3N85 | pdb_00003n85

Crystallographic trimer of HER2 extracellular regions in complex with tryptophan-rich antibody fragment

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 
    0.230 (Depositor), 0.229 (DCC) 
  • R-Value Work: 
    0.206 (Depositor), 0.205 (DCC) 
  • R-Value Observed: 
    0.207 (Depositor) 

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 3N85

This is version 2.2 of the entry. See complete history. 

Literature

Structure of the complex between HER2 and an antibody paratope formed by side chains from tryptophan and serine.

Fisher, R.D., Ultsch, M., Lingel, A., Schaefer, G., Shao, L., Birtalan, S., Sidhu, S.S., Eigenbrot, C.

(2010) J Mol Biology 402: 217-229

  • DOI: https://doi.org/10.1016/j.jmb.2010.07.027
  • Primary Citation Related Structures: 
    3N85

  • PubMed Abstract: 

    Engineered antibody paratopes with limited sequence diversity permit assessment of the roles played by different amino acid side chains in creating the high-affinity, high-specificity interactions characteristic of antibodies. We describe a paratope raised against the human ErbB family member HER2, using a binary diversity tryptophan/serine library displayed on phage. Fab37 binds to the extracellular domain of HER2 with sub-nanomolar affinity. An X-ray structure at 3.2 A resolution reveals a contact paratope composed almost entirely of tryptophan and serine residues. Mutagenesis experiments reveal which of these side chains are more important for direct antigen interactions and which are more important for conformational flexibility. The crystal lattice contains an unprecedented trimeric arrangement of HER2 closely related to previously observed homodimers of the related epidermal growth factor receptor.

    • Organizational Affiliation: 
    • Department of Protein Engineering, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA.

Macromolecule Content 

  • Total Structure Weight: 119.43 kDa 
  • Atom Count: 8,114 
  • Modeled Residue Count: 1,033 
  • Deposited Residue Count: 1,065 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:
|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Receptor tyrosine-protein kinase erbB-2624Homo sapiensMutation(s): 0 
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 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04626
Glycosylation
Glycosylation Sites: 2
Go to GlyGen: P04626-1
Sequence Annotations
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Reference Sequence
Find similar proteins by:
|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Fab37 Light ChainB [auth L]217Homo sapiensMutation(s): 0 
Find similar proteins by:
|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Fab37 Heavy ChainC [auth H]224Homo sapiensMutation(s): 0 

Oligosaccharides

Help  
Entity ID: 4
MoleculeChains Length2D Diagram GlycosylationD Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranoseD [auth B]4N-Glycosylation
Glycosylation Resources
GlyTouCan: G32152BH
GlyCosmos: G32152BH
GlyGen: G32152BH
Entity ID: 5
MoleculeChains Length2D Diagram GlycosylationD Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseE [auth C]3N-Glycosylation
Glycosylation Resources
GlyTouCan: G15407YE
GlyCosmos: G15407YE
GlyGen: G15407YE

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4

Query on SO4


Download:Ideal Coordinates CCD File
G [auth A]
H [auth A]
I [auth A]
J [auth A]
K [auth A]
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
O [auth A],
P [auth A],
Q [auth A],
R [auth A],
S [auth A],
T [auth L],
U [auth L],
V [auth H]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
CL

Query on CL


Download:Ideal Coordinates CCD File
F [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free:  0.230 (Depositor), 0.229 (DCC) 
  • R-Value Work:  0.206 (Depositor), 0.205 (DCC) 
  • R-Value Observed: 0.207 (Depositor) 
Space Group: P 63 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 182.22α = 90
b = 182.22β = 90
c = 330.851γ = 120
Software Package:
Software NamePurpose
Blu-Icedata collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-07-28
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2014-01-15
    Changes: Refinement description
  • Version 1.3: 2017-11-08
    Changes: Refinement description
  • Version 1.4: 2018-01-24
    Changes: Refinement description
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2023-09-06
    Changes: Data collection, Database references, Refinement description, Structure summary
  • Version 2.2: 2024-11-06
    Changes: Structure summary