Biological Assembly 1  

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

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

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

Macromolecule Content

• Total Structure Weight: 82.04 kDa 
• Atom Count: 5581 
• Modelled Residue Count: 671 
• Deposited Residue Count: 737 
• Unique protein chains: 2

5MY6

Crystal structure of a HER2-Nb complex

• PDB DOI: 10.2210/pdb5MY6/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens, Camelus dromedarius
• Expression System: Homo sapiens, Escherichia coli
• Mutation(s): No 


• Deposited: 2017-01-25 Released: 2017-08-09 
• Deposition Author(s): Sterckx, Y.G.-J., D'Huyvetter, M., Devoogdt, N.
• Funding Organization(s): FWO-Vlaanderen, Innoviris.Brussels, Stichting Tegen Kanker, BAEF, Germaine Eisendrath-Dubois Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 0.220 
• R-Value Work: 0.185 
• R-Value Observed: 0.187 

Literature

(131)I-labeled Anti-HER2 Camelid sdAb as a Theranostic Tool in Cancer Treatment.

D'Huyvetter, M., De Vos, J., Xavier, C., Pruszynski, M., Sterckx, Y.G.J., Massa, S., Raes, G., Caveliers, V., Zalutsky, M.R., Lahoutte, T., Devoogdt, N.

(2017) Clin Cancer Res 23: 6616-6628

• PubMed: 28751451 
• DOI: 10.1158/1078-0432.CCR-17-0310
• Primary Citation of Related Structures:  
  5MY6


• PubMed Abstract: 
  

Purpose: Camelid single-domain antibody-fragments (sdAb) have beneficial pharmacokinetic properties, and those targeted to HER2 can be used for imaging of HER2-overexpressing cancer. Labeled with a therapeutic radionuclide, they may be used for HER2-targeted therapy. Here, we describe the generation of a ¹³¹ I-labeled sdAb as a theranostic drug to treat HER2-overexpressing cancer. Experimental Design: Anti-HER2 sdAb 2Rs15d was labeled with ¹³¹ I using [ ¹³¹ I]SGMIB and evaluated in vitro Biodistribution was evaluated in two HER2 ⁺ murine xenograft models by micro-SPECT/CT imaging and at necropsy, and under challenge with trastuzumab and pertuzumab. The therapeutic potential of [ ¹³¹ I]SGMIB-2Rs15d was investigated in two HER2 ⁺ tumor mouse models. A single-dose toxicity study was performed in mice using unlabeled [ ¹²⁷ I]SGMIB-sdAb at 1.4 mg/kg. The structure of the 2Rs15d-HER2 complex was determined by X-ray crystallography. Results: [ ¹³¹ I]SGMIB-2Rs15d bound specifically to HER2 ⁺ cells ( K _d = 4.74 ± 0.39 nmol/L). High and specific tumor uptake was observed in both BT474/M1 and SKOV-3 tumor xenografted mice and surpassed kidney levels by 3 hours. Extremely low uptake values were observed in other normal tissues at all time points. The crystal structure revealed that 2Rs15d recognizes HER2 Domain 1, consistent with the lack of competition with trastuzumab and pertuzumab observed in vivo [ ¹³¹ I]SGMIB-2Rs15d alone, or in combination with trastuzumab, extended median survival significantly. No toxicity was observed after injecting [ ¹²⁷ I]SGMIB-2Rs15d. Conclusions: These findings demonstrate the theranostic potential of [ ¹³¹ I]SGMIB-2Rs15d. An initial scan using low radioactive [*I]SGMIB-2Rs15d allows patient selection and dosimetry calculations for subsequent therapeutic [ ¹³¹ I]SGMIB-2Rs15d and could thereby impact therapy outcome on HER2 ⁺ breast cancer patients. Clin Cancer Res; 23(21); 6616-28. ©2017 AACR .

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Organizational Affiliation: 

In Vivo Cellular and Molecular Imaging Laboratory, Vrije Universiteit Brussel, Brussels, Belgium.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Receptor tyrosine-protein kinase erbB-2	A	622	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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Nanobody 2Rs15d	B	115	Camelus dromedarius	Mutation(s): 0

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	C	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	D [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
GOL	E [auth A], F [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 0.220 
• R-Value Work: 0.185 
• R-Value Observed: 0.187 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.52	α = 90
b = 113.52	β = 90
c = 137.43	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data scaling
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2017-01-25 
• Released Date: 2017-08-09 
Deposition Author(s): Sterckx, Y.G.-J., D'Huyvetter, M., Devoogdt, N.

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Funding Organization	Location	Grant Number
FWO-Vlaanderen	Belgium	--
Innoviris.Brussels	Belgium	--
Stichting Tegen Kanker	Belgium	--
BAEF	Belgium	--
Germaine Eisendrath-Dubois Foundation	Belgium	--

Revision History  

• Version 1.0: 2017-08-09
  Type: Initial release
  
• Version 1.1: 2017-10-11
  Changes: Database references
• Version 1.2: 2017-11-15
  Changes: Database references
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary