6DDR

Crystal Structure Analysis of the Epitope of an Anti-MICA Antibody


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.208 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

High-resolution glycosylation site-engineering method identifies MICA epitope critical for shedding inhibition activity of anti-MICA antibodies.

Lombana, T.N.Matsumoto, M.L.Berkley, A.M.Toy, E.Cook, R.Gan, Y.Du, C.Schnier, P.Sandoval, W.Ye, Z.Schartner, J.M.Kim, J.Spiess, C.

(2019) MAbs 11: 75-93

  • DOI: 10.1080/19420862.2018.1532767
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • As an immune evasion strategy, MICA and MICB, the major histocompatibility complex class I homologs, are proteolytically cleaved from the surface of cancer cells leading to impairment of CD8 + T cell- and natural killer cell-mediated immune responses ...

    As an immune evasion strategy, MICA and MICB, the major histocompatibility complex class I homologs, are proteolytically cleaved from the surface of cancer cells leading to impairment of CD8 + T cell- and natural killer cell-mediated immune responses. Antibodies that inhibit MICA/B shedding from tumors have therapeutic potential, but the optimal epitopes are unknown. Therefore, we developed a high-resolution, high-throughput glycosylation-engineered epitope mapping (GEM) method, which utilizes site-specific insertion of N-linked glycans onto the antigen surface to mask local regions. We apply GEM to the discovery of epitopes important for shedding inhibition of MICA/B and validate the epitopes at the residue level by alanine scanning and X-ray crystallography (Protein Data Bank accession numbers 6DDM (1D5 Fab-MICA*008), 6DDR (13A9 Fab-MICA*008), 6DDV (6E1 Fab-MICA*008). Furthermore, we show that potent inhibition of MICA shedding can be achieved by antibodies that bind GEM epitopes adjacent to previously reported cleavage sites, and that these anti-MICA/B antibodies can prevent tumor growth in vivo.


    Organizational Affiliation

    c Translational Oncology , Genentech Inc ., South San Francisco , USA.,a Department of Antibody Engineering , Genentech Inc ., South San Francisco , USA.,d Biochemical and Cellular Pharmacology , Genentech Inc ., South San Francisco , USA.,f Cancer Immunology , Genentech Inc ., South San Francisco , USA.,b Structural Biology , Genentech Inc ., South San Francisco , USA.,e Microchemistry, Proteomics and Lipidomics , Genentech Inc ., South San Francisco , USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Anti-MICA Fab fragment light chain clone 13A9
A
214N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Anti-MICA Fab fragment heavy chain clone 13A9
B
221N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
MHC class I polypeptide-related sequence A
C
94Homo sapiensMutation(s): 0 
Gene Names: MICA
Find proteins for Q96QC4 (Homo sapiens)
Go to Gene View: MICA
Go to UniProtKB:  Q96QC4
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
C
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download SDF File 
Download CCD File 
B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, B, C
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.208 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 51.549α = 90.00
b = 61.833β = 90.00
c = 172.368γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2018-05-10 
  • Released Date: 2018-10-24 
  • Deposition Author(s): Matsumoto, M.L.

Revision History 

  • Version 1.0: 2018-10-24
    Type: Initial release
  • Version 1.1: 2018-12-05
    Type: Data collection, Database references
  • Version 1.2: 2019-01-23
    Type: Data collection, Database references