Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors and generated by PQS (software)

Macromolecule Content

• Total Structure Weight: 125.49 kDa 
• Atom Count: 7,989 
• Modelled Residue Count: 1,028 
• Deposited Residue Count: 1,118 
• Unique protein chains: 2

 2V5P

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

• PDB DOI:  https://doi.org/10.2210/pdb2V5P/pdb

• Classification: RECEPTOR/GLYCOPROTEIN
• Organism(s): Homo sapiens
• Expression System: Cricetulus griseus, Escherichia coli
• 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: 4.10 Å
• R-Value Free: 0.327 
• R-Value Work: 0.291 
• R-Value Observed: 0.293 

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: https://doi.org/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, B	492	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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
INSULIN-LIKE GROWTH FACTOR II	C, D	67	Homo sapiens	Mutation(s): 0  Gene Names: IGF2, PP1446
UniProt & NIH Common Fund Data Resources
Find proteins for P01344 (Homo sapiens) Explore P01344  Go to UniProtKB:  P01344
PHAROS:  P01344

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E	3		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE GlyCosmos:  G15407YE GlyGen:  G15407YE

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	F [auth A], G [auth A], H [auth B], I [auth B], J [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 4.10 Å
• R-Value Free: 0.327 
• R-Value Work: 0.291 
• R-Value Observed: 0.293 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 165.979	α = 90
b = 117.312	β = 123.41
c = 116.668	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• 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: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2018-02-28
  Changes: Source and taxonomy
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Other, Structure summary