Biological Assembly 1  

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

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Hetero 4-mer - A2B2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 152.21 kDa 
• Atom Count: 8892 
• Modelled Residue Count: 1115 
• Deposited Residue Count: 1350 
• Unique protein chains: 2

1IVO

Crystal Structure of the Complex of Human Epidermal Growth Factor and Receptor Extracellular Domains.

• PDB DOI: 10.2210/pdb1IVO/pdb

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


• Deposited: 2002-03-28 Released: 2002-10-16 
• Deposition Author(s): Ogiso, H., Ishitani, R., Nureki, O., Fukai, S., Yamanaka, M., Kim, J.H., Saito, K., Shirouzu, M., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.30 Å
• R-Value Free: 0.326 
• R-Value Work: 0.255 
• R-Value Observed: 0.258 

Literature

Crystal Structure of the Complex of Human Epidermal Growth Factor and Receptor Extracellular Domains.

Ogiso, H., Ishitani, R., Nureki, O., Fukai, S., Yamanaka, M., Kim, J.H., Saito, K., Inoue, M., Shirouzu, M., Yokoyama, S.

(2002) Cell 110: 775-787

• PubMed: 12297050 
• DOI: 10.1016/s0092-8674(02)00963-7
• Primary Citation of Related Structures:  
  1IVO


• PubMed Abstract: 
  

Epidermal growth factor (EGF) regulates cell proliferation and differentiation by binding to the EGF receptor (EGFR) extracellular region, comprising domains I-IV, with the resultant dimerization of the receptor tyrosine kinase. In this study, the crystal structure of a 2:2 complex of human EGF and the EGFR extracellular region has been determined at 3.3 A resolution. EGFR domains I-III are arranged in a C shape, and EGF is docked between domains I and III. The 1:1 EGF*EGFR complex dimerizes through a direct receptor*receptor interaction, in which a protruding beta-hairpin arm of each domain II holds the body of the other. The unique "receptor-mediated dimerization" was verified by EGFR mutagenesis.

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Organizational Affiliation: 

RIKEN Genomic Sciences Center, 1-7-22 Suehiro-cho, Tsurumi, 230-0045, Yokohama, Kanagawa, Japan.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Epidermal Growth Factor Receptor	A, B	622	Homo sapiens	Mutation(s): 0  Gene Names: EGFR, ERBB, ERBB1, HER1 EC: 2.7.1.112 (PDB Primary Data), 2.7.10.1 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P00533 (Homo sapiens) Explore P00533  Go to UniProtKB:  P00533
PHAROS:  P00533

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Epidermal growth factor	C, D	53	Homo sapiens	Mutation(s): 0  Gene Names: EGF
UniProt & NIH Common Fund Data Resources
Find proteins for P01133 (Homo sapiens) Explore P01133  Go to UniProtKB:  P01133
PHAROS:  P01133

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth B], L [auth B], M [auth B]	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: 0.326 
• R-Value Work: 0.255 
• R-Value Observed: 0.258 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 220.164	α = 90
b = 220.164	β = 90
c = 113.121	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MLPHARE	phasing
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2002-03-28 
• Released Date: 2002-10-16 
Deposition Author(s): Ogiso, H., Ishitani, R., Nureki, O., Fukai, S., Yamanaka, M., Kim, J.H., Saito, K., Shirouzu, M., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History  

• Version 1.0: 2002-10-16
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary