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: 2.96 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.209 

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:  
    3VE2, 3VE1

  • 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 ...

    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
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(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Transferrin-binding protein 2A, C658Neisseria meningitidis serogroup BMutation(s): 0 
Gene Names: tbpB, tbp2
UniProt
Find proteins for Q09057 (Neisseria meningitidis serogroup B)
Explore Q09057 
Go to UniProtKB:  Q09057
Protein Feature View
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  • Reference Sequence
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(by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
SerotransferrinB, D679Homo sapiensMutation(s): 0 
Gene Names: TF, PRO1400
UniProt & NIH Common Fund Data Resources
Find proteins for P02787 (Homo sapiens)
Explore P02787 
Go to UniProtKB:  P02787
PHAROS:  P02787
GTEx:  ENSG00000091513
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL
Download Ideal Coordinates CCD File 
E [auth A] , F [auth A] , I [auth B] , J [auth B] , K [auth B] , L [auth B] , M [auth B] , N [auth B] , 
E [auth A],  F [auth A],  I [auth B],  J [auth B],  K [auth B],  L [auth B],  M [auth B],  N [auth B],  O [auth C],  R [auth D],  S [auth D],  T [auth D],  U [auth D]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N		 Ligand Interaction
CO3
Query on CO3
Download Ideal Coordinates CCD File 
 G [auth B], P [auth D]CARBONATE ION
C O3
BVKZGUZCCUSVTD-UHFFFAOYSA-L		 Ligand Interaction
FE
Query on FE
Download Ideal Coordinates CCD File 
 H [auth B], Q [auth D]FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.96 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.209 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 128.023α = 90
b = 153.509β = 90
c = 169.511γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History  (Full details and data files)

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