7ZQT

Helicobacter pylori adhesin BabA bound to neutralising human antibody.

• PDB DOI: https://doi.org/10.2210/pdb7ZQT/pdb

• Classification: CELL ADHESION
• Organism(s): Helicobacter pylori, Lama glama, Homo sapiens
• Expression System: Escherichia coli, Drosophila melanogaster
• Mutation(s): No 


• Deposited: 2022-05-03 Released: 2023-05-17 
• Deposition Author(s): Moonens, K., Boren, T.
• Funding Organization(s): Research Foundation - Flanders (FWO)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.281 
• R-Value Work: 0.225 
• R-Value Observed: 0.228 

Literature

Helicobacter pylori adhesin BabA bound to neutralising human antibody.

Remaut, H.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A1B1C1D1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A2B1C1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: isothermal titration calorimetry

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A1B1C1D1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A2B1C1 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 218.35 kDa 
• Atom Count: 13,999 
• Modelled Residue Count: 1,859 
• Deposited Residue Count: 2,038 
• Unique protein chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Adhesin binding fucosylated histo-blood group antigen	A, E	466	Helicobacter pylori	Mutation(s): 0  Gene Names: babA2
UniProt
Find proteins for O52269 (Helicobacter pylori) Explore O52269  Go to UniProtKB:  O52269

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Nanobody Nb19	B, F	120	Lama glama	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
VH domain human IgG antibody ABbA	C, G	222	Homo sapiens	Mutation(s): 0

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
VL domain human IgG antibody ABbA	D, H	211	Homo sapiens	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	J [auth A], L [auth E]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO	I [auth A], K [auth E]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.281 
• R-Value Work: 0.225 
• R-Value Observed: 0.228 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.7	α = 90
b = 68.4	β = 104.4
c = 176.6	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-05-17 
Deposition Author(s): Moonens, K., Boren, T.

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Funding Organization	Location	Grant Number
Research Foundation - Flanders (FWO)	Belgium	G033717N

Revision History  

• Version 1.0: 2023-05-17
  Type: Initial release
  
• Version 1.1: 2024-02-07
  Changes: Data collection, Refinement description