1GP3 | pdb_00001gp3

Human IGF2R domain 11

• PDB DOI: https://doi.org/10.2210/pdb1GP3/pdb

• Classification: RECEPTOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2001-10-29 Released: 2002-02-28 
• Deposition Author(s): Brown, J., Esnouf, R.M., Jones, M.A., Linnell, J., Harlos, K., Hassan, A.B., Jones, E.Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 
  0.255 (Depositor), 0.258 (DCC) 
• R-Value Work: 
  0.206 (Depositor), 0.206 (DCC) 
• R-Value Observed: 
  0.206 (Depositor) 

Starting Model: experimental

Literature

Structure of a Functional Igf2R Fragment Determined from the Anomalous Scattering of Sulfur

Brown, J., Esnouf, R.M., Jones, M.A., Linnell, J., Harlos, K., Hassan, A.B., Jones, E.Y.

(2002) EMBO J 21: 1054

• PubMed: 11867533 
• DOI: https://doi.org/10.1093/emboj/21.5.1054
• Primary Citation Related Structures: 
  1GP0, 1GP3


• PubMed Abstract: 
  

  Insulin-like growth factor II receptor (IGF2R) is a multifunctional cell surface receptor implicated in tumour suppression. Its growth inhibitory activity has been associated with an ability to bind IGF-II. IGF2R contains 15 homologous extracellular domains, with domain 11 primarily responsible for IGF-II binding. We report a 1.4 A resolution crystal structure of domain 11, solved using the anomalous scattering signal of sulfur. The structure consists of two crossed beta-sheets forming a flattened beta-barrel. Structural analysis identifies the putative IGF-II binding site at one end of the beta-barrel whilst crystal lattice contacts suggest a model for the full-length IGF2R extracellular region. The structure factors and coordinates of IGF2R domain 11 have been deposited in the Protein Data Bank (accession codes 1GP0 and 1GP3).

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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, Roosevelt Drive, Headington, Oxford OX3 7BN, UK.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 15.56 kDa 
• Atom Count: 1,061 
• Modeled Residue Count: 129 
• Deposited Residue Count: 143 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CATION-INDEPENDENT MANNOSE-6-PHOSPHATE RECEPTOR	A	143	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P11717 (Homo sapiens) Explore P11717  Go to UniProtKB:  P11717
PHAROS:  P11717 GTEx:  ENSG00000197081

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free:  0.255 (Depositor), 0.258 (DCC) 
• R-Value Work:  0.206 (Depositor), 0.206 (DCC) 
• R-Value Observed: 0.206 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 31.373	α = 90
b = 49.843	β = 90
c = 83.03	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
EPMR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2002-02-28 
Deposition Author(s): Brown, J., Esnouf, R.M., Jones, M.A., Linnell, J., Harlos, K., Hassan, A.B., Jones, E.Y.

Revision History  

• Version 1.0: 2002-02-28
  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: 2019-04-10
  Changes: Data collection, Other, Source and taxonomy
• Version 1.4: 2023-12-13
  Changes: Data collection, Database references, Other, Refinement description
• Version 1.5: 2024-11-06
  Changes: Structure summary