8Q6J

Atomic structure and conformational variability of the HER2-Trastuzumab-Pertuzumab complex

• PDB DOI: https://doi.org/10.2210/pdb8Q6J/pdb
• EM Map EMD-18188: EMDB EMDataResource

• Classification: STRUCTURAL PROTEIN
• Organism(s): Homo sapiens
• Expression System: Cricetulus griseus, Homo sapiens
• Mutation(s): No 


• Deposited: 2023-08-11 Released: 2023-09-20 
• Deposition Author(s): Ruedas, R., Vuillemot, R., Tubiana, T., Winter, J.M., Pieri, L., Arteni, A.A., Samson, C., Jonic, J., Mathieu, M., Bressanelli, S.
• Funding Organization(s): Centre National de la Recherche Scientifique (CNRS), Other private

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.30 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Atomic structure and conformational variability of the HER2-Trastuzumab-Pertuzumab complex

Ruedas, R., Vuillemot, R., Tubiana, T., Winter, J.M., Pieri, L., Arteni, A.A., Samson, C., Jonic, J., Mathieu, M., Bressanelli, S.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 5-mer - A2B2C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 5-mer - A4B1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content

• Total Structure Weight: 164.74 kDa 
• Atom Count: 11,535 
• Modelled Residue Count: 1,494 
• Deposited Residue Count: 1,494 
• Unique protein chains: 5

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Trastuzumab fab light chain	A	214	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Trastuzumab Fab heavy chain	B	220	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Pertuzumab Fab light chain	C	214	Homo sapiens	Mutation(s): 0

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Pertuzumab Fab heavy chain	D	222	Homo sapiens	Mutation(s): 0

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Receptor tyrosine-protein kinase erbB-2	E	624	Homo sapiens	Mutation(s): 0  Gene Names: ERBB2
UniProt & NIH Common Fund Data Resources
Find proteins for P04626 (Homo sapiens) Explore P04626  Go to UniProtKB:  P04626
PHAROS:  P04626 GTEx:  ENSG00000141736

Oligosaccharides

Help

Entity ID: 6
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	F [auth G], G [auth J]	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	H [auth E], I [auth E], J [auth E]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.30 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.20.1
MODEL REFINEMENT	Coot	0.8.9.2
RECONSTRUCTION	cryoSPARC	4.1.2

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-09-20 
Deposition Author(s): Ruedas, R., Vuillemot, R., Tubiana, T., Winter, J.M., Pieri, L., Arteni, A.A., Samson, C., Jonic, J., Mathieu, M., Bressanelli, S.

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Funding Organization	Location	Grant Number
Centre National de la Recherche Scientifique (CNRS)	France	--
Other private		--

Revision History  

• Version 1.0: 2023-09-20
  Type: Initial release