6KBI

Crystal structure of ErbB3 N418Q mutant

• PDB DOI: https://doi.org/10.2210/pdb6KBI/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Cricetulus griseus
• Mutation(s): Yes 


• Deposited: 2019-06-25 Released: 2020-07-01 
• Deposition Author(s): Kato, K., Yao, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 0.278 
• R-Value Work: 0.221 
• R-Value Observed: 0.224 

Starting Model: experimental

Literature

Crystal structure of ErbB3 N418Q mutant

Takahashi, M., Kato, K., Yao, M.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 140.33 kDa 
• Atom Count: 8,967 
• Modelled Residue Count: 1,138 
• Deposited Residue Count: 1,240 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Receptor tyrosine-protein kinase erbB-3	A, B	620	Homo sapiens	Mutation(s): 1  Gene Names: ERBB3, HER3 EC: 2.7.10.1
UniProt & NIH Common Fund Data Resources
Find proteins for P21860 (Homo sapiens) Explore P21860  Go to UniProtKB:  P21860
PHAROS:  P21860 GTEx:  ENSG00000065361
Glycosylation
Glycosylation Sites: 8		Go to GlyGen: P21860-1

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C, D	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth B], L [auth B], M [auth B], N [auth B], O [auth B], P [auth B], Q [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: 3.00 Å
• R-Value Free: 0.278 
• R-Value Work: 0.221 
• R-Value Observed: 0.224 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 236.105	α = 90
b = 49.458	β = 125.62
c = 190.919	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-07-01 
Deposition Author(s): Kato, K., Yao, M.

Revision History  

• Version 1.0: 2020-07-01
  Type: Initial release
  
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2023-11-22
  Changes: Data collection, Database references, Refinement description, Structure summary
• Version 2.2: 2024-10-30
  Changes: Structure summary