7QVK | pdb_00007qvk

NM-02 in complex with HER2-ECD

• PDB DOI: https://doi.org/10.2210/pdb7QVK/pdb

• Classification: ONCOPROTEIN
• Organism(s): Homo sapiens, Camelus bactrianus
• Expression System: Homo sapiens, Cricetulus griseus
• Mutation(s): No 


• Deposited: 2022-01-21 Released: 2023-02-01 
• Deposition Author(s): Cowan, R., Hall, G., Carr, M.
• Funding Organization(s): Other private

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free: 
  0.330 (Depositor), 0.338 (DCC) 
• R-Value Work: 
  0.275 (Depositor), 0.282 (DCC) 
• R-Value Observed: 
  0.275 (Depositor) 

Starting Model: experimental

Literature

Co-crystallisation and humanisation of an anti-HER2 single-domain antibody as a theranostic tool.

Sawmynaden, K., Wong, N., Davies, S., Cowan, R., Brown, R., Tang, D., Henry, M., Tickle, D., Matthews, D., Carr, M., Bakrania, P., Hoi Ting, H., Hall, G.

(2023) PLoS One 18: e0288259-e0288259

• PubMed: 37459326 
• DOI: https://doi.org/10.1371/journal.pone.0288259
• Primary Citation Related Structures: 
  7QVK


• PubMed Abstract: 
  

  Human epidermal growth factor receptor-2 (HER2) is a well-recognised biomarker associated with 25% of breast cancers. In most cases, early detection and/or treatment correlates with an increased chance of survival. This study, has identified and characterised a highly specific anti-HER2 single-domain antibody (sdAb), NM-02, as a potential theranostic tool. Complete structural description by X-ray crystallography has revealed a non-overlapping epitope with current anti-HER2 antibodies. To reduce the immunogenicity risk, NM-02 underwent a humanisation process and retained wild type-like binding properties. To further de-risk the progression towards chemistry, manufacturing and control (CMC) we performed full developability profiling revealing favourable thermal and physical biochemical 'drug-like' properties. Finally, the application of the lead humanised NM-02 candidate (variant K) for HER2-specific imaging purposes was demonstrated using breast cancer HER2+/BT474 xenograft mice.

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Organizational Affiliation: 
• LifeArc, Open Innovation Campus, Stevenage, United Kingdom.
NanoMab, Shanghai, China.
Department of Molecular and Cell Biology, Leicester Institute of Structural and Chemical Biology, University of Leicester, Leicester, United Kingdom.

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 Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 84.77 kDa 
• Atom Count: 4,836 
• Modeled Residue Count: 627 
• Deposited Residue Count: 762 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Receptor tyrosine-protein kinase erbB-2	A [auth AAA]	630	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: 2		Go to GlyGen: P04626-1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
NM-02	B [auth BBB]	132	Camelus bactrianus	Mutation(s): 0

Oligosaccharides

Help  

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

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free:  0.330 (Depositor), 0.338 (DCC) 
• R-Value Work:  0.275 (Depositor), 0.282 (DCC) 
• R-Value Observed: 0.275 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 105.767	α = 90
b = 105.767	β = 90
c = 185.882	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-02-01 
Deposition Author(s): Cowan, R., Hall, G., Carr, M.

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Funding Organization	Location	Grant Number
Other private		--

Revision History  

• Version 1.0: 2023-02-01
  Type: Initial release
  
• Version 1.1: 2023-07-26
  Changes: Database references, Derived calculations
• Version 1.2: 2024-02-07
  Changes: Data collection, Refinement description
• Version 1.3: 2024-11-06
  Changes: Structure summary