6GJE

Structure of the Amnionless(20-357)-Cubilin(36-135) complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.212 

wwPDB Validation   3D Report Full Report


This is version 3.0 of the entry. See complete history


Literature

Structural assembly of the megadalton-sized receptor for intestinal vitamin B12uptake and kidney protein reabsorption.

Larsen, C.Etzerodt, A.Madsen, M.Skjodt, K.Moestrup, S.K.Andersen, C.B.F.

(2018) Nat Commun 9: 5204-5204

  • DOI: https://doi.org/10.1038/s41467-018-07468-4
  • Primary Citation of Related Structures:  
    6GJE

  • PubMed Abstract: 

    The endocytic receptor cubam formed by the 460-kDa protein cubilin and the 45-kDa transmembrane protein amnionless (AMN), is essential for intestinal vitamin B 12 (B 12 ) uptake and for protein (e.g. albumin) reabsorption from the kidney filtrate. Loss of function of any of the two components ultimately leads to serious B 12 deficiency and urinary protein loss in humans (Imerslund-Gräsbeck's syndrome, IGS). Here, we present the crystal structure of AMN in complex with the amino-terminal region of cubilin, revealing a sophisticated assembly of three cubilin subunits combining into a single intertwined β-helix domain that docks to a corresponding three-faced β-helix domain in AMN. This β-helix-β-helix association thereby anchors three ligand-binding cubilin subunits to the transmembrane AMN. Electron microscopy of full-length cubam reveals a 700-800 Å long tree-like structure with the potential of dimerization into an even larger complex. Furthermore, effects of known human mutations causing IGS are explained by the structural information.


  • Organizational Affiliation

    Department of Biomedicine, Aarhus University, 8000, Aarhus C, Denmark. cbfa@biomed.au.dk.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protein amnionless338Homo sapiensMutation(s): 0 
Gene Names: AMNUNQ513/PRO1028
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BXJ7 (Homo sapiens)
Explore Q9BXJ7 
Go to UniProtKB:  Q9BXJ7
PHAROS:  Q9BXJ7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9BXJ7
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Cubilin
B, C, D
110Homo sapiensMutation(s): 0 
Gene Names: CUBNIFCR
UniProt & NIH Common Fund Data Resources
Find proteins for O60494 (Homo sapiens)
Explore O60494 
Go to UniProtKB:  O60494
PHAROS:  O60494
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO60494
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.212 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.28α = 90
b = 158.84β = 90
c = 237.16γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Danish Council for Independent ResearchDenmark--

Revision History  (Full details and data files)

  • Version 1.0: 2018-12-19
    Type: Initial release
  • Version 1.1: 2018-12-26
    Changes: Data collection, Database references
  • Version 2.0: 2019-02-27
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary
  • Version 3.0: 2019-06-12
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Experimental preparation, Polymer sequence, Source and taxonomy, Structure summary