Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 118.20 kDa 
• Atom Count: 7472 
• Residue Count: 960 
• Unique protein chains: 3

5O4G

HER2 in complex with Fab MF3958

• DOI: 10.2210/pdb5O4G/pdb

• Classification: ONCOPROTEIN
• Organism(s): Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2017-05-29 Released: 2018-05-16 
• Deposition Author(s): De Nardis, C., Gros, P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 0.271 
• R-Value Work: 0.229 
• R-Value Observed: 0.231 

Literature

Unbiased Combinatorial Screening Identifies a Bispecific IgG1 that Potently Inhibits HER3 Signaling via HER2-Guided Ligand Blockade.

Geuijen, C.A.W., De Nardis, C., Maussang, D., Rovers, E., Gallenne, T., Hendriks, L.J.A., Visser, T., Nijhuis, R., Logtenberg, T., de Kruif, J., Gros, P., Throsby, M.

(2018) Cancer Cell 33: 922-936.e10

• PubMed: 29763625 
• DOI: 10.1016/j.ccell.2018.04.003
• Primary Citation of Related Structures:  
  5O4O, 5O4G, 5O7P


• PubMed Abstract: 
  

HER2-driven cancers require phosphatidylinositide-3 kinase (PI3K)/Akt signaling through HER3 to promote tumor growth and survival. The therapeutic benefit of HER2-targeting agents, which depend on PI3K/Akt inhibition, can be overcome by hyperactivation of the heregulin (HRG)/HER3 pathway. Here we describe an unbiased phenotypic combinatorial screening approach to identify a bispecific immunoglobulin G1 (IgG1) antibody against HER2 and HER3. In tumor models resistant to HER2-targeting agents, the bispecific IgG1 potently inhibits the HRG/HER3 pathway and downstream PI3K/Akt signaling via a "dock & block" mechanism. This bispecific IgG1 is a potentially effective therapy for breast cancer and other tumors with hyperactivated HRG/HER3 signaling.

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Organizational Affiliation: 

Merus NV, 3584 Utrecht, the Netherlands. Electronic address: [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Receptor tyrosine-protein kinase erbB-2	C	606	Homo sapiens	Mutation(s): 0  Gene Names: ERBB2, HER2, MLN19, NEU, NGL EC: 2.7.10.1
Find proteins for P04626 (Homo sapiens) Explore P04626  Go to UniProtKB:  P04626
NIH Common Fund Data Resources
PHAROS  P04626 GTEx  ENSG00000141736

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
MF3958 FAB light chain	A	214	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
MF3958 FAB heavy chain	B	247	Homo sapiens	Mutation(s): 0

Oligosaccharides

Help

Entity ID: 4
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	D	6		N-Glycosylation

Entity ID: 5
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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	C	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 0.271 
• R-Value Work: 0.229 
• R-Value Observed: 0.231 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.79	α = 90
b = 113.5	β = 101.92
c = 113.49	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
iMOSFLM	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2017-05-29 
• Released Date: 2018-05-16 
Deposition Author(s): De Nardis, C., Gros, P.

Revision History 

• Version 1.0: 2018-05-16
  Type: Initial release
  
• Version 1.1: 2018-05-23
  Changes: Data collection, Database references
• Version 1.2: 2019-02-20
  Changes: Advisory, Data collection, Derived calculations
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary