5O4G | pdb_00005o4g

HER2 in complex with Fab MF3958

• PDB DOI: https://doi.org/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 (Depositor), 0.274 (DCC) 
• R-Value Work: 
  0.229 (Depositor), 0.234 (DCC) 
• R-Value Observed: 
  0.231 (Depositor) 

Starting Models: experimental

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: https://doi.org/10.1016/j.ccell.2018.04.003
• Primary Citation Related Structures: 
  5O4G, 5O4O, 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.
Crystal and Structural Chemistry, Bijvoet Center for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, 3584 Utrecht, the Netherlands.
Merus NV, 3584 Utrecht, the Netherlands. Electronic address: [e-mail].

Biological Assembly 1  

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: 118.2 kDa 
• Atom Count: 7,472 
• Modeled Residue Count: 960 
• Deposited Residue Count: 1,067 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Receptor tyrosine-protein kinase erbB-2	A [auth C]	606	Homo sapiens	Mutation(s): 0  Gene Names: ERBB2, HER2, MLN19, NEU, NGL EC: 2.7.10.1
UniProt & NIH Common Fund Data Resources
Find proteins for P04626 (Homo sapiens) Explore P04626  Go to UniProtKB:  P04626
PHAROS:  P04626 GTEx:  ENSG00000141736
Glycosylation
Glycosylation Sites: 3		Go to GlyGen: P04626-1

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

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

Oligosaccharides

Help  

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
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
Glycosylation Resources
GlyTouCan: G09724ZC GlyCosmos: G09724ZC GlyGen: G09724ZC

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
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 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 (Depositor), 0.274 (DCC) 
• R-Value Work:  0.229 (Depositor), 0.234 (DCC) 
• R-Value Observed: 0.231 (Depositor) 

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

• 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
• Version 2.1: 2024-01-17
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary
• Version 2.2: 2024-10-16
  Changes: Structure summary