1SM3

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

• PDB DOI:  https://doi.org/10.2210/pdb1SM3/pdb

• Classification: COMPLEX (ANTIBODY/PEPTIDE EPITOPE)
• Organism(s): Mus musculus
• Mutation(s): No 


• Deposited: 1997-12-23 Released: 1999-03-23 
• Deposition Author(s): Dokurno, P., Bates, P.A., Band, H.A., Stewart, L.M.D., Lally, J.M., Burchell, J.M., Taylor-Papadimitriou, J., Sternberg, M.J.E., Snary, D., Freemont, P.S.

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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 

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

• PubMed: 9826510 
• DOI: https://doi.org/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 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.

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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

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 48.84 kDa 
• Atom Count: 3,564 
• Modelled Residue Count: 430 
• Deposited Residue Count: 446 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SM3 ANTIBODY	A [auth L]	215	Mus musculus	Mutation(s): 0
UniProt
Find proteins for P01723 (Mus musculus) Explore P01723  Go to UniProtKB:  P01723

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
SM3 ANTIBODY	B [auth H]	218	Mus musculus	Mutation(s): 0
UniProt
Find proteins for P01801 (Mus musculus) Explore P01801  Go to UniProtKB:  P01801

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
PEPTIDE EPITOPE	C [auth P]	13	N/A	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P15941 (Homo sapiens) Explore P15941  Go to UniProtKB:  P15941
PHAROS:  P15941

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CD	D [auth L], E [auth L], F [auth L], G [auth L], H, I [auth H], J [auth H], K [auth H]	CADMIUM ION Cd WLZRMCYVCSSEQC-UHFFFAOYSA-N
CL	L [auth H], M [auth H]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

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 = 42.2	α = 90
b = 83.73	β = 93.3
c = 67.24	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
Agrovata	data reduction
CCP4	data reduction
X-PLOR	model building
X-PLOR	refinement
Agrovata	data scaling
CCP4	data scaling
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1999-03-23 
Deposition Author(s): Dokurno, P., Bates, P.A., Band, H.A., Stewart, L.M.D., Lally, J.M., Burchell, J.M., Taylor-Papadimitriou, J., Sternberg, M.J.E., Snary, D., Freemont, P.S.

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
• Version 1.3: 2023-08-09
  Changes: Data collection, Database references, Derived calculations, Refinement description