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- PDB-21im: E coli CNF1 -

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Basic information

Entry
Database: PDB / ID: 21im
TitleE coli CNF1
ComponentsCytotoxic necrotizing factor 1
KeywordsTOXIN / E coli CNF1 toxin
Function / homology
Function and homology information


symbiont-mediated perturbation of host cell-cell junction
Similarity search - Function
Cytotoxic necrotizing factor, Rho-activating domain / Domain of unknown function DUF4765 / Cytotoxic necrotizing factor, Rho-activating domain superfamily / Rho-activating domain of cytotoxic necrotizing factor / Domain of unknown function (DUF4765) / Domain of unknown function DUF6543 / Dermonecrotic toxin, N-terminal domain / Cytotoxic necrotizing factor-like, catalytic
Similarity search - Domain/homology
Cytotoxic necrotizing factor 1
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 Å
AuthorsZhou, C. / Zheng, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: E coli CNF1
Authors: Zhou, C. / Zheng, Y.
History
DepositionDec 13, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Sep 30, 2026Provider: repository / Type: Initial release
Revision 1.0Sep 30, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cytotoxic necrotizing factor 1


Theoretical massNumber of molelcules
Total (without water)114,0011
Polymers114,0011
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Cytotoxic necrotizing factor 1


Mass: 114000.633 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: cnf1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q47106
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: E coli CNF1 toxin / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 110 kDa/nm / Experimental value: YES
Source (natural)Organism: Escherichia coli (E. coli)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
SpecimenConc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid type: Quantifoil R1.2/1.3
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: 52 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.3particle selection
2PHENIX1.21.2_5419model refinement
5cryoSPARCCTF correction
11cryoSPARC4.3final Euler assignment
13cryoSPARC4.33D reconstruction
CTF correctionDetails: Patch CTF / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 8635282 / Details: Autopick
3D reconstructionResolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 252548 / Symmetry type: POINT
RefinementHighest resolution: 3 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0047476
ELECTRON MICROSCOPYf_angle_d0.83110126
ELECTRON MICROSCOPYf_dihedral_angle_d6.3891006
ELECTRON MICROSCOPYf_chiral_restr0.0521138
ELECTRON MICROSCOPYf_plane_restr0.0061299

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