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- EMDB-67696: E coli CNF1 -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-67696
TitleE coli CNF1
Map data
Sample
  • Complex: E coli CNF1 toxin
    • Protein or peptide: Cytotoxic necrotizing factor 1
KeywordsE coli CNF1 toxin / 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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsZhou C / Zheng Y
Funding support China, 1 items
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, 2025-
Header (metadata) releaseSep 30, 2026-
Map releaseSep 30, 2026-
UpdateSep 30, 2026-
Current statusSep 30, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_67696.png

Downloads & links

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Map

FileDownload / File: emd_67696.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.93 Å/pix.
x 256 pix.
= 238.08 Å		0.93 Å/pix.
x 256 pix.
= 238.08 Å		0.93 Å/pix.
x 256 pix.
= 238.08 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.93 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.165
Minimum - Maximum-1.5006495 - 1.973537
Average (Standard dev.)0.00042022273 (±0.036782186)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 238.08 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_67696_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_67696_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : E coli CNF1 toxin

EntireName: E coli CNF1 toxin
Components
  • Complex: E coli CNF1 toxin
    • Protein or peptide: Cytotoxic necrotizing factor 1

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Supramolecule #1: E coli CNF1 toxin

SupramoleculeName: E coli CNF1 toxin / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 110 kDa/nm

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Macromolecule #1: Cytotoxic necrotizing factor 1

MacromoleculeName: Cytotoxic necrotizing factor 1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 114.000633 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGNQWQQKYL LEYNELVSNF PSPERVVSDY IKNCFKTDLP WFSRIDPDNA YFICFSQNRS NSRSYTGWDH LGKYKTEVLT LTQAALINI GYRFDVFDDA NSSTGIYKTK SADVFNEENE EKMLPSEYLH FLQKCDFAGV YGKTLSDYWS KYYDKFKLLL K NYYISSAL ...String:
MGNQWQQKYL LEYNELVSNF PSPERVVSDY IKNCFKTDLP WFSRIDPDNA YFICFSQNRS NSRSYTGWDH LGKYKTEVLT LTQAALINI GYRFDVFDDA NSSTGIYKTK SADVFNEENE EKMLPSEYLH FLQKCDFAGV YGKTLSDYWS KYYDKFKLLL K NYYISSAL YLYKNGELDE REYNFSMNAL NRSDNISLLF FDIYGYYASD IFVAKNNDKV MLFIPGAKKP FLFKKNIADL RL TLKELIK DSDKQQLLSQ HFSLYSRQDG VSYAGVNSVL HAIENDGNFN ESYFLYSNKT LSNKDVFDAI AISVKKRSFS DGD IVIKSN SEAQRDYALT ILQTILSMTP IFDIVVPEVS VPLGLGIITS SMGISFDQLI NGDTYEERRS AIPGLATNAV LLGL SFAIP LLISKAGINQ EVLSSVINNE GRTLNETNID IFLKEYGIAE DSISSTNLLD VKLKSSGQHV NIVKLSDEDN QIVAV KGSS LSGIYYEVDI ETGYEILSRR IYRTEYNNEI LWTRGGGLKG GQPFDFESLN IPVFFKDEPY SAVTGSPLSF INDDSS LLY PDTNPKLPQP TSEMDIVNYV KGSGSFGDRF VTLMRGATEE EAWNIASYHT AGGSTEELHE ILLGQGPQSS LGFTEYT SN VNSADAASRR HFLVVIKVHV KYITNNNVSY VNHWAIPDEA PVEVLAVVDR RFNFPEPSTP PDISTIRKLL SLRYFKES I ESTSKSNFQK LSRGNIDVLK GRGSISSTRQ RAIYPYFEAA NADEQQPLFF YIKKDRFDNH GYDQYFYDNT VGLNGIPTL NTYTGEIPSD SSSLGSTYWK KYNLTNETSI IRVSNSARGA NGIKIALEEV QEGKPVIITS GNLSGCTTIV ARKEGYIYKV HTGTTKSLA GFTSTTGVKK AVEVLELLTK EPIPRVEGIM SNDFLVDYLS ENFEDSLITY SSSEKKPDSQ ITIIRDNVSV F PYFLDNIP EHGFGTSATV LVRVDGNVVV RSLSESYSLN ADASEISVLK VFSKKF

UniProtKB: Cytotoxic necrotizing factor 1

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration2 mg/mL
BufferpH: 7.5
GridModel: Quantifoil R1.2/1.3
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 52.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 8635282 / Details: Autopick
CTF correctionSoftware - Name: cryoSPARC / Details: Patch CTF / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.3) / Number images used: 252548
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Details: Ab initio reconstruction
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.3) / Details: Non uniform refinement

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