3U7U

Crystal structure of extracellular region of human epidermal growth factor receptor 4 in complex with neuregulin-1 beta

• PDB DOI:  https://doi.org/10.2210/pdb3U7U/pdb

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


• Deposited: 2011-10-14 Released: 2012-08-29 
• Deposition Author(s): Liu, P., Cleveland IV, T.E., Bouyain, S., Longo, P.A., Leahy, D.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.03 Å
• R-Value Free: 0.227 
• R-Value Work: 0.190 
• R-Value Observed: 0.191 

Literature

A single ligand is sufficient to activate EGFR dimers.

Liu, P., Cleveland, T.E., Bouyain, S., Byrne, P.O., Longo, P.A., Leahy, D.J.

(2012) Proc Natl Acad Sci U S A 109: 10861-10866

• PubMed: 22699492 
• DOI: https://doi.org/10.1073/pnas.1201114109
• Primary Citation of Related Structures:  
  3U7U


• PubMed Abstract: 
  

Crystal structures of human epidermal growth factor receptor (EGFR) with bound ligand revealed symmetric, doubly ligated receptor dimers thought to represent physiologically active states. Such complexes fail to rationalize negative cooperativity of epidermal growth factor (EGF) binding to EGFR and the behavior of the ligandless EGFR homolog ErbB2/HER2, however. We report cell-based assays that provide evidence for active, singly ligated dimers of human EGFR and its homolog, ErbB4/HER4. We also report crystal structures of the ErbB4/HER4 extracellular region complexed with its ligand Neuregulin-1β that resolve two types of ErbB dimer when compared to EGFR:Ligand complexes. One type resembles the recently reported asymmetric dimer of Drosophila EGFR with a single high-affinity ligand bound and provides a model for singly ligated human ErbB dimers. These results unify models of vertebrate and invertebrate EGFR/ErbB signaling, imply that the tethered conformation of unliganded ErbBs evolved to prevent crosstalk among ErbBs, and establish a molecular basis for both negative cooperativity of ligand binding to vertebrate ErbBs and the absence of active ErbB2/HER2 homodimers in normal conditions.

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Organizational Affiliation: 

Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, 725 N. Wolfe Street, Baltimore, MD 21205, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 4 assigned by authors and generated by PISA (software)

Biological Assembly 5  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 5 assigned by authors and generated by PISA (software)

Biological Assembly 6  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 6 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 455.34 kDa 
• Atom Count: 30,527 
• Modelled Residue Count: 3,835 
• Deposited Residue Count: 4,020 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Receptor tyrosine-protein kinase erbB-4	A, B, C, D, E, F	615	Homo sapiens	Mutation(s): 0  Gene Names: ERBB4, HER4 EC: 2.7.10.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q15303 (Homo sapiens) Explore Q15303  Go to UniProtKB:  Q15303
PHAROS:  Q15303

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Neuregulin 1	G, H, I, J, K, L	55	Homo sapiens	Mutation(s): 0  Gene Names: NRG1, GGF, HGL, HRGA, NDF, SMDF
UniProt & NIH Common Fund Data Resources
Find proteins for Q02297 (Homo sapiens) Explore Q02297  Go to UniProtKB:  Q02297
PHAROS:  Q02297

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	AA [auth D], BA [auth D], CA [auth D], DA [auth E], EA [auth E], FA [auth E], GA [auth F], HA [auth F], IA [auth F], JA [auth F], KA [auth F], LA [auth F], M [auth A], N [auth A], O [auth A], P [auth A], Q [auth B], R [auth B], S [auth B], T [auth B], U [auth B], V [auth B], W [auth C], X [auth C], Y [auth D], Z [auth D]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.03 Å
• R-Value Free: 0.227 
• R-Value Work: 0.190 
• R-Value Observed: 0.191 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.73	α = 90
b = 223.51	β = 99.72
c = 146.92	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
BUSTER-TNT	refinement
PDB_EXTRACT	data extraction
JBluIce-EPICS	data collection
BUSTER	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-08-29 
Deposition Author(s): Liu, P., Cleveland IV, T.E., Bouyain, S., Longo, P.A., Leahy, D.J.

Revision History  

• Version 1.0: 2012-08-29
  Type: Initial release
  
• Version 1.1: 2017-11-08
  Changes: Refinement description
• Version 1.2: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Database references, Derived calculations, Structure summary
• Version 1.3: 2023-09-13
  Changes: Data collection, Database references, Refinement description, Structure summary