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- PDB-1kb5: MURINE T-CELL RECEPTOR VARIABLE DOMAIN/FAB COMPLEX -

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Basic information

Entry
Database: PDB / ID: 1kb5
TitleMURINE T-CELL RECEPTOR VARIABLE DOMAIN/FAB COMPLEX
Components
  • (ANTIBODY DESIRE-1) x 2
  • (KB5-C20 T-CELL ANTIGEN RECEPTOR) x 2
KeywordsCOMPLEX (IMMUNOGLOBULIN/RECEPTOR) / T-CELL RECEPTOR / STRAND SWITCH / FAB / ANTICLONOTYPIC / (IMMUNOGLOBULIN/RECEPTOR) / COMPLEX (IMMUNOGLOBULIN-RECEPTOR) COMPLEX
Function / homology
Function and homology information


positive regulation of B cell activation / early endosome to late endosome transport / humoral immune response mediated by circulating immunoglobulin / phagocytosis, recognition / positive regulation of type IIa hypersensitivity / regulation of proteolysis / positive regulation of type I hypersensitivity / antibody-dependent cellular cytotoxicity / Fc-gamma receptor I complex binding / T cell receptor complex ...positive regulation of B cell activation / early endosome to late endosome transport / humoral immune response mediated by circulating immunoglobulin / phagocytosis, recognition / positive regulation of type IIa hypersensitivity / regulation of proteolysis / positive regulation of type I hypersensitivity / antibody-dependent cellular cytotoxicity / Fc-gamma receptor I complex binding / T cell receptor complex / phagocytosis, engulfment / endosome to lysosome transport / positive regulation of endocytosis / immunoglobulin complex, circulating / IgG immunoglobulin complex / immunoglobulin receptor binding / immunoglobulin mediated immune response / antigen processing and presentation / positive regulation of phagocytosis / complement activation, classical pathway / antigen binding / multivesicular body / B cell differentiation / response to bacterium / peptide antigen binding / positive regulation of immune response / antibacterial humoral response / adaptive immune response / extracellular space / extracellular region / plasma membrane / cytosol
Similarity search - Function
Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. ...Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
: / Immunoglobulin kappa constant / Ig gamma-2A chain C region, membrane-bound form / T-cell receptor beta chain V region E1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsHousset, D. / Mazza, G. / Gregoire, C. / Piras, C. / Malissen, B. / Fontecilla-Camps, J.C.
Citation
Journal: EMBO J. / Year: 1997
Title: The three-dimensional structure of a T-cell antigen receptor V alpha V beta heterodimer reveals a novel arrangement of the V beta domain.
Authors: Housset, D. / Mazza, G. / Gregoire, C. / Piras, C. / Malissen, B. / Fontecilla-Camps, J.C.
#1: Journal: Science / Year: 1996
Title: An Alphabeta T Cell Receptor Structure at 2.5 A and its Orientation in the Tcr-Mhc Complex
Authors: Garcia, K.C. / Degano, M. / Stanfield, R.L. / Brunmark, A. / Jackson, M.R. / Peterson, P.A. / Teyton, L. / Wilson, I.A.
#2: Journal: Nature / Year: 1996
Title: Structure of the Complex between Human T-Cell Receptor, Viral Peptide and Hla-A2
Authors: Garboczi, D.N. / Ghosh, P. / Utz, U. / Fan, Q.R. / Biddison, W.E. / Wiley, D.C.
#3: Journal: Science / Year: 1995
Title: Crystal Structure of the Beta Chain of a T Cell Antigen Receptor
Authors: Bentley, G.A. / Boulot, G. / Karjalainen, K. / Mariuzza, R.A.
#4: Journal: Science / Year: 1995
Title: Crystal Structure of the V Alpha Domain of a T Cell Antigen Receptor
Authors: Fields, B.A. / Ober, B. / Malchiodi, E.L. / Lebedeva, M.I. / Braden, B.C. / Ysern, X. / Kim, J.K. / Shao, X. / Ward, E.S. / Mariuzza, R.A.
#5: Journal: Proc.Natl.Acad.Sci.USA / Year: 1991
Title: Engineered Secreted T-Cell Receptor Alpha Beta Heterodimers
Authors: Gregoire, C. / Rebai, N. / Schweisguth, F. / Necker, A. / Mazza, G. / Auphan, N. / Millward, A. / Schmitt-Verhulst, A.M. / Malissen, B.
History
DepositionApr 6, 1997Processing site: BNL
Revision 1.0Apr 8, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Apr 11, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_beamline
Revision 1.5Aug 9, 2023Group: Database references / Refinement description
Category: database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: KB5-C20 T-CELL ANTIGEN RECEPTOR
B: KB5-C20 T-CELL ANTIGEN RECEPTOR
L: ANTIBODY DESIRE-1
H: ANTIBODY DESIRE-1


Theoretical massNumber of molelcules
Total (without water)73,5014
Polymers73,5014
Non-polymers00
Water4,792266
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)187.310, 80.950, 52.080
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein KB5-C20 T-CELL ANTIGEN RECEPTOR / TCR VAPLHA VBETA DOMAIN


Mass: 12809.139 Da / Num. of mol.: 1 / Fragment: FV FRAGMENT, VARIABLE DOMAIN
Source method: isolated from a genetically manipulated source
Details: 24 RESIDUE LINK BETWEEN VALPHA C-TERMINUS AND VBETA N-TERMINUS
Source: (gene. exp.) Mus musculus (house mouse) / Cell: T-CELL / Cellular location: SURFACE / Cellular location (production host): MYELOMA / Production host: Mus musculus (house mouse) / References: GenBank: 554285
#2: Protein KB5-C20 T-CELL ANTIGEN RECEPTOR / TCR VAPLHA VBETA DOMAIN


Mass: 13381.247 Da / Num. of mol.: 1 / Fragment: FV FRAGMENT, VARIABLE DOMAIN
Source method: isolated from a genetically manipulated source
Details: 24 RESIDUE LINK BETWEEN VALPHA C-TERMINUS AND VBETA N-TERMINUS
Source: (gene. exp.) Mus musculus (house mouse) / Cell: T-CELL / Cellular location: SURFACE / Cellular location (production host): MYELOMA / Production host: Mus musculus (house mouse) / References: UniProt: P04214
#3: Antibody ANTIBODY DESIRE-1


Mass: 23624.062 Da / Num. of mol.: 1 / Fragment: FAB / Source method: isolated from a natural source / Details: CLEAVED BY PAPAIN / Source: (natural) Mus musculus (house mouse) / Strain: IGG2A / References: UniProt: P01837
#4: Antibody ANTIBODY DESIRE-1


Mass: 23686.391 Da / Num. of mol.: 1 / Fragment: FAB / Source method: isolated from a natural source / Details: CLEAVED BY PAPAIN / Source: (natural) Mus musculus (house mouse) / Strain: IGG2A / References: UniProt: P01865
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 266 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE TCR FV FRAGMENT AND THE VARIABLE REGIONS OF THE FAB DESIRE-1 HAVE BEEN NUMBERED AS DESCRIBED IN ...THE TCR FV FRAGMENT AND THE VARIABLE REGIONS OF THE FAB DESIRE-1 HAVE BEEN NUMBERED AS DESCRIBED IN KABAT ET AL., 1991. A FEW DISORDERED SIDE CHAINS LOCATED AT THE SURFACE HAVE A 0.5 OCCUPANCY. ASP A 120 IS THE FIRST RESIDUE OF THE LINKER BETWEEN VALPHA AND VBETA CHAINS.

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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: 54.18 %
Crystal growpH: 7.2
Details: 15% PEG6000, 100MM HEPES PH 6.9-7.5, 200MM NACL, 0.1% NAN3, pH 7.2
PH range: 6.9-7.5
Crystal
*PLUS
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / PH range low: 7.5 / PH range high: 6.9
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
115 %PEG60001reservoir
2100 mMHEPES1reservoir
3200 mM1reservoirNaCl
40.1 %1reservoirNaN3

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM02 / Wavelength: 0.9786
DetectorDetector: CCD / Date: Oct 1, 1996 / Details: MIRRORS
RadiationMonochromator: SI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2.5→25 Å / Num. obs: 24517 / % possible obs: 86.7 % / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Biso Wilson estimate: 76 Å2 / Rsym value: 0.086
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 1.7 % / Rsym value: 0.395 / % possible all: 64.9
Reflection
*PLUS
Observed criterion σ(F): 3 / Num. measured all: 75774 / Rmerge(I) obs: 0.086

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Processing

Software
NameClassification
XDSdata scaling
XSCALEdata scaling
AMoREphasing
REFMACrefinement
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 1VFA, 1MLB, 1FLR, 1BEC

1vfa

1mlb

1flr

1bec


Resolution: 2.5→10 Å / σ(F): 0
Details: BULK SOLVENT CORRECTION USED R VALUE (WORKING + TEST SET) : 0.221
RfactorNum. reflection% reflectionSelection details
Rwork0.219 ---
obs0.221 20232 --
Rfree-1048 5 %RANDOM
Displacement parametersBiso mean: 48.9 Å2
Refinement stepCycle: LAST / Resolution: 2.5→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5172 0 0 266 5438
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0130.02
X-RAY DIFFRACTIONp_angle_d0.0340.03
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.1120.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it0.591
X-RAY DIFFRACTIONp_mcangle_it1.121.5
X-RAY DIFFRACTIONp_scbond_it0.751.5
X-RAY DIFFRACTIONp_scangle_it1.262
X-RAY DIFFRACTIONp_plane_restr0.0140.02
X-RAY DIFFRACTIONp_chiral_restr0.2130.2
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Num. reflection all: 20232 / Num. reflection obs: 18105 / σ(F): 3 / Rfactor all: 0.221 / Rfactor obs: 0.21 / Rfactor Rfree: 0.315
Solvent computation
*PLUS
Displacement parameters
*PLUS

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