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- PDB-8iew: Cas005-crRNA-DNA complex -

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Open data


ID or keywords:

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Basic information

Entry
Database: PDB / ID: 8iew
TitleCas005-crRNA-DNA complex
Components
  • (DNA (55-MER)) x 2
  • Cas005
  • RNA (38-MER)
KeywordsRNA BINDING PROTEIN/RNA/DNA / CRISPR/Cas005 / RNA BINDING PROTEIN-RNA-DNA complex
Function / homologyDNA / DNA (> 10) / RNA / RNA (> 10)
Function and homology information
Biological speciesBiggievirus Mos11
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsZhang, X. / Duan, Z.Q. / Zhu, J.K.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, China) China
CitationJournal: To Be Published
Title: Cryo-EM structure of Cas005-crRNA-DNA complex at 3.1 Angstroms resolution
Authors: Zhang, X. / Duan, Z.Q. / Zhu, J.K.
History
DepositionFeb 16, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Feb 28, 2024Provider: repository / Type: Initial release
Revision 1.1Jul 16, 2025Group: Data collection / Structure summary / Category: em_software / pdbx_entry_details / Item: _em_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cas005
B: RNA (38-MER)
C: DNA (55-MER)
D: DNA (55-MER)


Theoretical massNumber of molelcules
Total (without water)129,4034
Polymers129,4034
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Cas005


Mass: 83449.094 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Biggievirus Mos11 / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: RNA chain RNA (38-MER)


Mass: 12058.124 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Biggievirus Mos11 / Production host: Escherichia coli BL21(DE3) (bacteria)
#3: DNA chain DNA (55-MER)


Mass: 16994.910 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Biggievirus Mos11 / Production host: Escherichia coli BL21(DE3) (bacteria)
#4: DNA chain DNA (55-MER)


Mass: 16900.799 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Biggievirus Mos11 / Production host: Escherichia coli BL21(DE3) (bacteria)
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: Ternary complex of Cas005 with crRNA and target DNA / Type: COMPLEX / Entity ID: all / Source: MULTIPLE SOURCES
Source (natural)Organism: Biggievirus Mos11
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 7.4
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 FIELD / Nominal defocus max: 5000 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 50 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
EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 59719 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0065569
ELECTRON MICROSCOPYf_angle_d0.6967833
ELECTRON MICROSCOPYf_dihedral_angle_d20.0521265
ELECTRON MICROSCOPYf_chiral_restr0.041898
ELECTRON MICROSCOPYf_plane_restr0.008775

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