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- EMDB-54245: NetF - ANTXR2 local refinement focused -

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Basic information

Entry
Database: EMDB / ID: EMD-54245
TitleNetF - ANTXR2 local refinement focused
Map datafocused local refinement map NetF-CMG2/ANTXR2 complex
Sample
  • Complex: local focused refinement of NetF bound to ANTXR2/CMG2 - ternary complex
    • Protein or peptide: Anthrax toxin receptor 2
    • Protein or peptide: Leukocidin/Hemolysin toxin family
KeywordsNetF / clostridium perfringens / hemolysin / CMG2 / ANTXR2 / toxin receptor interaction / transmembrane beta-barrel / TOXIN
Function / homology
Function and homology information


cytolysis in another organism / collagen fibril organization / uterus development / Uptake and function of anthrax toxins / single fertilization / transmembrane signaling receptor activity / endosome membrane / external side of plasma membrane / endoplasmic reticulum membrane / cell surface ...cytolysis in another organism / collagen fibril organization / uterus development / Uptake and function of anthrax toxins / single fertilization / transmembrane signaling receptor activity / endosome membrane / external side of plasma membrane / endoplasmic reticulum membrane / cell surface / extracellular region / metal ion binding / plasma membrane
Similarity search - Function
Anthrax toxin receptor / Anthrax toxin receptor, C-terminal / Anthrax toxin receptor, extracellular domain / Anthrax receptor C-terminus region / Anthrax receptor extracellular domain / Bi-component toxin, staphylococci / Leukocidin/Hemolysin toxin / Leukocidin/Hemolysin toxin family / Leukocidin/porin MspA superfamily / von Willebrand factor type A domain ...Anthrax toxin receptor / Anthrax toxin receptor, C-terminal / Anthrax toxin receptor, extracellular domain / Anthrax receptor C-terminus region / Anthrax receptor extracellular domain / Bi-component toxin, staphylococci / Leukocidin/Hemolysin toxin / Leukocidin/Hemolysin toxin family / Leukocidin/porin MspA superfamily / von Willebrand factor type A domain / VWFA domain profile. / von Willebrand factor (vWF) type A domain / von Willebrand factor, type A / von Willebrand factor A-like domain superfamily
Similarity search - Domain/homology
Leukocidin/Hemolysin toxin family / Anthrax toxin receptor 2
Similarity search - Component
Biological speciesHomo sapiens (human) / Clostridium perfringens (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.6 Å
AuthorsWang C / Iacovache I / Zuber B
Funding support Switzerland, 1 items
OrganizationGrant numberCountry
Swiss National Science Foundation10000175 Switzerland
CitationJournal: To Be Published
Title: Anthrax toxin receptor 2 is the Receptor for Clostridium perfringens NetF: Structural Insights into Toxin Binding and Pore Formation
Authors: Wang C / Cattalani F / Iacovache I / Arunasalam N / Posthaus H / Zuber B
History
DepositionJul 2, 2025-
Header (metadata) releaseFeb 18, 2026-
Map releaseFeb 18, 2026-
UpdateFeb 18, 2026-
Current statusFeb 18, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_54245.png

Downloads & links

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Map

FileDownload / File: emd_54245.map.gz / Format: CCP4 / Size: 476.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationfocused local refinement map NetF-CMG2/ANTXR2 complex
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.56 Å/pix.
x 500 pix.
= 281.5 Å		0.56 Å/pix.
x 500 pix.
= 281.5 Å		0.56 Å/pix.
x 500 pix.
= 281.5 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.563 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.05
Minimum - Maximum-0.4887072 - 0.8613046
Average (Standard dev.)0.00020468252 (±0.006234686)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions500500500
Spacing500500500
CellA=B=C: 281.5 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: half map A focused local refinement

Fileemd_54245_half_map_1.map
Annotationhalf map A focused local refinement
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map B focused local refinement

Fileemd_54245_half_map_2.map
Annotationhalf map B focused local refinement
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : local focused refinement of NetF bound to ANTXR2/CMG2 - ternary c...

EntireName: local focused refinement of NetF bound to ANTXR2/CMG2 - ternary complex
Components
  • Complex: local focused refinement of NetF bound to ANTXR2/CMG2 - ternary complex
    • Protein or peptide: Anthrax toxin receptor 2
    • Protein or peptide: Leukocidin/Hemolysin toxin family

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Supramolecule #1: local focused refinement of NetF bound to ANTXR2/CMG2 - ternary c...

SupramoleculeName: local focused refinement of NetF bound to ANTXR2/CMG2 - ternary complex
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 418 KDa

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Macromolecule #1: Anthrax toxin receptor 2

MacromoleculeName: Anthrax toxin receptor 2 / type: protein_or_peptide / ID: 1
Details: ANTXR2/CMG2 extracellular domain C terminally Flag and hexahistidine tagged
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 38.765117 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGTLSAPPCT QRIKWKGLLL TASLLNFWNL PTTAGQEQPS CRRAFDLYFV LDKSGSVANN WIEIYNFVQQ LAERFVSPEM RLSFIVFSS QATIILPLTG DRGKISKGLE DLKRVSPVGE TYIHEGLKLA NEQIQKAGGL KTSSIIIALT DGKLDGLVPS Y AEKEAKIS ...String:
MGTLSAPPCT QRIKWKGLLL TASLLNFWNL PTTAGQEQPS CRRAFDLYFV LDKSGSVANN WIEIYNFVQQ LAERFVSPEM RLSFIVFSS QATIILPLTG DRGKISKGLE DLKRVSPVGE TYIHEGLKLA NEQIQKAGGL KTSSIIIALT DGKLDGLVPS Y AEKEAKIS RSLGASVYCV GVLDFEQAQL ERIADSKEQV FPVKGGFQAL KGIINSILAQ SCTEILELQP SSVCVGEEFQ IV LSGRGFM LGSRNGSVLC TYTVNETYTT SVKPVSVQLN SMLCPAPILN KAGETLDVSV SFNGGKSVIS GSLIVTATEC SNG RTENLY FQGGAGARSI EGRIVKDYKD DDDKHHHHHH

UniProtKB: Anthrax toxin receptor 2

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Macromolecule #2: Leukocidin/Hemolysin toxin family

MacromoleculeName: Leukocidin/Hemolysin toxin family / type: protein_or_peptide / ID: 2 / Details: N-terminally hexahistidine tagged NetF / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Clostridium perfringens (bacteria)
Molecular weightTheoretical: 32.87459 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MVHHHHHHNS FPESIINSKG KQAEVYTSSD ASERDGIKTS LSASFIEDPN SNNLTALVSL KGFIPSGLIK TGTYYSANMY WPSKYNINI ETTDEKNNVK ILESIPSNTI ETVRVTESMG YSIGGNVSVS KKSSSVGANA GFNVQRSVQY EQPDFKTIQK S DGIRKASW ...String:
MVHHHHHHNS FPESIINSKG KQAEVYTSSD ASERDGIKTS LSASFIEDPN SNNLTALVSL KGFIPSGLIK TGTYYSANMY WPSKYNINI ETTDEKNNVK ILESIPSNTI ETVRVTESMG YSIGGNVSVS KKSSSVGANA GFNVQRSVQY EQPDFKTIQK S DGIRKASW NIVFNKTKDG YDQNSYHALY GNQLFMKSRL HNTGAKNLVE DKDLSPLISG GFTPNMVIAL KAPKGTKKSM IN LNYNLYQ DLYTLEWYKT QWWGENRVAK EPYYTYQTYE LDWENHTVEF IY

UniProtKB: Leukocidin/Hemolysin toxin family

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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

Concentration0.1 mg/mL
BufferpH: 8
VitrificationCryogen name: ETHANE / Chamber humidity: 100 %

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 30.0 µm / Nominal defocus min: 10.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Details: same processing as for EMD-54238 but masked and local refined.
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 268296
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: Other / Chain - Initial model type: other / Details: modelangelo
RefinementProtocol: OTHER
Output model

PDB-9rt4:
NetF - ANTXR2 local refinement focused

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