4ZXB

Structure of the human insulin receptor ectodomain, IRDeltabeta construct, in complex with four Fab molecules


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.207 

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This is version 2.0 of the entry. See complete history

Re-refinement Note

This entry reflects an alternative modeling of the original data in: 2DTG 3LOH


Literature

Higher-Resolution Structure of the Human Insulin Receptor Ectodomain: Multi-Modal Inclusion of the Insert Domain.

Croll, T.I.Smith, B.J.Margetts, M.B.Whittaker, J.Weiss, M.A.Ward, C.W.Lawrence, M.C.

(2016) Structure 24: 469-476

  • DOI: https://doi.org/10.1016/j.str.2015.12.014
  • Primary Citation of Related Structures:  
    4ZXB

  • PubMed Abstract: 

    Insulin receptor (IR) signaling is critical to controlling nutrient uptake and metabolism. However, only a low-resolution (3.8 Å) structure currently exists for the IR ectodomain, with some segments ill-defined or unmodeled due to disorder. Here, we revise this structure using new diffraction data to 3.3 Å resolution that allow improved modeling of the N-linked glycans, the first and third fibronectin type III domains, and the insert domain. A novel haptic interactive molecular dynamics strategy was used to aid fitting to low-resolution electron density maps. The resulting model provides a foundation for investigation of structural transitions in IR upon ligand binding.


  • Organizational Affiliation

    Institute of Health and Biomedical Innovation, Queensland University of Technology, QLD 4059, Australia.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Fab 83-7 heavy chain219Mus musculusMutation(s): 0 
UniProt
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UniProt GroupU5LP42
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Fab 83-7 light chain219Mus musculusMutation(s): 0 
UniProt
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UniProt GroupP01837
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Fab 83-14 heavy chain220Mus musculusMutation(s): 0 
UniProt
Find proteins for P01865 (Mus musculus)
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Fab 83-14 light chain214Mus musculusMutation(s): 0 
UniProt
Find proteins for A2P1G9 (Mus musculus)
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UniProt GroupA2P1G9
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Insulin receptor894Homo sapiensMutation(s): 5 
UniProt & NIH Common Fund Data Resources
Find proteins for P06213 (Homo sapiens)
Explore P06213 
Go to UniProtKB:  P06213
PHAROS:  P06213
GTEx:  ENSG00000171105 
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Oligosaccharides

Help

Entity ID: 6
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose
F, H, K
3N-Glycosylation
Glycosylation Resources
GlyTouCan:  G21290RB
GlyCosmos:  G21290RB
GlyGen:  G21290RB
Entity ID: 7
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
G
3N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE
GlyCosmos:  G15407YE
GlyGen:  G15407YE
Entity ID: 8
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose
I
6N-Glycosylation
Glycosylation Resources
GlyTouCan:  G39203UC
GlyCosmos:  G39203UC
GlyGen:  G39203UC
Entity ID: 9
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose
J, L
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G86851RC
GlyCosmos:  G86851RC
GlyGen:  G86851RC
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.207 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 121.87α = 90
b = 321.25β = 90
c = 199.4γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
XSCALEdata scaling
BUSTERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Health and Medical Research Council (NHMRC, Australia)Australia1005896
National Health and Medical Research Council (NHMRC, Australia)Australia1058233
Hazel and Pip Appel FundAustralia--
National Health and Medical Research Council (NHMRC, Australia)Australia361646
Victorian State Government Operational Infrastructure Support GrantAustralia--

Revision History  (Full details and data files)

  • Version 1.0: 2016-02-24
    Type: Initial release
  • Version 1.1: 2016-03-09
    Changes: Database references
  • Version 1.2: 2017-09-06
    Changes: Author supporting evidence, Data collection, Database references, Derived calculations
  • Version 1.3: 2020-01-08
    Changes: Author supporting evidence, Data collection
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary