1SM3

CRYSTAL STRUCTURE OF THE TUMOR SPECIFIC ANTIBODY SM3 COMPLEX WITH ITS PEPTIDE EPITOPE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.213 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structure at 1.95 A resolution of the breast tumour-specific antibody SM3 complexed with its peptide epitope reveals novel hypervariable loop recognition.

Dokurno, P.Bates, P.A.Band, H.A.Stewart, L.M.Lally, J.M.Burchell, J.M.Taylor-Papadimitriou, J.Snary, D.Sternberg, M.J.Freemont, P.S.

(1998) J.Mol.Biol. 284: 713-728

  • DOI: 10.1006/jmbi.1998.2209

  • PubMed Abstract: 
  • The anti-breast tumour antibody SM3 has a high selectivity in reacting specifically with carcinoma-associated mucin. SM3 recognises the core repeating motif (Pro-Asp-Thr-Arg-Pro) of aberrantly glycosylated epithelial mucin MUC1, and has potential as ...

    The anti-breast tumour antibody SM3 has a high selectivity in reacting specifically with carcinoma-associated mucin. SM3 recognises the core repeating motif (Pro-Asp-Thr-Arg-Pro) of aberrantly glycosylated epithelial mucin MUC1, and has potential as a therapeutic and diagnostic tool. Here we report the crystal structure of the Fab fragment of SM3 in complex with a 13-residue MUC1 peptide antigen (Thr1P-Ser2P-Ala3P-Pro4P-Asp5P-Thr6P -Arg7P-Pro8P-Ala9P-Pro10P-Gly11P- Ser12P-Thr13P). The SM3-MUC1 peptide structure was solved by molecular replacement, and the current model is refined at 1.95 A resolution with an R-factor of 21.3% and R-free 28.3%. The MUC1 peptide is bound both by non-polar interactions and hydrogen bonds in an elongated groove in the antibody-combining site through interactions with Complimentarity Determining Regions (CDRs), three of the light chain (L1, L2, L3) and two of the heavy chain (H1 and H3). The conformation of the peptide is mainly extended with no discernable standard secondary structure. There is a single non-proline cis-peptide bond in H3 (Val95H-Gly96H-Gln97H-Phe98H-Ala101H-Ty r102H) between Gly96H and Gln97H, which appears to play a role in SM3-peptide antigen interactions, and represents the first such example within an antibody hypervariable loop. The SM3-MUC1 peptide structure has implications for rational therapeutic and diagnostic antibody engineering.


    Related Citations: 
    • Crystallization of an Antitumour Antibody Sm3 Complexed with a Peptide Epitope
      Dokurno, P.,Lally, J.M.,Bates, P.A.,Taylor-Papadimitriou, J.,Band, H.A.,Snary, D.,Freemont, P.S.
      (1997) Acta Crystallogr.,Sect.D 53: 780


    Organizational Affiliation

    Molecular Structure and Function Laboratory, Imperial Cancer Research Fund, London, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
SM3 ANTIBODY
L
215Mus musculusMutation(s): 0 
Find proteins for P01723 (Mus musculus)
Go to UniProtKB:  P01723
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
SM3 ANTIBODY
H
218Mus musculusMutation(s): 0 
Find proteins for P01801 (Mus musculus)
Go to UniProtKB:  P01801
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
PEPTIDE EPITOPE
P
13Homo sapiensMutation(s): 0 
Gene Names: MUC1 (PUM)
Find proteins for P15941 (Homo sapiens)
Go to Gene View: MUC1
Go to UniProtKB:  P15941
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
H
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
CD
Query on CD

Download SDF File 
Download CCD File 
H, L
CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.213 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 42.200α = 90.00
b = 83.730β = 93.30
c = 67.240γ = 90.00
Software Package:
Software NamePurpose
X-PLORrefinement
DENZOdata reduction
AGROVATAdata scaling
AGROVATAdata reduction
CCP4data reduction
X-PLORmodel building
CCP4data scaling
X-PLORphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-03-23
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance