3VE1

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


Experimental Data Snapshot

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

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

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

  • DOI: 10.1038/nsmb.2251
  • Primary Citation of Related Structures:  

  • 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 ...

    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.


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Transferrin-binding protein 2
A, C
658Neisseria meningitidis serogroup BMutation(s): 0 
Gene Names: tbpB (tbp2)
Find proteins for Q09057 (Neisseria meningitidis serogroup B)
Go to UniProtKB:  Q09057
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Serotransferrin
B, D
679Homo sapiensMutation(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
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, B, C, D
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
FE
Query on FE

Download SDF File 
Download CCD File 
B, D
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
 Ligand Interaction
CO3
Query on CO3

Download SDF File 
Download CCD File 
B, D
CARBONATE ION
C O3
BVKZGUZCCUSVTD-UHFFFAOYSA-L
 Ligand Interaction
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 = 128.023α = 90.00
b = 153.509β = 90.00
c = 169.511γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
DENZOdata reduction
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

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