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- PDB-8vba: The secreted adhesin EtpA of Enterotoxigenic Escherichia coli in ... -

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Basic information

Entry
Database: PDB / ID: 8vba
TitleThe secreted adhesin EtpA of Enterotoxigenic Escherichia coli in complex with the mouse mAb 1C08
Components
  • EtpA
  • mAb 1C08 Heavy Chain
  • mAb 1C08 Light Chain
KeywordsCELL ADHESION / Adhesin / glycoprotein / lectin / antibody-antigen complex
Function / homology
Function and homology information


extracellular region
Similarity search - Function
: / Filamentous haemagglutinin FhaB/tRNA nuclease CdiA-like, TPS domain / TPS secretion domain / haemagglutination activity domain / ESPR domain / Extended Signal Peptide of Type V secretion system / Parallel beta-helix repeat / Parallel beta-helix repeats / Pectin lyase fold / Pectin lyase fold/virulence factor
Similarity search - Domain/homology
beta-D-glucopyranose / EtpA
Similarity search - Component
Biological speciesEscherichia coli ETEC H10407 (bacteria)
Mus musculus (house mouse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.29 Å
AuthorsBerndsen, Z.T. / Ward, A.B.
Funding support United States, 7items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI126887 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI089894 United States
Department of Veterans Affairs (VA, United States)5I01BX001469-05). United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)T32AI007172 United States
Consortia for HIV/AIDS Vaccine DevelopmentUM1 AI144462 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)UM1 AI100663 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI113867 United States
CitationJournal: To Be Published
Title: Structure and Antigenicity of the Secreted Glycoprotein Adhesin EtpA of Enterotoxigenic Escherichia coli
Authors: Berndsen, Z.T. / Akhtar, M. / Thapa, M. / Vickers, T. / Schmitz, A. / Torres, J.L. / Baboo, S. / Kumar, P. / Khatoom, N. / Sheikh, A. / Hamrick, M. / Diedrich, J.K. / Bartolome, S.M. / ...Authors: Berndsen, Z.T. / Akhtar, M. / Thapa, M. / Vickers, T. / Schmitz, A. / Torres, J.L. / Baboo, S. / Kumar, P. / Khatoom, N. / Sheikh, A. / Hamrick, M. / Diedrich, J.K. / Bartolome, S.M. / Garrett, P.T. / Yates III, J.R. / Turner, J.S. / Dell, A. / Haslam, S. / Paulson, J.C. / Ellebedy, A.H. / Fleckenstein, J.M. / Ward, A.B.
History
DepositionDec 12, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 11, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2024Group: Data collection / Structure summary
Category: em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: EtpA
H: mAb 1C08 Heavy Chain
L: mAb 1C08 Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)240,78842
Polymers233,7623
Non-polymers7,02639
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: Protein EtpA


Mass: 157456.922 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli ETEC H10407 (bacteria)
Gene: etpA / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q29XT7
#2: Antibody mAb 1C08 Heavy Chain


Mass: 50965.383 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): Expi293F / Production host: Homo sapiens (human)
#3: Antibody mAb 1C08 Light Chain


Mass: 25339.232 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): Expi293 / Production host: Homo sapiens (human)
#4: Sugar...
ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / glucose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 39 / Source method: obtained synthetically / Formula: C6H12O6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranoseCOMMON NAMEGMML 1.0
b-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0
Has ligand of interestY
Has protein modificationY

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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: EtpA in complex with the mAb 1C08 Fab / Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT
Molecular weightValue: .220 MDa / Experimental value: YES
Source (natural)Organism: Escherichia coli ETEC H10407 (bacteria)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 6
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K

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Electron microscopy imaging

MicroscopyModel: TFS GLACIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1500 nm / Nominal defocus min: 500 nm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 47 e/Å2 / Film or detector model: TFS FALCON 4i (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARC2particle selection
2EPU2image acquisition
4cryoSPARC2CTF correction
7UCSF Chimeramodel fitting
9cryoSPARC2initial Euler assignment
10cryoSPARCfinal Euler assignment
11cryoSPARC2classification
12cryoSPARC3D reconstruction
13PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.29 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 215360 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Atomic model buildingSource name: AlphaFold / Type: in silico model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0049506
ELECTRON MICROSCOPYf_angle_d0.96212926
ELECTRON MICROSCOPYf_dihedral_angle_d3.9091349
ELECTRON MICROSCOPYf_chiral_restr0.0511656
ELECTRON MICROSCOPYf_plane_restr0.0041633

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