8VBA

The secreted adhesin EtpA of Enterotoxigenic Escherichia coli in complex with the mouse mAb 1C08

PDB DOI: https://doi.org/10.2210/pdb8VBA/pdb
EM Map EMD-43118: EMDB EMDataResource

Classification: CELL ADHESION
Organism(s): Escherichia coli ETEC H10407, Mus musculus
Expression System: Escherichia coli BL21(DE3), Homo sapiens
Mutation(s): No

Deposited: 2023-12-12 Released: 2024-09-11
Deposition Author(s): Berndsen, Z.T., Ward, A.B.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), Department of Veterans Affairs (VA, United States), Consortia for HIV/AIDS Vaccine Development

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.29 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Structure and Antigenicity of the Secreted Glycoprotein Adhesin EtpA of Enterotoxigenic Escherichia coli

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.

To be published.

Macromolecule Content

Total Structure Weight: 240.79 kDa
Atom Count: 9,416
Modelled Residue Count: 1,260
Deposited Residue Count: 2,263
Unique protein chains: 3

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
EtpA	A	1,564	Escherichia coli ETEC H10407	Mutation(s): 0 Gene Names: etpA
UniProt
Find proteins for Q29XT7 (Escherichia coli) Explore Q29XT7 Go to UniProtKB: Q29XT7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q29XT7
Glycosylation
Glycosylation Sites: 39	Glycosylation Focus chain A
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
mAb 1C08 Heavy Chain	B [auth H]	466	Mus musculus	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
mAb 1C08 Light Chain	C [auth L]	233	Mus musculus	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BGC (Subject of Investigation/LOI) Query on BGC Download Ideal Coordinates CCD File SDF format, chain AA [auth A] SDF format, chain BA [auth A] SDF format, chain CA [auth A] SDF format, chain D [auth A] SDF format, chain DA [auth A] SDF format, chain E [auth A] SDF format, chain EA [auth A] SDF format, chain F [auth A] SDF format, chain FA [auth A] SDF format, chain G [auth A] SDF format, chain GA [auth A] SDF format, chain H [auth A] SDF format, chain HA [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain JA [auth A] SDF format, chain K [auth A] SDF format, chain KA [auth A] SDF format, chain LA [auth A] SDF format, chain M [auth A] SDF format, chain MA [auth A] SDF format, chain N [auth A] SDF format, chain NA [auth A] SDF format, chain O [auth A] SDF format, chain OA [auth A] SDF format, chain PA [auth A] SDF format, chain Q [auth A] SDF format, chain S [auth A] SDF format, chain U [auth A] SDF format, chain V [auth A] SDF format, chain W [auth A] SDF format, chain X [auth A] SDF format, chain Y [auth A] SDF format, chain Z [auth A] SDF format, chain IA [auth A] SDF format, chain L [auth A] SDF format, chain P [auth A] SDF format, chain R [auth A] SDF format, chain T [auth A] MOL2 format, chain AA [auth A] MOL2 format, chain BA [auth A] MOL2 format, chain CA [auth A] MOL2 format, chain D [auth A] MOL2 format, chain DA [auth A] MOL2 format, chain E [auth A] MOL2 format, chain EA [auth A] MOL2 format, chain F [auth A] MOL2 format, chain FA [auth A] MOL2 format, chain G [auth A] MOL2 format, chain GA [auth A] MOL2 format, chain H [auth A] MOL2 format, chain HA [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain JA [auth A] MOL2 format, chain K [auth A] MOL2 format, chain KA [auth A] MOL2 format, chain LA [auth A] MOL2 format, chain M [auth A] MOL2 format, chain MA [auth A] MOL2 format, chain N [auth A] MOL2 format, chain NA [auth A] MOL2 format, chain O [auth A] MOL2 format, chain OA [auth A] MOL2 format, chain PA [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain S [auth A] MOL2 format, chain U [auth A] MOL2 format, chain V [auth A] MOL2 format, chain W [auth A] MOL2 format, chain X [auth A] MOL2 format, chain Y [auth A] MOL2 format, chain Z [auth A] MOL2 format, chain IA [auth A] MOL2 format, chain L [auth A] MOL2 format, chain P [auth A] MOL2 format, chain R [auth A] MOL2 format, chain T [auth A]	AA [auth A] BA [auth A] CA [auth A] D [auth A] DA [auth A] AA [auth A], BA [auth A], CA [auth A], D [auth A], DA [auth A], E [auth A], EA [auth A], F [auth A], FA [auth A], G [auth A], GA [auth A], H [auth A], HA [auth A], I [auth A], IA [auth A], J [auth A], JA [auth A], K [auth A], KA [auth A], L [auth A], LA [auth A], M [auth A], MA [auth A], N [auth A], NA [auth A], O [auth A], OA [auth A], P [auth A], PA [auth A], Q [auth A], R [auth A], S [auth A], T [auth A], U [auth A], V [auth A], W [auth A], X [auth A], Y [auth A], Z [auth A]	beta-D-glucopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-VFUOTHLCSA-N		Interactions Focus chain AA [auth A] Focus chain BA [auth A] Focus chain CA [auth A] Focus chain D [auth A] Focus chain DA [auth A] Focus chain E [auth A] Focus chain EA [auth A] Focus chain F [auth A] Focus chain FA [auth A] Focus chain G [auth A] Focus chain GA [auth A] Focus chain H [auth A] Focus chain HA [auth A] Focus chain I [auth A] Focus chain IA [auth A] Focus chain J [auth A] Focus chain JA [auth A] Focus chain K [auth A] Focus chain KA [auth A] Focus chain L [auth A] Focus chain LA [auth A] Focus chain M [auth A] Focus chain MA [auth A] Focus chain N [auth A] Focus chain NA [auth A] Focus chain O [auth A] Focus chain OA [auth A] Focus chain P [auth A] Focus chain PA [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A] Focus chain U [auth A] Focus chain V [auth A] Focus chain W [auth A] Focus chain X [auth A] Focus chain Y [auth A] Focus chain Z [auth A] Interactions & Density Focus chain AA [auth A] Focus chain BA [auth A] Focus chain CA [auth A] Focus chain D [auth A] Focus chain DA [auth A] Focus chain E [auth A] Focus chain EA [auth A] Focus chain F [auth A] Focus chain FA [auth A] Focus chain G [auth A] Focus chain GA [auth A] Focus chain H [auth A] Focus chain HA [auth A] Focus chain I [auth A] Focus chain IA [auth A] Focus chain J [auth A] Focus chain JA [auth A] Focus chain K [auth A] Focus chain KA [auth A] Focus chain L [auth A] Focus chain LA [auth A] Focus chain M [auth A] Focus chain MA [auth A] Focus chain N [auth A] Focus chain NA [auth A] Focus chain O [auth A] Focus chain OA [auth A] Focus chain P [auth A] Focus chain PA [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A] Focus chain U [auth A] Focus chain V [auth A] Focus chain W [auth A] Focus chain X [auth A] Focus chain Y [auth A] Focus chain Z [auth A]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.29 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC
MODEL REFINEMENT	PHENIX

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2024-09-11

Deposition Author(s):

Berndsen, Z.T.

Ward, A.B.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	R01 AI126887
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	R01 AI089894
Department of Veterans Affairs (VA, United States)	United States	5I01BX001469-05).
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	T32AI007172
Consortia for HIV/AIDS Vaccine Development	United States	UM1 AI144462
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	UM1 AI100663
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	R01 AI113867