Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PQS (software)

Macromolecule Content

• Total Structure Weight: 70.07 kDa 
• Atom Count: 4686 
• Modelled Residue Count: 604 
• Deposited Residue Count: 627 
• Unique protein chains: 1

2V5O

STRUCTURE OF HUMAN IGF2R DOMAINS 11-14

• PDB DOI: 10.2210/pdb2V5O/pdb

• Classification: RECEPTOR
• Organism(s): Homo sapiens
• Expression System: Cricetulus griseus
• Mutation(s): No 


• Deposited: 2007-07-06 Released: 2007-12-11 
• Deposition Author(s): 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.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.91 Å
• R-Value Free: 0.304 
• R-Value Work: 0.257 
• R-Value Observed: 0.259 

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

• PubMed: 18046459 
• DOI: 10.1038/sj.emboj.7601938
• Primary Citation of Related Structures:  
  2V5N, 2V5O, 2V5P


• 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 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.

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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

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CATION-INDEPENDENT MANNOSE-6-PHOSPHATE RECEPTOR	A	627	Homo sapiens	Mutation(s): 0  Gene Names: IGF2R, MPRI
UniProt & NIH Common Fund Data Resources
Find proteins for P11717 (Homo sapiens) Explore P11717  Go to UniProtKB:  P11717
PHAROS:  P11717

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	B [auth A], C [auth A], D [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
CL	E [auth A], F [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.91 Å
• R-Value Free: 0.304 
• R-Value Work: 0.257 
• R-Value Observed: 0.259 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 138.554	α = 90
b = 69.247	β = 103.25
c = 98.012	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2007-07-06 
• Released Date: 2007-12-11 
Deposition Author(s): 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.

Revision History  

• Version 1.0: 2007-12-11
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2018-02-28
  Changes: Source and taxonomy
• Version 1.3: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Other, Structure summary