6J71

HuA21-scFv in complex with the extracellular domain(ECD) of HER2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.918 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.208 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural insight into a matured humanized monoclonal antibody HuA21 against HER2-overexpressing cancer cells.

Wang, Z.Cheng, L.Guo, G.Cheng, B.Hu, S.Zhang, H.Zhu, Z.Niu, L.

(2019) Acta Crystallogr D Struct Biol 75: 554-563

  • DOI: 10.1107/S2059798319006995

  • PubMed Abstract: 
  • HER2, a member of the epidermal growth factor receptor (EGFR) family, has been associated with human breast, ovarian and gastric cancers. Anti-HER2 monoclonal antibodies (mAbs) have demonstrated clinical efficacy for HER2-overexpressing breast cancer ...

    HER2, a member of the epidermal growth factor receptor (EGFR) family, has been associated with human breast, ovarian and gastric cancers. Anti-HER2 monoclonal antibodies (mAbs) have demonstrated clinical efficacy for HER2-overexpressing breast cancer. A chimeric antibody chA21 that specifically inhibits the growth of HER2-overexpressing cancer cells both in vitro and in vivo has previously been developed. To reduce a potential human anti-mouse immune response, the humanized antibody HuA21 was developed and was further subjected to affinity maturation by phage display on the basis of chA21. Here, the crystal structure of HuA21-scFv in complex with the extracellular domain of HER2 is reported, which demonstrates that HuA21 binds almost the same epitope as chA21 and also provides insight into how substitutions in HuA21 improve the binding affinity compared with chA21, which could facilitate structure-based optimization in the future. Furthermore, the effects of HuA21 variants with constant domains of different lengths were explored and it was noticed that the deletion of constant domain 1 could improve the inhibition efficacy in a cell-proliferation assay, possibly functioning via increased internalization, which might guide the design of other monoclonal antibodies.


    Organizational Affiliation

    Department of Biology, Southern University of Science and Technology, Shenzhen, Guangdong 518000, People's Republic of China.,Hanke Mab Biotechnologies Inc., Hefei, Anhui 230026, People's Republic of China.,Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230026, People's Republic of China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Receptor tyrosine-protein kinase erbB-2
A
618Homo sapiensMutation(s): 0 
Gene Names: ERBB2 (HER2, MLN19, NEU, NGL)
EC: 2.7.10.1
Find proteins for P04626 (Homo sapiens)
Go to Gene View: ERBB2
Go to UniProtKB:  P04626
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
anti-HER2 humanized antibody HuA21
B
254N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BMA
Query on BMA

Download SDF File 
Download CCD File 
A
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.918 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.208 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 146.987α = 90.00
b = 78.073β = 107.47
c = 125.769γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
PDB_EXTRACTdata extraction
SCALEPACKdata scaling
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of ChinaChinaU1632124
National Natural Science Foundation of ChinaChina31270770
National Natural Science Foundation of ChinaChina31621002
Ministry of Science and Technology (China)China2017YFA0503600
Ministry of Science and Technology (China)China2017YFA0504903
Ministry of Science and Technology (China)China2012CB917200

Revision History 

  • Version 1.0: 2019-02-27
    Type: Initial release
  • Version 1.1: 2019-06-26
    Type: Data collection, Database references