9MTX | pdb_00009mtx

CryoEM structure of extracellular domain of human HER2 complexed with nano-bodies 29E09

PDB DOI: https://doi.org/10.2210/pdb9MTX/pdb
EM Map EMD-48615: EMDB EMDataResource

Classification: TRANSFERASE
Organism(s): Lama glama, Homo sapiens
Expression System: Escherichia coli, Homo sapiens
Mutation(s): No

Deposited: 2025-01-12 Released: 2025-11-19
Deposition Author(s): Bruch, E.M., Rak, A.
Funding Organization(s): Other private

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.06 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

TPP-45142, an Anti-HER2 T-cell Engager Designed for Selective HER2-Low Cancer Immune TherapyImmunotherapy

De Tavernier, E., Kim, P., Bruch, E.M., Crotez-Retamozo, V., Rak, A., Vintem, A.P.B.

To be published.

Macromolecule Content

Total Structure Weight: 82.77 kDa
Atom Count: 3,762
Modeled Residue Count: 510
Deposited Residue Count: 752
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nanobody VHH 29E09	A	122	Lama glama	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
receptor protein-tyrosine kinase	B	630	Homo sapiens	Mutation(s): 0 Gene Names: HER-2, ERBB2, hCG_28177 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 Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P04626
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.06 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.20.1_4487

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2025-11-19

Deposition Author(s):

Funding Organization	Location	Grant Number
Other private	United States	--

Revision History (Full details and data files)

Version 1.0: 2025-11-19
Type: Initial release

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.