1S78

Insights into ErbB signaling from the structure of the ErbB2-pertuzumab complex

• PDB DOI: https://doi.org/10.2210/pdb1S78/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens, Mus musculus
• Expression System: Cricetulus griseus, Escherichia coli
• Mutation(s): No 


• Deposited: 2004-01-29 Released: 2004-04-27 
• Deposition Author(s): Franklin, M.C., Carey, K.D., Vajdos, F.F., Leahy, D.J., de Vos, A.M., Sliwkowski, M.X.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.25 Å
• R-Value Free: 0.268 
• R-Value Work: 0.224 
• R-Value Observed: 0.227 

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 PISA (software)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 235.73 kDa 
• Atom Count: 15,481 
• Modelled Residue Count: 1,995 
• Deposited Residue Count: 2,128 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Receptor protein-tyrosine kinase erbB-2	A, B	624	Homo sapiens	Mutation(s): 0  Gene Names: ERBB2, HER2, NGL, NEU EC: 2.7.1.112
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
Pertuzumab Fab light chain	C, E	214	Mus musculus	Mutation(s): 0
UniProt
Find proteins for Q7Z3Y4 (Homo sapiens) Explore Q7Z3Y4  Go to UniProtKB:  Q7Z3Y4

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Pertuzumab Fab heavy chain	D, F	226	Mus musculus	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	G, H, I, K	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Entity ID: 5
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	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	L [auth A], M [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.25 Å
• R-Value Free: 0.268 
• R-Value Work: 0.224 
• R-Value Observed: 0.227 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 139.412	α = 90
b = 139.412	β = 90
c = 356.873	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-04-27 
Deposition Author(s): Franklin, M.C., Carey, K.D., Vajdos, F.F., Leahy, D.J., de Vos, A.M., Sliwkowski, M.X.

Revision History  

• Version 1.0: 2004-04-27
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2023-08-23
  Changes: Data collection, Database references, Refinement description, Structure summary