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 
  • R-Value Observed: 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
  • Primary Citation of Related Structures:  
    1SM3

  • 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 D Biol Crystallogr 53: 780

    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
SM3 ANTIBODYL215Mus musculusMutation(s): 0 
Find proteins for P01723 (Mus musculus)
Explore P01723 
Go to UniProtKB:  P01723
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
SM3 ANTIBODYH218Mus musculusMutation(s): 0 
Find proteins for P01801 (Mus musculus)
Explore P01801 
Go to UniProtKB:  P01801
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
PEPTIDE EPITOPEP13N/AMutation(s): 0 
Find proteins for P15941 (Homo sapiens)
Explore P15941 
Go to UniProtKB:  P15941
NIH Common Fund Data Resources
PHAROS  P15941
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CD
Query on CD

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H, L
CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

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H
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 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 
  • R-Value Observed: 0.213 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.2α = 90
b = 83.73β = 93.3
c = 67.24γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
AGROVATAdata reduction
CCP4data reduction
X-PLORmodel building
X-PLORrefinement
AGROVATAdata scaling
CCP4data scaling
X-PLORphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

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