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- PDB-9uer: AcrIE10-Cas7-IR complex -

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Basic information

Entry
Database: PDB / ID: 9uer
TitleAcrIE10-Cas7-IR complex
Components
  • AcrIE10
  • CRISPR-associated protein Cse4
  • DNA (5'-D(P*GP*TP*AP*TP*GP*AP*CP*AP*GP*AP*TP*GP*TP*CP*AP*TP*AP*CP*AP*A)-3')
  • DNA (5'-D(P*TP*GP*TP*AP*TP*GP*AP*CP*AP*TP*CP*TP*GP*TP*CP*AP*TP*AP*C)-3')
KeywordsTRANSCRIPTION / Anti-CRISPR / Transcription inhibitor
Function / homologyCRISPR-associated protein, CT1975 / CT1975-like protein / DNA / DNA (> 10) / Uncharacterized protein / CRISPR-associated protein Cse4
Function and homology information
Biological speciesKlebsiella pneumoniae (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.64 Å
AuthorsTsui, W.T. / Ma, J.B.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Cryo-EM structure of AcrIE10-Cas7-IR complex
Authors: Tsui, W.T. / Ma, J.B.
History
DepositionApr 9, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Apr 15, 2026Provider: repository / Type: Initial release
Revision 1.0Apr 15, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Apr 15, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Apr 15, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 15, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 15, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Apr 15, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
G: DNA (5'-D(P*TP*GP*TP*AP*TP*GP*AP*CP*AP*TP*CP*TP*GP*TP*CP*AP*TP*AP*C)-3')
H: DNA (5'-D(P*GP*TP*AP*TP*GP*AP*CP*AP*GP*AP*TP*GP*TP*CP*AP*TP*AP*CP*AP*A)-3')
A: AcrIE10
B: AcrIE10
C: AcrIE10
D: AcrIE10
E: CRISPR-associated protein Cse4
F: CRISPR-associated protein Cse4


Theoretical massNumber of molelcules
Total (without water)141,3518
Polymers141,3518
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: DNA chain DNA (5'-D(P*TP*GP*TP*AP*TP*GP*AP*CP*AP*TP*CP*TP*GP*TP*CP*AP*TP*AP*C)-3')


Mass: 5794.771 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Klebsiella pneumoniae (bacteria)
#2: DNA chain DNA (5'-D(P*GP*TP*AP*TP*GP*AP*CP*AP*GP*AP*TP*GP*TP*CP*AP*TP*AP*CP*AP*A)-3')


Mass: 6166.030 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Klebsiella pneumoniae (bacteria)
#3: Protein
AcrIE10


Mass: 13185.825 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: FME62_29170, GNF00_17735, H3G96_028615 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A218NFC2
#4: Protein CRISPR-associated protein Cse4 / Type I-E CRISPR-associated protein Cas7/Cse4/CasC


Mass: 38323.203 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: cas7e, HV185_05140, LS45_06975 / Production host: Escherichia coli (E. coli) / References: UniProt: A0AAJ5AUD1
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: AcrIE10-Cas7*-IR complex / Type: COMPLEX / Details: Cas7* binds to AcrIE10-IR complex / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.2 MDa / Experimental value: NO
Source (natural)Organism: Klebsiella pneumoniae (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.8 / Details: 20mM Tris-HCl, 150mM NaCl
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK I / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
MicroscopyModel: FEI POLARA 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1200 nm
Image recordingAverage exposure time: 1.2 sec. / Electron dose: 50 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.18.2_3874: / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.64 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 108754 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0068093
ELECTRON MICROSCOPYf_angle_d0.83711143
ELECTRON MICROSCOPYf_dihedral_angle_d18.1821371
ELECTRON MICROSCOPYf_chiral_restr0.0471268
ELECTRON MICROSCOPYf_plane_restr0.0061329

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