2V5P

COMPLEX STRUCTURE OF HUMAN IGF2R DOMAINS 11-13 BOUND TO IGF-II


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.1 Å
  • R-Value Free: 0.327 
  • R-Value Work: 0.291 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structure and Functional Analysis of the Igf-II/Igf2R Interaction

Brown, J.Delaine, C.Zaccheo, O.J.Siebold, C.Gilbert, R.J.Van Boxel, G.Denley, A.Wallace, J.C.Hassan, A.B.Forbes, B.E.Jones, E.Y.

(2008) Embo J. 27: 265

  • DOI: 10.1038/sj.emboj.7601938
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Embryonic development and normal growth require exquisite control of insulin-like growth factors (IGFs). In mammals the extracellular region of the cation-independent mannose-6-phosphate receptor has gained an IGF-II-binding function and is termed ty ...

    Embryonic development and normal growth require exquisite control of insulin-like growth factors (IGFs). In mammals the extracellular region of the cation-independent mannose-6-phosphate receptor has gained an IGF-II-binding function and is termed type II IGF receptor (IGF2R). IGF2R sequesters IGF-II; imbalances occur in cancers and IGF2R is implicated in tumour suppression. We report crystal structures of IGF2R domains 11-12, 11-12-13-14 and domains 11-12-13/IGF-II complex. A distinctive juxtaposition of these domains provides the IGF-II-binding unit, with domain 11 directly interacting with IGF-II and domain 13 modulating binding site flexibility. Our complex shows that Phe19 and Leu53 of IGF-II lock into a hydrophobic pocket unique to domain 11 of mammalian IGF2Rs. Mutagenesis analyses confirm this IGF-II 'binding-hotspot', revealing that IGF-binding proteins and IGF2R have converged on the same high-affinity site.


    Organizational Affiliation

    Cancer Research UK Receptor Structure Research Group, Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Headington, Oxford, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CATION-INDEPENDENT MANNOSE-6-PHOSPHATE RECEPTOR
A, B
492Homo sapiensMutation(s): 0 
Gene Names: IGF2R (MPRI)
Find proteins for P11717 (Homo sapiens)
Go to Gene View: IGF2R
Go to UniProtKB:  P11717
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
INSULIN-LIKE GROWTH FACTOR II
C, D
67Homo sapiensMutation(s): 0 
Gene Names: IGF2
Find proteins for P01344 (Homo sapiens)
Go to Gene View: IGF2
Go to UniProtKB:  P01344
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BMA
Query on BMA

Download SDF File 
Download CCD File 
A
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A, B
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.1 Å
  • R-Value Free: 0.327 
  • R-Value Work: 0.291 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 165.979α = 90.00
b = 117.312β = 123.41
c = 116.668γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
XDSdata scaling
MOLREPphasing
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-12-11
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2018-02-28
    Type: Source and taxonomy