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- PDB-4ndm: Structure of the AB18.1 TCR -

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Basic information

Entry
Database: PDB / ID: 4ndm
TitleStructure of the AB18.1 TCR
Components
  • Human nkt tcr alpha chain
  • T-cell gamma protein,T-cell receptor beta-2 chain C region
KeywordsIMMUNE SYSTEM / Immunoglobulin / Histocompatibility antigens / T cell receptor / Immunological / lymphocytes / T cell recognition / activation / gamma delta T cell / Human / intraepithelial lymphocytes / CD1d / glycolipids / non-classical MHC / Glycoproteins / Cell-surface receptors
Function / homology
Function and homology information


response to bacterium
Similarity search - Function
T-cell receptor alpha chain, constant domain / Domain of unknown function (DUF1968) / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. ...T-cell receptor alpha chain, constant domain / Domain of unknown function (DUF1968) / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / 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
: / T-cell gamma protein / Human nkt tcr alpha chain / TRA@ protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.0065 Å
AuthorsLuoma, A.M. / Adams, E.J.
CitationJournal: Immunity / Year: 2013
Title: Crystal Structure of V delta 1 T Cell Receptor in Complex with CD1d-Sulfatide Shows MHC-like Recognition of a Self-Lipid by Human gamma delta T Cells.
Authors: Luoma, A.M. / Castro, C.D. / Mayassi, T. / Bembinster, L.A. / Bai, L. / Picard, D. / Anderson, B. / Scharf, L. / Kung, J.E. / Sibener, L.V. / Savage, P.B. / Jabri, B. / Bendelac, A. / Adams, E.J.
History
DepositionOct 27, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 18, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2014Group: Database references
Revision 1.2Jun 14, 2017Group: Database references / Source and taxonomy / Structure summary
Category: entity / entity_name_com ...entity / entity_name_com / entity_src_gen / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity.pdbx_description / _entity.pdbx_fragment ..._entity.pdbx_description / _entity.pdbx_fragment / _struct_ref.db_code / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq.seq_align_end
Revision 1.3Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Sep 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: T-cell gamma protein,T-cell receptor beta-2 chain C region
B: Human nkt tcr alpha chain


Theoretical massNumber of molelcules
Total (without water)55,7072
Polymers55,7072
Non-polymers00
Water181
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4390 Å2
ΔGint-31 kcal/mol
Surface area22160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.078, 142.213, 77.684
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein T-cell gamma protein,T-cell receptor beta-2 chain C region


Mass: 29324.668 Da / Num. of mol.: 1 / Fragment: AB18.1 TCR gamma chain / Mutation: S173C, C191A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRBC2 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A2NUW5, UniProt: A0A0G2JNG9
#2: Protein Human nkt tcr alpha chain / Human nkt tcr beta chain


Mass: 26382.443 Da / Num. of mol.: 1 / Fragment: AB18.1 TCR delta chain / Mutation: T167C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, HDCMA22P / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q6PJ56, UniProt: K7N5M3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1 / 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: 2.73 Å3/Da / Density % sol: 54.92 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop
Details: 20% PEG3350, 0.2 M trisodium citrate, 2% Ethylene Glycol, VAPOR DIFFUSION, SITTING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 2, 2011
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. all: 12399 / Num. obs: 12399 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 6 %
Reflection shellResolution: 3→3.05 Å / Redundancy: 5.2 % / Mean I/σ(I) obs: 2.94 / % possible all: 98.3

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry 3OMZ and 2EYR

3omz

2eyr


Resolution: 3.0065→43.539 Å / SU ML: 0.51 / σ(F): 1.74 / Phase error: 29.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2797 611 4.93 %
Rwork0.2424 --
obs0.2441 12398 99.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.0065→43.539 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3438 0 0 1 3439
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023534
X-RAY DIFFRACTIONf_angle_d0.6314822
X-RAY DIFFRACTIONf_dihedral_angle_d11.2861215
X-RAY DIFFRACTIONf_chiral_restr0.045537
X-RAY DIFFRACTIONf_plane_restr0.003619
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0065-3.3090.38791560.31952848X-RAY DIFFRACTION98
3.309-3.78760.28791680.26042888X-RAY DIFFRACTION100
3.7876-4.7710.23661420.22392986X-RAY DIFFRACTION100
4.771-43.54330.27691450.22913065X-RAY DIFFRACTION100

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