Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 226.24 kDa 
• Atom Count: 6469 
• Modelled Residue Count: 800 
• Deposited Residue Count: 1971 
• Unique protein chains: 2

6VWI

Head region of the closed conformation of the human type 1 insulin-like growth factor receptor ectodomain in complex with human insulin-like growth factor II.

• PDB DOI: 10.2210/pdb6VWI/pdb
• EM Map EMD-21417: EMDB EMDataResource

• Classification: SIGNALING PROTEIN
• Organism(s): Homo sapiens, Saccharomyces cerevisiae S288C
• Expression System: Cricetulus griseus, Escherichia coli
• Mutation(s): No 


• Deposited: 2020-02-19 Released: 2020-05-13 
• Deposition Author(s): Xu, Y., Kirk, N.S., Lawrence, M.C., Croll, T.I.
• Funding Organization(s): National Health and Medical Research Council (NHMRC, Australia), Wellcome Trust

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.70 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

How IGF-II Binds to the Human Type 1 Insulin-like Growth Factor Receptor.

Xu, Y., Kirk, N.S., Venugopal, H., Margetts, M.B., Croll, T.I., Sandow, J.J., Webb, A.I., Delaine, C.A., Forbes, B.E., Lawrence, M.C.

(2020) Structure 28: 786-798.e6

• PubMed: 32459985 
• DOI: 10.1016/j.str.2020.05.002
• Primary Citation of Related Structures:  
  6VWG, 6VWH, 6VWI, 6VWJ


• PubMed Abstract: 
  

Human type 1 insulin-like growth factor receptor (IGF-1R) signals chiefly in response to the binding of insulin-like growth factor I. Relatively little is known about the role of insulin-like growth factor II signaling via IGF-1R, despite the affinity of insulin-like growth factor II for IGF-1R being within an order of magnitude of that of insulin-like growth factor I. Here, we describe the cryoelectron microscopy structure of insulin-like growth factor II bound to a leucine-zipper-stabilized IGF-1R ectodomain, determined in two conformations to a maximum average resolution of 3.2 Å. The two conformations differ in the relative separation of their respective points of membrane entry, and comparison with the structure of insulin-like growth factor I bound to IGF-1R reveals long-suspected differences in the way in which the critical C domain of the respective growth factors interact with IGF-1R.

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Organizational Affiliation: 

Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, VIC 3050, Australia. Electronic address: [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Leucine-zippered human type 1 insulin-like growth factor receptor ectodomain	A, B	952	Homo sapiens, Saccharomyces cerevisiae S288C This entity is chimeric	Mutation(s): 0  Gene Names: IGF1R, GCN4, AAS3, ARG9, YEL009C EC: 2.7.10.1
UniProt & NIH Common Fund Data Resources
Find proteins for P03069 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P03069  Go to UniProtKB:  P03069
Find proteins for P08069 (Homo sapiens) Explore P08069  Go to UniProtKB:  P08069
PHAROS:  P08069
UniProt Groups	P03069P08069

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Insulin-like growth factor II	C [auth I]	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

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.70 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2020-02-19 
• Released Date: 2020-05-13 
Deposition Author(s): Xu, Y., Kirk, N.S., Lawrence, M.C., Croll, T.I.

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Funding Organization	Location	Grant Number
National Health and Medical Research Council (NHMRC, Australia)	Australia	APP1128553
Wellcome Trust	United Kingdom	209407/Z/17/

Revision History  

• Version 1.0: 2020-05-13
  Type: Initial release
  
• Version 1.1: 2020-05-20
  Changes: Structure summary
• Version 1.2: 2020-07-15
  Changes: Database references
• Version 1.3: 2020-07-22
  Changes: Database references
• Version 1.4: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary