5U8R

Structure of the ectodomain of the human Type 1 insulin-like growth factor receptor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00002 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.256 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

How ligand binds to the type 1 insulin-like growth factor receptor.

Xu, Y.Kong, G.K.Menting, J.G.Margetts, M.B.Delaine, C.A.Jenkin, L.M.Kiselyov, V.V.De Meyts, P.Forbes, B.E.Lawrence, M.C.

(2018) Nat Commun 9: 821-821

  • DOI: 10.1038/s41467-018-03219-7
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Human type 1 insulin-like growth factor receptor is a homodimeric receptor tyrosine kinase that signals into pathways directing normal cellular growth, differentiation and proliferation, with aberrant signalling implicated in cancer. Insulin-like gro ...

    Human type 1 insulin-like growth factor receptor is a homodimeric receptor tyrosine kinase that signals into pathways directing normal cellular growth, differentiation and proliferation, with aberrant signalling implicated in cancer. Insulin-like growth factor binding is understood to relax conformational restraints within the homodimer, initiating transphosphorylation of the tyrosine kinase domains. However, no three-dimensional structures exist for the receptor ectodomain to inform atomic-level understanding of these events. Here, we present crystal structures of the ectodomain in apo form and in complex with insulin-like growth factor I, the latter obtained by crystal soaking. These structures not only provide a wealth of detail of the growth factor interaction with the receptor's primary ligand-binding site but also indicate that ligand binding separates receptor domains by a mechanism of induced fit. Our findings are of importance to the design of agents targeting IGF-1R and its partner protein, the human insulin receptor.


    Organizational Affiliation

    The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC, 3052, Australia.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Insulin-like growth factor 1 receptor
A
885Homo sapiensMutation(s): 0 
Gene Names: IGF1R
EC: 2.7.10.1
Find proteins for P08069 (Homo sapiens)
Go to Gene View: IGF1R
Go to UniProtKB:  P08069
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Fv 24-60 heavy chain
H
126N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Fv 24-60 light chain
L
108N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
MLT
Query on MLT

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Download CCD File 
A
D-MALATE
(2R)-2-HYDROXYBUTANEDIOIC ACID; 2-HYDROXY-SUCCINIC ACID
C4 H6 O5
BJEPYKJPYRNKOW-UWTATZPHSA-N
 Ligand Interaction
IMD
Query on IMD

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Download CCD File 
H
IMIDAZOLE
C3 H5 N2
RAXXELZNTBOGNW-UHFFFAOYSA-O
 Ligand Interaction
NAG
Query on NAG

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00002 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.256 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 95.030α = 90.00
b = 201.730β = 90.00
c = 117.750γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
phenix.refinerefinement
PHASERphasing
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2016-12-14 
  • Released Date: 2018-02-28 
  • Deposition Author(s): Lawrence, M., Xu, Y.

Funding OrganizationLocationGrant Number
National Health and Medical Research Council (Australia)AustraliaAPP1070526
National Health and Medical Research Council (Australia)AustraliaAPP1128553
National Health and Medical Research Council (Australia)AustraliaIRIISS
Victorian State GovernmentAustraliaVictorian State Government Operational Infrastructure Support

Revision History 

  • Version 1.0: 2018-02-28
    Type: Initial release
  • Version 1.1: 2018-03-14
    Type: Database references