Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Protein Workshop | Ligand Explorer

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - AB 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - AB 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 294815.22 
• Atom Count: 19071 
• Residue Count: 2674 
• Unique protein chains: 2

3VE1

The 2.9 angstrom crystal structure of Transferrin binding protein B (TbpB) from serogroup B M982 Neisseria meningitidis in complex with human transferrin

• DOI: 10.2210/pdb3VE1/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Neisseria meningitidis serogroup B, Homo sapiens
• Expression System: Escherichia coli BL21(DE3), Pichia pastoris


• Deposited: 2012-01-06 Released: 2012-02-22 
• Deposition Author(s): Calmettes, C., Moraes, T.F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.956 Å
• R-Value Free: 0.249 
• R-Value Work: 0.207 

Literature

The structural basis of transferrin sequestration by transferrin-binding protein B.

Calmettes, C., Alcantara, J., Yu, R.H., Schryvers, A.B., Moraes, T.F.

(2012) Nat.Struct.Mol.Biol. 19: 358-360

• PubMed: 22343719 
• DOI: 10.1038/nsmb.2251
• Primary Citation of Related Structures:  
  3VE2


• PubMed Abstract: 
  

Neisseria meningitidis, the causative agent of bacterial meningitis, acquires the essential element iron from the host glycoprotein transferrin during infection through a surface transferrin receptor system composed of proteins TbpA and TbpB. Here we present the crystal structures of TbpB from N. meningitidis in its apo form and in complex with human transferrin. The structure reveals how TbpB sequesters and initiates iron release from human transferrin.

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Organizational Affiliation: 

Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Transferrin-binding protein 2	A, C	658	Neisseria meningitidis serogroup B	Mutation(s): 0  Gene Names: tbpB (tbp2)
Find proteins for Q09057 (Neisseria meningitidis serogroup B) Go to UniProtKB:  Q09057

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
Serotransferrin	B, D	679	Homo sapiens	Mutation(s): 0  Gene Names: TF
Find proteins for P02787 (Homo sapiens) Go to Gene View: TF Go to UniProtKB:  P02787

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
GOL	A, B, C, D	GLYCEROL GLYCERIN; PROPANE-1,2,3-TRIOL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
FE	B, D	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N
CO3	B, D	CARBONATE ION C O3 BVKZGUZCCUSVTD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.956 Å
• R-Value Free: 0.249 
• R-Value Work: 0.207 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 128.023	α = 90.00
b = 153.509	β = 90.00
c = 169.511	γ = 90.00

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
DENZO	data reduction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2012-01-06 
• Released Date: 2012-02-22 
• Deposition Author(s): Calmettes, C., Moraes, T.F.

Revision History 

• Version 1.0: 2012-02-22
  Type: Initial release
• Version 1.1: 2012-09-05
  Type: Database references
• Version 1.2: 2013-09-18
  Type: Derived calculations