2BB5

Structure of Human Transcobalamin in complex with Cobalamin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.257 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structural basis for mammalian vitamin B12 transport by transcobalamin.

Wuerges, J.Garau, G.Geremia, S.Fedosov, S.N.Petersen, T.E.Randaccio, L.

(2006) Proc.Natl.Acad.Sci.Usa 103: 4386-4391

  • DOI: 10.1073/pnas.0509099103
  • Primary Citation of Related Structures:  2BB6, 2BBC

  • PubMed Abstract: 
  • Cobalamin (Cbl, vitamin B(12)) serves for two essential cofactors in mammals. The pathway for its intestinal absorption, plasma transport, and cellular uptake uses cell surface receptors and three Cbl-transporting proteins, haptocorrin, intrinsic fac ...

    Cobalamin (Cbl, vitamin B(12)) serves for two essential cofactors in mammals. The pathway for its intestinal absorption, plasma transport, and cellular uptake uses cell surface receptors and three Cbl-transporting proteins, haptocorrin, intrinsic factor, and transcobalamin (TC). We present the structure determination of a member of the mammalian Cbl-transporter family. The crystal structures of recombinant human and bovine holo-TCs reveal a two-domain architecture, with an N-terminal alpha(6)-alpha(6) barrel and a smaller C-terminal domain. One Cbl molecule in base-on conformation is buried inside the domain interface. Structural data combined with previous binding assays indicate a domain motion in the first step of Cbl binding. In a second step, the weakly coordinated ligand H(2)O at the upper axial side of added H(2)O-Cbl is displaced by a histidine residue of the alpha(6)-alpha(6) barrel. Analysis of amino acid conservation on TC's surface in orthologous proteins suggests the location of the TC-receptor-recognition site in an extended region on the alpha(6)-alpha(6) barrel. The TC structure allows for the mapping of sites of amino acid variation due to polymorphisms of the human TC gene. Structural information is used to predict the overall fold of haptocorrin and intrinsic factor and permits a rational approach to the design of new Cbl-based bioconjugates for diagnostic or therapeutic drug delivery.


    Organizational Affiliation

    Centre of Excellence in Biocrystallography, Department of Chemical Sciences, University of Trieste, Via L. Giorgieri 1, I-34127 Trieste, Italy.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Transcobalamin II
A, B
409Homo sapiensGene Names: TCN2 (TC2)
Find proteins for P20062 (Homo sapiens)
Go to Gene View: TCN2
Go to UniProtKB:  P20062
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
B12
Query on B12

Download SDF File 
Download CCD File 
A, B
COBALAMIN
C62 H89 Co N13 O14 P
LKVIQTCSMMVGFU-DWSMJLPVSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.257 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 49.127α = 90.00
b = 145.497β = 90.00
c = 165.043γ = 90.00
Software Package:
Software NamePurpose
AMoREphasing
REFMACrefinement
PDB_EXTRACTdata extraction
CCP4data scaling
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-04-04
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Advisory, Version format compliance
  • Version 1.3: 2012-10-24
    Type: Non-polymer description