5NRP

Beta domain of human transcobalamin bound to cobinamide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.57 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.180 

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Ligand Structure Quality Assessment 


This is version 2.1 of the entry. See complete history


Literature

Structure of the human transcobalamin beta domain in four distinct states.

Bloch, J.S.Ruetz, M.Krautler, B.Locher, K.P.

(2017) PLoS One 12: e0184932-e0184932

  • DOI: 10.1371/journal.pone.0184932
  • Primary Citation of Related Structures:  
    5NO0, 5NP4, 5NRP, 5NSA

  • PubMed Abstract: 
  • Vitamin B12 (cyanocobalamin, CNCbl) is an essential cofactor-precursor for two biochemical reactions in humans. When ingested, cobalamins (Cbl) are transported via a multistep transport system into the bloodstream, where the soluble protein transcobalamin (TC) binds Cbl and the complex is taken up into the cells via receptor mediated endocytosis ...

    Vitamin B12 (cyanocobalamin, CNCbl) is an essential cofactor-precursor for two biochemical reactions in humans. When ingested, cobalamins (Cbl) are transported via a multistep transport system into the bloodstream, where the soluble protein transcobalamin (TC) binds Cbl and the complex is taken up into the cells via receptor mediated endocytosis. Crystal structures of TC in complex with CNCbl have been solved previously. However, the initial steps of holo-TC assembly have remained elusive. Here, we present four crystal structures of the beta domain of human TC (TC-beta) in different substrate-bound states. These include the apo and CNCbl-bound states, providing insight into the early steps of holo-TC assembly. We found that in vitro assembly of TC-alpha and TC-beta to a complex was Cbl-dependent. We also determined the structure of TC-beta in complex with cobinamide (Cbi), an alternative substrate, shedding light on the specificity of TC. We finally determined the structure of TC-beta in complex with an inhibitory antivitamin B12 (anti-B12). We used this structure to model the binding of anti-B12 into full-length holo-TC and could rule out that the inhibitory function of anti-B12 was based on an inability to form a functional complex with TC.


    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Transcobalamin-2A108Homo 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
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CBY (Subject of Investigation/LOI)
Query on CBY

Download Ideal Coordinates CCD File 
B [auth A], C [auth A]COB(II)INAMIDE
C48 H72 Co N11 O8
GFVWZOGCSKVPRA-NZMQITGIDF
 Ligand Interaction
CYN
Query on CYN

Download Ideal Coordinates CCD File 
D [auth A]CYANIDE ION
C N
XFXPMWWXUTWYJX-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.57 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.180 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.859α = 90
b = 59.859β = 90
c = 70.114γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-09-27
    Type: Initial release
  • Version 2.0: 2019-10-16
    Changes: Atomic model, Data collection
  • Version 2.1: 2019-11-20
    Changes: Derived calculations