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- PDB-1nfd: AN ALPHA-BETA T CELL RECEPTOR (TCR) HETERODIMER IN COMPLEX WITH A... -

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Basic information

Entry
Database: PDB / ID: 1nfd
TitleAN ALPHA-BETA T CELL RECEPTOR (TCR) HETERODIMER IN COMPLEX WITH AN ANTI-TCR FAB FRAGMENT DERIVED FROM A MITOGENIC ANTIBODY
Components
  • (H57 FAB) x 2
  • (N15 ALPHA-BETA T-CELL RECEPTOR) x 2
KeywordsCOMPLEX (IMMUNORECEPTOR/IMMUNOGLOBULIN) / COMPLEX (IMMUNORECEPTOR-IMMUNOGLOBULIN) / COMPLEX (IMMUNORECEPTOR-IMMUNOGLOBULIN) complex
Function / homology
Function and homology information


Phosphorylation of CD3 and TCR zeta chains / Translocation of ZAP-70 to Immunological synapse / Co-inhibition by PD-1 / Generation of second messenger molecules / Downstream TCR signaling / alpha-beta T cell receptor complex / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / T cell receptor complex / adaptive immune response
Similarity search - Function
T-cell receptor alpha chain, constant domain / Domain of unknown function (DUF1968) / : / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold ...T-cell receptor alpha chain, constant domain / Domain of unknown function (DUF1968) / : / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
T-cell receptor alpha chain constant / T-cell receptor beta-1 chain C region
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT, MAD PHASING / Resolution: 2.8 Å
AuthorsWang, J.-H. / Lim, K. / Smolyar, A. / Teng, M.-K. / Sacchittini, J. / Reinherz, E.L.
Citation
Journal: EMBO J. / Year: 1998
Title: Atomic structure of an alphabeta T cell receptor (TCR) heterodimer in complex with an anti-TCR fab fragment derived from a mitogenic antibody.
Authors: Wang, J. / Lim, K. / Smolyar, A. / Teng, M. / Liu, J. / Tse, A.G. / Liu, J. / Hussey, R.E. / Chishti, Y. / Thomson, C.T. / Sweet, R.M. / Nathenson, S.G. / Chang, H.C. / Sacchettini, J.C. / Reinherz, E.L.
#1: Journal: J.Biol.Chem. / Year: 1996
Title: Crystallization of a Deglycosylated T Cell Receptor (Tcr) Complexed with an Anti-Tcr Fab Fragment
Authors: Liu, J. / Tse, A.G. / Chang, H.C. / Liu, J.H. / Wang, J. / Hussey, R.E. / Chishti, Y. / Rheinhold, B. / Spoerl, R. / Nathenson, S.G. / Sacchettini, J.C. / Reinherz, E.L.
History
DepositionAug 4, 1997Processing site: BNL
Revision 1.0Jan 28, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Jul 5, 2017Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.process_site
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_validate_chiral / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _pdbx_nonpoly_scheme.entity_id / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _struct_asym.entity_id / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _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.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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Aug 9, 2023Group: Database references / Refinement description / Structure summary
Category: chem_comp / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Dec 25, 2024Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature / pdbx_validate_close_contact / struct_conn

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: N15 ALPHA-BETA T-CELL RECEPTOR
B: N15 ALPHA-BETA T-CELL RECEPTOR
C: N15 ALPHA-BETA T-CELL RECEPTOR
D: N15 ALPHA-BETA T-CELL RECEPTOR
E: H57 FAB
F: H57 FAB
G: H57 FAB
H: H57 FAB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)197,63822
Polymers194,5418
Non-polymers3,09714
Water00
1
C: N15 ALPHA-BETA T-CELL RECEPTOR
D: N15 ALPHA-BETA T-CELL RECEPTOR
G: H57 FAB
H: H57 FAB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,81911
Polymers97,2714
Non-polymers1,5487
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
A: N15 ALPHA-BETA T-CELL RECEPTOR
B: N15 ALPHA-BETA T-CELL RECEPTOR
E: H57 FAB
F: H57 FAB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,81911
Polymers97,2714
Non-polymers1,5487
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
A: N15 ALPHA-BETA T-CELL RECEPTOR
B: N15 ALPHA-BETA T-CELL RECEPTOR
hetero molecules

E: H57 FAB
F: H57 FAB

C: N15 ALPHA-BETA T-CELL RECEPTOR
D: N15 ALPHA-BETA T-CELL RECEPTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,28920
Polymers147,1926
Non-polymers3,09714
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
crystal symmetry operation2_546-x,y-1/2,-z+11
Buried area24260 Å2
ΔGint-54 kcal/mol
Surface area81950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.740, 122.300, 115.840
Angle α, β, γ (deg.)90.00, 107.95, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.923569, -0.383429, 0.001392), (-0.382049, 0.920543, 0.081477), (-0.032522, 0.074718, -0.996674)47.4757, 4.4272, 117.9216
2given(-0.931432, -0.363879, 0.005052), (-0.357016, 0.91638, 0.181073), (-0.070518, 0.166854, -0.983456)45.17395, -1.53481, 107.36128
3given(-0.914571, -0.403693, -0.024328), (-0.403989, 0.909131, 0.101363), (-0.018802, 0.102532, -0.994552)50.45118, 4.7913, 114.72173
4given(-0.918457, -0.394715, -0.025235), (-0.393772, 0.906539, 0.152087), (-0.037155, 0.149622, -0.988045)49.80048, 0.99606, 109.58141
5given(-0.77875, -0.61828, -0.106195), (-0.619703, 0.731854, 0.283473), (-0.097546, 0.286564, -0.953082)70.68728, 4.57725, 97.536
6given(-0.742508, -0.655816, -0.136335), (-0.664198, 0.694491, 0.276628), (-0.086734, 0.295952, -0.951257)74.42132, 10.43213, 95.96081
7given(-0.767263, -0.628236, -0.128943), (-0.635315, 0.717069, 0.286682), (-0.087643, 0.30188, -0.949309)73.15421, 5.50508, 96.33139
8given(-0.750416, -0.649633, -0.121871), (-0.650863, 0.694162, 0.307436), (-0.115123, 0.310026, -0.943732)73.12054, 6.12949, 95.89676

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Components

#1: Protein N15 ALPHA-BETA T-CELL RECEPTOR


Mass: 22611.205 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Description: CODON IN / Gene: N15 T-CELL RECEPTOR / Plasmid: PEE14-GS / Cell line (production host): CH0 LEC 3.2.8.1 / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P01849*PLUS
#2: Protein N15 ALPHA-BETA T-CELL RECEPTOR


Mass: 27310.598 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Description: CODON IN / Gene: N15 T-CELL RECEPTOR / Plasmid: PEE14-GS / Cell line (production host): CH0 LEC 3.2.8.1 / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P01852
#3: Antibody H57 FAB


Mass: 23045.672 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Description: CODON IN / Gene: N15 T-CELL RECEPTOR / Plasmid: PEE14-GS / Cell line (production host): CH0 LEC 3.2.8.1 / Production host: Cricetulus griseus (Chinese hamster)
#4: Antibody H57 FAB


Mass: 24303.168 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Description: CODON IN / Gene: N15 T-CELL RECEPTOR / Plasmid: PEE14-GS / Cell line (production host): CH0 LEC 3.2.8.1 / Production host: Cricetulus griseus (Chinese hamster)
#5: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 14
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
Has protein modificationY

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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: 2.46 Å3/Da / Density % sol: 50 %
Crystal growpH: 5.5 / Details: 8-10% PEG8000, 0.2 M KCL, 0.1 M 2 ACETATE, PH5.5
Crystal grow
*PLUS
Method: unknown / Details: Liu, J., (1996) J.Biol.Chem., 271, 33639.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
18-10 %PEG800011
20.2 M11KCl
30.1 Macetate11

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1.086
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 26, 1996
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.086 Å / Relative weight: 1
ReflectionResolution: 2.8→15 Å / Num. obs: 37321 / % possible obs: 76.6 % / Observed criterion σ(I): 1 / Redundancy: 3.1 % / Rmerge(I) obs: 0.078 / Rsym value: 0.078 / Net I/σ(I): 12.1
Reflection shellResolution: 2.8→2.9 Å / Rmerge(I) obs: 0.263 / Rsym value: 0.263 / % possible all: 51.1
Reflection shell
*PLUS
% possible obs: 51.1 % / Redundancy: 1.3 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT, MAD PHASING
Starting model: PDB ENTRY 1TCR FOR TCR AND A PARTIALLY REFINED FAB FROM SACCHETTINI GROUP

1tcr


Resolution: 2.8→15 Å / σ(F): 2
Details: SOLVENT CORRECTION APPLIED. ANISOTROPIC B-FACTOR CORRECTION APPLIED TO FO.
RfactorNum. reflection% reflection
Rfree0.309 3584 10 %
Rwork0.243 --
obs0.243 35885 73.5 %
Displacement parametersBiso mean: 26.59 Å2
Refine analyzeLuzzati coordinate error obs: 0.38 Å
Refinement stepCycle: LAST / Resolution: 2.8→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13688 0 196 0 13884
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.006
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_deg1.2
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.5
X-RAY DIFFRACTIONx_mcangle_it2
X-RAY DIFFRACTIONx_scbond_it2
X-RAY DIFFRACTIONx_scangle_it2.5
LS refinement shellResolution: 2.8→2.9 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.369 260 10 %
Rwork0.309 2659 -
obs--48.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM3_MOD.CHOTOPH3.CHO
Software
*PLUS
Name: X-PLOR / Version: 3.85 / Classification: refinement
Refine LS restraints
*PLUS
Type: x_improper_angle_deg / Dev ideal: 0.7

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