3W13

Insulin receptor ectodomain construct comprising domains L1-CR in complex with high-affinity insulin analogue [D-PRO-B26]-DTI-NH2, alphact peptide(693-719) and FAB 83-7


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.30 Å
  • R-Value Free: 0.335 
  • R-Value Work: 0.289 
  • R-Value Observed: 0.291 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

How insulin engages its primary binding site on the insulin receptor

Menting, J.G.Whittaker, J.Margetts, M.B.Whittaker, L.J.Kong, G.K.-W.Smith, B.J.Watson, C.J.Zakova, L.Kletvikova, E.Jiracek, J.Chan, S.J.Steiner, D.F.Dodson, G.G.Brzozowski, A.M.Weiss, M.A.Ward, C.W.Lawrence, M.C.

(2013) Nature 493: 241-245

  • DOI: 10.1038/nature11781
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Insulin receptor signalling has a central role in mammalian biology, regulating cellular metabolism, growth, division, differentiation and survival. Insulin resistance contributes to the pathogenesis of type 2 diabetes mellitus and the onset of Alzhe ...

    Insulin receptor signalling has a central role in mammalian biology, regulating cellular metabolism, growth, division, differentiation and survival. Insulin resistance contributes to the pathogenesis of type 2 diabetes mellitus and the onset of Alzheimer's disease; aberrant signalling occurs in diverse cancers, exacerbated by cross-talk with the homologous type 1 insulin-like growth factor receptor (IGF1R). Despite more than three decades of investigation, the three-dimensional structure of the insulin-insulin receptor complex has proved elusive, confounded by the complexity of producing the receptor protein. Here we present the first view, to our knowledge, of the interaction of insulin with its primary binding site on the insulin receptor, on the basis of four crystal structures of insulin bound to truncated insulin receptor constructs. The direct interaction of insulin with the first leucine-rich-repeat domain (L1) of insulin receptor is seen to be sparse, the hormone instead engaging the insulin receptor carboxy-terminal α-chain (αCT) segment, which is itself remodelled on the face of L1 upon insulin binding. Contact between insulin and L1 is restricted to insulin B-chain residues. The αCT segment displaces the B-chain C-terminal β-strand away from the hormone core, revealing the mechanism of a long-proposed conformational switch in insulin upon receptor engagement. This mode of hormone-receptor recognition is novel within the broader family of receptor tyrosine kinases. We support these findings by photo-crosslinking data that place the suggested interactions into the context of the holoreceptor and by isothermal titration calorimetry data that dissect the hormone-insulin receptor interface. Together, our findings provide an explanation for a wealth of biochemical data from the insulin receptor and IGF1R systems relevant to the design of therapeutic insulin analogues.


    Organizational Affiliation

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



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Insulin receptor domains L1-CR
E
310Homo sapiensMutation(s): 0 
Gene Names: INSR
EC: 2.7.10.1
Find proteins for P06213 (Homo sapiens)
Go to UniProtKB:  P06213
NIH Common Fund Data Resources
PHAROS  P06213
Protein Feature View
  • Reference Sequence

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
monoclonal antibody fab 83-7 fragment - heavy chain
C
116Mus musculusMutation(s): 0 
Protein Feature View
  • Reference Sequence

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
monoclonal antibody fab 83-7 fragment - light chain
D
114Mus musculusMutation(s): 0 
Protein Feature View
  • Reference Sequence

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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Insulin A chain
A
21Homo sapiensMutation(s): 0 
Gene Names: INS
Find proteins for P01308 (Homo sapiens)
Go to UniProtKB:  P01308
NIH Common Fund Data Resources
PHAROS  P01308
Protein Feature View
  • Reference Sequence

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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Insulin B chain
B
26Homo sapiensMutation(s): 0 
Gene Names: INS
Find proteins for P01308 (Homo sapiens)
Go to UniProtKB:  P01308
NIH Common Fund Data Resources
PHAROS  P01308
Protein Feature View
  • Reference Sequence

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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
Insulin receptor alphact peptide
F
23Homo sapiensMutation(s): 0 
Gene Names: INSR
EC: 2.7.10.1
Find proteins for P06213 (Homo sapiens)
Go to UniProtKB:  P06213
NIH Common Fund Data Resources
PHAROS  P06213
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download CCD File 
E
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
BMA
Query on BMA

Download CCD File 
E
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
MAN
Query on MAN

Download CCD File 
E
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
PR9
Query on PR9
BD-PEPTIDE LINKINGC5 H10 N2 OPRO
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.30 Å
  • R-Value Free: 0.335 
  • R-Value Work: 0.289 
  • R-Value Observed: 0.291 
  • Space Group: P 2 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 169.228α = 90
b = 169.228β = 90
c = 169.228γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
MOLREPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-01-09
    Type: Initial release
  • Version 1.1: 2013-01-16
    Changes: Database references
  • Version 1.2: 2013-09-04
    Changes: Database references