4ZXB

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

• PDB DOI: https://doi.org/10.2210/pdb4ZXB/pdb
• Entry: 4ZXB supersedes: 2DTG, 3LOH

• Classification: HORMONE RECEPTOR/IMMUNE SYSTEM
• Organism(s): Mus musculus, Homo sapiens
• Expression System: Mus musculus, Cricetulus griseus
• Mutation(s): Yes 


• Deposited: 2015-05-20 Released: 2016-02-24 
• Deposition Author(s): Croll, T., Smith, B.J., Margetts, M.B., Whittaker, J., Weiss, M.A., Ward, C.W., Lawrence, M.C.
• Funding Organization(s): National Health and Medical Research Council (NHMRC, Australia), Hazel and Pip Appel Fund, Victorian State Government Operational Infrastructure Support Grant

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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 

Re-refinement Note

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

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 10-mer - A2B2C2D2E2 Pseudo Symmetry: Cyclic - C2  (Explore in 3D)
Pseudo Stoichiometry: Hetero 10-mer - A4B4C2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 202.01 kDa 
• Atom Count: 12,918 
• Modelled Residue Count: 1,601 
• Deposited Residue Count: 1,766 
• Unique protein chains: 5

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab 83-7 heavy chain	A	219	Mus musculus	Mutation(s): 0
UniProt
Find proteins for U5LP42 (Mus musculus) Explore U5LP42  Go to UniProtKB:  U5LP42

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab 83-7 light chain	B	219	Mus musculus	Mutation(s): 0
UniProt
Find proteins for P01837 (Mus musculus) Explore P01837  Go to UniProtKB:  P01837

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab 83-14 heavy chain	C	220	Mus musculus	Mutation(s): 0
UniProt
Find proteins for P01865 (Mus musculus) Explore P01865  Go to UniProtKB:  P01865

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab 83-14 light chain	D	214	Mus musculus	Mutation(s): 0
UniProt
Find proteins for A2P1G9 (Mus musculus) Explore A2P1G9  Go to UniProtKB:  A2P1G9

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Insulin receptor	E	894	Homo sapiens	Mutation(s): 5
UniProt & NIH Common Fund Data Resources
Find proteins for P06213 (Homo sapiens) Explore P06213  Go to UniProtKB:  P06213
PHAROS:  P06213 GTEx:  ENSG00000171105

Oligosaccharides

Help

Entity ID: 6
Molecule	Chains	Length	2D Diagram	Glycosylation	3D 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	3		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G21290RB GlyCosmos:  G21290RB GlyGen:  G21290RB

Entity ID: 7
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	G	3		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE GlyCosmos:  G15407YE GlyGen:  G15407YE

Entity ID: 8
Molecule	Chains	Length	2D Diagram	Glycosylation	3D 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	6		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G39203UC GlyCosmos:  G39203UC GlyGen:  G39203UC

Entity ID: 9
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose	J, L	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G86851RC GlyCosmos:  G86851RC GlyGen:  G86851RC

Small Molecules

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

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 = 121.87	α = 90
b = 321.25	β = 90
c = 199.4	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
XSCALE	data scaling
BUSTER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2016-02-24 
Deposition Author(s): Croll, T., Smith, B.J., Margetts, M.B., Whittaker, J., Weiss, M.A., Ward, C.W., Lawrence, M.C.
• This entry supersedes: 2DTG, 3LOH

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Funding Organization	Location	Grant Number
National Health and Medical Research Council (NHMRC, Australia)	Australia	1005896
National Health and Medical Research Council (NHMRC, Australia)	Australia	1058233
Hazel and Pip Appel Fund	Australia	--
National Health and Medical Research Council (NHMRC, Australia)	Australia	361646
Victorian State Government Operational Infrastructure Support Grant	Australia	--

Revision History  

• 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