4ZRP

TC:CD320


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.184 

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Ligand Structure Quality Assessment 


This is version 2.0 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:  
    4ZRP, 4ZRQ

  • 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 extracellular domain of CD320, visualizing the structural basis of the TC-CD320 interaction ...

    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
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Transcobalamin-2A, B409Homo sapiensMutation(s): 0 
Gene Names: TCN2TC2
UniProt & NIH Common Fund Data Resources
Find proteins for P20062 (Homo sapiens)
Explore P20062 
Go to UniProtKB:  P20062
PHAROS:  P20062
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
CD320 antigenC, D119Homo sapiensMutation(s): 0 
Gene Names: CD3208D6AUNQ198/PRO224
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NPF0 (Homo sapiens)
Explore Q9NPF0 
Go to UniProtKB:  Q9NPF0
PHAROS:  Q9NPF0
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CNC (Subject of Investigation/LOI)
Query on CNC

Download Ideal Coordinates CCD File 
E [auth A], M [auth B]CYANOCOBALAMIN
C63 H89 Co N14 O14 P
SYZBZQWSWIJYAR-UVKKECPRSA-M
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], N [auth B]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download Ideal Coordinates CCD File 
F [auth A], G [auth A], O [auth C], P [auth C], Q [auth D], R [auth D]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.184 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 98.099α = 90
b = 98.099β = 90
c = 355.979γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PDB_EXTRACTdata extraction
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

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

Revision History  (Full details and data files)

  • Version 1.0: 2016-07-20
    Type: Initial release
  • Version 1.1: 2016-07-27
    Changes: Database references
  • Version 1.2: 2018-10-10
    Changes: Data collection, Database references, Source and taxonomy, Structure summary
  • Version 2.0: 2021-08-25
    Changes: Advisory, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary