3C09

Crystal structure the Fab fragment of matuzumab (Fab72000) in complex with domain III of the extracellular region of EGFR


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.299 
  • R-Value Work: 0.242 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Matuzumab binding to EGFR prevents the conformational rearrangement required for dimerization.

Schmiedel, J.Blaukat, A.Li, S.Knochel, T.Ferguson, K.M.

(2008) Cancer Cell 13: 365-373

  • DOI: 10.1016/j.ccr.2008.02.019
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • An increasing number of therapeutic antibodies targeting tumors that express the epidermal growth factor receptor (EGFR) are in clinical use or late stages of clinical development. Here we investigate the molecular basis for inhibition of EGFR activa ...

    An increasing number of therapeutic antibodies targeting tumors that express the epidermal growth factor receptor (EGFR) are in clinical use or late stages of clinical development. Here we investigate the molecular basis for inhibition of EGFR activation by the therapeutic antibody matuzumab (EMD72000). We describe the X-ray crystal structure of the Fab fragment of matuzumab (Fab72000) in complex with isolated domain III from the extracellular region of EGFR. Fab72000 interacts with an epitope on EGFR that is distinct from the ligand-binding region on domain III and from the cetuximab/Erbitux epitope. Matuzumab blocks ligand-induced receptor activation indirectly by sterically preventing the domain rearrangement and local conformational changes that must occur for high-affinity ligand binding and receptor dimerization.


    Organizational Affiliation

    Department of Physiology, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Matuzumab Fab Light chain
L, B
212N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Matuzumab Fab Heavy chain
H, C
223N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Epidermal growth factor receptor
A, D
214Homo sapiensMutation(s): 0 
Gene Names: EGFR (ERBB, ERBB1, HER1)
EC: 2.7.10.1
Find proteins for P00533 (Homo sapiens)
Go to Gene View: EGFR
Go to UniProtKB:  P00533
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MAN
Query on MAN

Download SDF File 
Download CCD File 
A
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
BMA
Query on BMA

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

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.299 
  • R-Value Work: 0.242 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 141.073α = 90.00
b = 205.035β = 117.49
c = 81.577γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
PDB_EXTRACTdata extraction
PHASERphasing
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-04-15
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Non-polymer description, Version format compliance
  • Version 1.2: 2017-10-25
    Type: Refinement description