8VQD

HER2 S310F in complex with TL1 Fab

• PDB DOI: https://doi.org/10.2210/pdb8VQD/pdb
• EM Map EMD-43439: EMDB EMDataResource

• Classification: SIGNALING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Homo sapiens, Escherichia coli
• Mutation(s): Yes 


• Deposited: 2024-01-18 Released: 2024-10-09 
• Deposition Author(s): Bang, I., Koide, S.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.61 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Models: experimental, in silico

Literature

Selective targeting of oncogenic hotspot mutations of the HER2 extracellular domain

Bang, I., Hattori, T., Leloup, N., Corrado, A., Koide, A., Geles, K., Buck, E., Koide, S.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

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

Biological Assembly Evidence: electron microscopy

Macromolecule Content

• Total Structure Weight: 150.54 kDa 
• Atom Count: 5,686 
• Modelled Residue Count: 736 
• Deposited Residue Count: 1,366 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Receptor tyrosine-protein kinase erbB-2/hIgG1 Fc domain fusion	A	894	Homo sapiens	Mutation(s): 1  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: 1		Go to GlyGen: P04626-1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Variable Heavy chain of TL1 Fab	B [auth C]	257	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Variable Light chain of TL1 Fab	C [auth B]	215	Homo sapiens	Mutation(s): 0

Oligosaccharides

Help

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	D	2		N-Glycosylation

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.61 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.20.1_4487
MODEL REFINEMENT	Coot	0.9.8.1
RECONSTRUCTION	cryoSPARC	4.2.1

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-10-09 
Deposition Author(s): Bang, I., Koide, S.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2024-10-09
  Type: Initial release