4ZRP

TC:CD320


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.184 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural basis of transcobalamin recognition by human CD320 receptor.

Alam, A.Woo, J.S.Schmitz, J.Prinz, B.Root, K.Chen, F.Bloch, J.S.Zenobi, R.Locher, K.P.

(2016) Nat Commun 7: 12100-12100

  • DOI: 10.1038/ncomms12100
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Cellular uptake of vitamin B12 (cobalamin) requires capture of transcobalamin (TC) from the plasma by CD320, a ubiquitous cell surface receptor of the LDLR family. Here we present the crystal structure of human holo-TC in complex with the extracellul ...

    Cellular uptake of vitamin B12 (cobalamin) requires capture of transcobalamin (TC) from the plasma by CD320, a ubiquitous cell surface receptor of the LDLR family. Here we present the crystal structure of human holo-TC in complex with the extracellular domain of CD320, visualizing the structural basis of the TC-CD320 interaction. The observed interaction chemistry can rationalize the high affinity of CD320 for TC and lack of haptocorrin binding. The in vitro affinity and complex stability of TC-CD320 were quantitated using a solid-phase binding assay and thermostability analysis. Stable complexes with TC were also observed for the disease-causing CD320ΔE88 mutant and for the isolated LDLR-A2 domain. We also determined the structure of the TC-CD320ΔE88 complex, which revealed only minor changes compared with the wild-type complex. Finally, we demonstrate significantly reduced in vitro affinity of TC for CD320 at low pH, recapitulating the proposed ligand release during the endocytic pathway.


    Organizational Affiliation

    Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, 8093 Zurich, Switzerland.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Transcobalamin-2
A, B
409Homo sapiensMutation(s): 0 
Gene Names: TCN2 (TC2)
Find proteins for P20062 (Homo sapiens)
Go to Gene View: TCN2
Go to UniProtKB:  P20062
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
CD320 antigen
C, D
119Homo sapiensMutation(s): 0 
Gene Names: CD320 (8D6A)
Find proteins for Q9NPF0 (Homo sapiens)
Go to Gene View: CD320
Go to UniProtKB:  Q9NPF0
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

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

Download SDF File 
Download CCD File 
A, C, D
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
CNC
Query on CNC

Download SDF File 
Download CCD File 
A, B
CO-CYANOCOBALAMIN
C63 H88 Co N14 O14 P
OEEKSCBDGPRZJZ-BYLSPCLQSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.184 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 98.099α = 90.00
b = 98.099β = 90.00
c = 355.979γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
PHENIXphasing
PDB_EXTRACTdata extraction
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2015-05-12 
  • Released Date: 2016-07-20 
  • Deposition Author(s): Alam, A., Locher, K.P.

Revision History 

  • Version 1.0: 2016-07-20
    Type: Initial release
  • Version 1.1: 2016-07-27
    Type: Database references
  • Version 1.2: 2018-10-10
    Type: Data collection, Database references, Source and taxonomy, Structure summary