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- PDB-1sm3: CRYSTAL STRUCTURE OF THE TUMOR SPECIFIC ANTIBODY SM3 COMPLEX WITH... -

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Basic information

Entry
Database: PDB / ID: 1sm3
TitleCRYSTAL STRUCTURE OF THE TUMOR SPECIFIC ANTIBODY SM3 COMPLEX WITH ITS PEPTIDE EPITOPE
Components
  • (SM3 ANTIBODY) x 2
  • PEPTIDE EPITOPE
KeywordsCOMPLEX (ANTIBODY/PEPTIDE EPITOPE) / ANTIBODY / PEPTIDE ANTIGEN / ANTITUMOR ANTIBODY / COMPLEX (ANTIBODY-PEPTIDE EPITOPE) / COMPLEX (ANTIBODY-PEPTIDE EPITOPE) complex
Function / homology
Function and homology information


Defective GALNT3 causes HFTC / Defective C1GALT1C1 causes TNPS / Defective GALNT12 causes CRCS1 / Termination of O-glycan biosynthesis / O-linked glycosylation of mucins / negative regulation of cell adhesion mediated by integrin / negative regulation of transcription by competitive promoter binding / immunoglobulin complex / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / Dectin-2 family ...Defective GALNT3 causes HFTC / Defective C1GALT1C1 causes TNPS / Defective GALNT12 causes CRCS1 / Termination of O-glycan biosynthesis / O-linked glycosylation of mucins / negative regulation of cell adhesion mediated by integrin / negative regulation of transcription by competitive promoter binding / immunoglobulin complex / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / Dectin-2 family / DNA damage response, signal transduction by p53 class mediator / immunoglobulin mediated immune response / localization / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / transcription coregulator activity / antigen binding / Golgi lumen / p53 binding / Interleukin-4 and Interleukin-13 signaling / adaptive immune response / vesicle / blood microparticle / immune response / apical plasma membrane / RNA polymerase II cis-regulatory region sequence-specific DNA binding / chromatin / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular exosome / nucleus / plasma membrane
Similarity search - Function
Domain found in sea urchin sperm protein, enterokinase, agrin / SEA domain superfamily / SEA domain profile. / SEA domain / SEA domain / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin ...Domain found in sea urchin sperm protein, enterokinase, agrin / SEA domain superfamily / SEA domain profile. / SEA domain / SEA domain / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
: / Ig lambda-1 chain V region / Ig heavy chain V-III region J606 / Mucin-1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsDokurno, 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.
Citation
Journal: J.Mol.Biol. / Year: 1998
Title: Crystal structure at 1.95 A resolution of the breast tumour-specific antibody SM3 complexed with its peptide epitope reveals novel hypervariable loop recognition.
Authors: 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.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1997
Title: Crystallization of an Antitumour Antibody Sm3 Complexed with a Peptide Epitope
Authors: Dokurno, P. / Lally, J.M. / Bates, P.A. / Taylor-Papadimitriou, J. / Band, H.A. / Snary, D. / Freemont, P.S.
History
DepositionDec 23, 1997Processing site: BNL
Revision 1.0Mar 23, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: database_2 / diffrn_source ...database_2 / diffrn_source / pdbx_initial_refinement_model / pdbx_struct_conn_angle / software / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _software.name / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: SM3 ANTIBODY
H: SM3 ANTIBODY
P: PEPTIDE EPITOPE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,83813
Polymers47,8683
Non-polymers97010
Water5,963331
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5510 Å2
ΔGint-90 kcal/mol
Surface area18520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.200, 83.730, 67.240
Angle α, β, γ (deg.)90.00, 93.30, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein/peptide , 1 types, 1 molecules P

#3: Protein/peptide PEPTIDE EPITOPE


Mass: 1258.316 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: ANTI-BREAST TUMOUR ANTIBODY SM3 AGAINST EPITHELIAL MUCIN MUC1
References: UniProt: P15941

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Antibody , 2 types, 2 molecules LH

#1: Antibody SM3 ANTIBODY


Mass: 23149.592 Da / Num. of mol.: 1 / Fragment: FAB FRAGMENT / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Organ: BREAST / Tissue: EPITHELIAL / References: UniProt: P01723
#2: Antibody SM3 ANTIBODY


Mass: 23460.197 Da / Num. of mol.: 1 / Fragment: FAB FRAGMENT / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Organ: BREAST / Tissue: EPITHELIAL / References: UniProt: P01801

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Non-polymers , 3 types, 341 molecules

#4: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cd
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 331 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 51 %
Crystal growpH: 6 / Details: pH 6.0
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
119 %(w/v)PEG40001reservoir
20.1 Macetate1reservoir
30.2 M1reservoirCdCl2

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.912
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 1, 1996
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.912 Å / Relative weight: 1
ReflectionResolution: 1.95→30 Å / Num. obs: 33093 / % possible obs: 96.6 % / Observed criterion σ(I): 1 / Redundancy: 3.4 % / Biso Wilson estimate: 16.2 Å2 / Rmerge(I) obs: 0.069 / Rsym value: 0.069 / Net I/σ(I): 8.1
Reflection shellResolution: 1.95→2.06 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.254 / Mean I/σ(I) obs: 3 / Rsym value: 0.254 / % possible all: 93.2
Reflection shell
*PLUS
% possible obs: 93.2 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
Agrovatadata reduction
CCP4data reduction
X-PLOR3.8model building
X-PLOR3.8refinement
Agrovatadata scaling
CCP4data scaling
X-PLOR3.8phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1MFE

1mfe


Resolution: 1.95→8 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 100000 / Data cutoff low absF: 0.01 / Isotropic thermal model: UNRESTRAINED / Cross valid method: THROUGHOUT / σ(F): 4
Details: TOPOLOGY AND PARAMETERS FILES WERE ALTERED TO ALLOW THE CIS-GLN
RfactorNum. reflection% reflectionSelection details
Rfree0.283 1442 4.3 %RANDOM
Rwork0.213 ---
obs0.213 28735 85.6 %-
Displacement parametersBiso mean: 16.4 Å2
Refinement stepCycle: LAST / Resolution: 1.95→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3227 0 10 331 3568
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.017
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.604
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d28
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.36
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 1.95→2.04 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.288 143 3.4 %
Rwork0.263 2809 -
obs--70.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2TOPH19.PEP
X-RAY DIFFRACTION3TOPH19.SOL
Software
*PLUS
Name: X-PLOR / Version: 3.8 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg28
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.36
LS refinement shell
*PLUS
Rfactor obs: 0.263

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