1D0B | pdb_00001d0b

INTERNALIN B LEUCINE RICH REPEAT DOMAIN

• PDB DOI: https://doi.org/10.2210/pdb1D0B/pdb

• Classification: CELL ADHESION
• Organism(s): Listeria monocytogenes
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 1999-09-09 Released: 2000-01-07 
• Deposition Author(s): Marino, M., Braun, L., Cossart, P., Ghosh, P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.86 Å
• R-Value Free: 
  0.235 (Depositor), 0.235 (DCC) 
• R-Value Work: 
  0.207 (Depositor), 0.207 (DCC) 
• R-Value Observed: 
  0.210 (Depositor) 

Literature

Structure of the lnlB leucine-rich repeats, a domain that triggers host cell invasion by the bacterial pathogen L. monocytogenes.

Marino, M., Braun, L., Cossart, P., Ghosh, P.

(1999) Mol Cell 4: 1063-1072

• PubMed: 10635330 
• DOI: https://doi.org/10.1016/s1097-2765(00)80234-8
• Primary Citation Related Structures: 
  1D0B


• PubMed Abstract: 
  

  The L. monocytogenes protein lnlB activates phosphoinositide 3-kinase and induces phagocytosis in several mammalian cell types. The 1.86 A resolution X-ray crystal structure of the leucine-rich repeat domain of lnlB that is both necessary and sufficient to induce phagocytosis is presented here. The structure supports a crucial role for calcium in host cell invasion by L. monocytogenes and supplies a rationale for its function. Calciums are bound to the protein in an unusually exposed manner that suggests that the metals may act as a bridge between lnlB and mammalian cell surface receptors. The structure also identifies surfaces on the curved and elongated molecule that may constitute additional interaction sites in forming a bacterial-mammalian signaling complex.

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Organizational Affiliation: 
• Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla 92093-0314, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 23.84 kDa 
• Atom Count: 1,771 
• Modeled Residue Count: 207 
• Deposited Residue Count: 213 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
INTERNALIN B	A	213	Listeria monocytogenes	Mutation(s): 0
UniProt
Find proteins for P0DQD2 (Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e)) Explore P0DQD2  Go to UniProtKB:  P0DQD2

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	B [auth A], C [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.86 Å
• R-Value Free:  0.235 (Depositor), 0.235 (DCC) 
• R-Value Work:  0.207 (Depositor), 0.207 (DCC) 
• R-Value Observed: 0.210 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.41	α = 90
b = 56.92	β = 90
c = 84.35	γ = 90

Software Package:

Software Name	Purpose
CCP4	model building
SOLVE	phasing
SHARP	phasing
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
CCP4	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2000-01-07 
Deposition Author(s): Marino, M., Braun, L., Cossart, P., Ghosh, P.

Revision History  

• Version 1.0: 2000-01-07
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-02-07
  Changes: Data collection, Database references, Derived calculations