InlB392_T332E: T332E variant of Listeria monocytogenes InlB (internalin B) residues 36-392

Experimental Data Snapshot

  • Resolution: 2.05 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.189 

wwPDB Validation   3D Report Full Report

This is version 1.2 of the entry. See complete history


A recurring packing contact in crystals of InlB pinpoints functional binding sites in the internalin domain and the B repeat.

Geerds, C.Bleymuller, W.M.Meyer, T.Widmann, C.Niemann, H.H.

(2022) Acta Crystallogr D Struct Biol 78: 310-320

  • DOI: https://doi.org/10.1107/S2059798322000432
  • Primary Citation of Related Structures:  
    7NMS, 7PV8, 7PV9

  • PubMed Abstract: 

    InlB, a bacterial agonist of the human receptor tyrosine kinase MET, consists of an N-terminal internalin domain, a central B repeat and three C-terminal GW domains. In all previous structures of full-length InlB or an InlB construct lacking the GW domains (InlB 392 ), there was no interpretable electron density for the B repeat. Here, three InlB 392 crystal structures in which the B repeat is resolved are described. These are the first structures to reveal the relative orientation of the internalin domain and the B repeat. A wild-type structure and two structures of the T332E variant together contain five crystallographically independent molecules. Surprisingly, the threonine-to-glutamate substitution in the B repeat substantially improved the crystallization propensity and crystal quality of the T332E variant. The internalin domain and B repeat are quite rigid internally, but are flexibly linked to each other. The new structures show that inter-domain flexibility is the most likely cause of the missing electron density for the B repeat in previous InlB structures. A potential binding groove between B-repeat strand β2 and an adjacent loop forms an important crystal contact in all five crystallographically independent chains. This region may represent a hydrophobic `sticky patch' that supports protein-protein interactions. This assumption agrees with the previous finding that all known inactivating point mutations in the B repeat lie within strand β2. The groove formed by strand β2 and the adjacent loop may thus represent a functionally important protein-protein interaction site in the B repeat.

  • Organizational Affiliation

    Department of Chemistry, Bielefeld University, Universitätsstrasse 25, 33615 Bielefeld, Germany.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Internalin B362Listeria monocytogenes EGD-eMutation(s): 1 
Gene Names: inlBlmo0434
Find proteins for P0DQD2 (Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e))
Explore P0DQD2 
Go to UniProtKB:  P0DQD2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0DQD2
Sequence Annotations
  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.58α = 90
b = 54.59β = 90
c = 226.72γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2022-01-26
    Type: Initial release
  • Version 1.1: 2022-03-16
    Changes: Database references
  • Version 1.2: 2024-01-31
    Changes: Data collection, Refinement description