CP*GP*GP*GP*TP*CP*AP*AP*AP*TP*G)-3')


Mass: 11502.379 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) metagenome (others) / Production host: Escherichia coli (E. coli)
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
Has ligand of interestN
Has protein modificationN

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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 / Type: COMPLEX / Entity ID: #1-#4 / Source: RECOMBINANT
Source (natural)Organism: metagenome (others)
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: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1600 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING ONLY
3D reconstructionResolution: 2.65 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 171509 / Symmetry type: POINT
RefinementHighest resolution: 2.65 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0047940
ELECTRON MICROSCOPYf_angle_d0.67311566
ELECTRON MICROSCOPYf_dihedral_angle_d18.4812626
ELECTRON MICROSCOPYf_chiral_restr0.0381430
ELECTRON MICROSCOPYf_plane_restr0.005793

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