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- PDB-4lfh: Crystal Structure of 9C2 TCR -

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Basic information

Entry
Database: PDB / ID: 4lfh
TitleCrystal Structure of 9C2 TCR
Components
  • 9C2 TCR delta chain
  • 9C2 TCR gamma chain
KeywordsIMMUNE SYSTEM / NKT cells / GammaDelta TCR / CD1d / lipid recognition / PBS-44
Function / homology
Function and homology information


gamma-delta T cell receptor complex / gamma-delta T cell activation / small molecule binding / T cell receptor signaling pathway / adaptive immune response / external side of plasma membrane / plasma membrane
Similarity search - Function
Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain ...Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / 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
ACETATE ION / T cell receptor gamma constant 1 / TRA@ protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å
AuthorsUldrich, A.P. / Le Nours, J. / Pellicci, D.G. / Gras, S. / Rossjohn, J. / Godfrey, D.I.
CitationJournal: Nat.Immunol. / Year: 2013
Title: CD1d-lipid antigen recognition by the gamma delta TCR.
Authors: Uldrich, A.P. / Le Nours, J. / Pellicci, D.G. / Gherardin, N.A. / McPherson, K.G. / Lim, R.T. / Patel, O. / Beddoe, T. / Gras, S. / Rossjohn, J. / Godfrey, D.I.
History
DepositionJun 26, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 2, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2013Group: Database references
Revision 1.2Nov 6, 2013Group: Database references
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_unobs_or_zero_occ_atoms / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _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.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 20, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _chem_comp.pdbx_synonyms / _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
D: 9C2 TCR delta chain
G: 9C2 TCR gamma chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,4726
Polymers54,9422
Non-polymers5294
Water3,873215
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5040 Å2
ΔGint-39 kcal/mol
Surface area21900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.534, 118.534, 89.127
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP42212

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Components

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Antibody / Protein / Sugars , 3 types, 3 molecules DG

#1: Antibody 9C2 TCR delta chain


Mass: 26265.854 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pHLsec / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: Q6PJ56*PLUS
#2: Protein 9C2 TCR gamma chain


Mass: 28676.480 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pHLsec / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: P0CF51*PLUS
#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE

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Non-polymers , 3 types, 218 molecules

#4: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 215 / 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: 2.85 Å3/Da / Density % sol: 56.83 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 40% PEG300, 0.1 M sodium cacodylate, pH 6.5, 0.2 M calcium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.954 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Jun 13, 2013
RadiationMonochromator: double Si(111) with sagittaly bent second crystal
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
ReflectionResolution: 2.3→83.816 Å / Num. all: 28824 / Num. obs: 28824 / % possible obs: 100 % / Redundancy: 14.4 % / Rsym value: 0.155
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 14.8 % / Rmerge(I) obs: 0.383 / Mean I/σ(I) obs: 2.2 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALA3.3.20data scaling
PHASERphasing
BUSTER-TNTrefinement
PDB_EXTRACT3.11data extraction
Blu-Icedata collection
XDSdata reduction
BUSTER2.10.0refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 3OMZ AND 1HXM

3omz

1hxm


Resolution: 2.3→41.71 Å / Cor.coef. Fo:Fc: 0.9461 / Cor.coef. Fo:Fc free: 0.9126 / Occupancy max: 1 / Occupancy min: 0 / SU R Cruickshank DPI: 0.219 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.229 / SU Rfree Blow DPI: 0.197 / SU Rfree Cruickshank DPI: 0.195
RfactorNum. reflection% reflectionSelection details
Rfree0.2376 1457 5.06 %RANDOM
Rwork0.1866 ---
obs0.1891 28780 99.97 %-
Displacement parametersBiso max: 159.64 Å2 / Biso mean: 57.2649 Å2 / Biso min: 27.5 Å2
Baniso -1Baniso -2Baniso -3
1--2.2774 Å20 Å20 Å2
2---2.2774 Å20 Å2
3---4.5549 Å2
Refine analyzeLuzzati coordinate error obs: 0.338 Å
Refinement stepCycle: LAST / Resolution: 2.3→41.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3397 0 34 215 3646
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1625SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes80HARMONIC2
X-RAY DIFFRACTIONt_gen_planes502HARMONIC5
X-RAY DIFFRACTIONt_it3537HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion477SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3785SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d3537HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg4801HARMONIC21.18
X-RAY DIFFRACTIONt_omega_torsion3.65
X-RAY DIFFRACTIONt_other_torsion3.18
LS refinement shellResolution: 2.3→2.39 Å / Total num. of bins used: 14
RfactorNum. reflection% reflection
Rfree0.2517 136 4.59 %
Rwork0.2173 2828 -
all0.2188 2964 -
obs--99.97 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.2085-0.61261.10461.3123-0.70110.55980.2780.46550.3935-0.4663-0.2839-0.2080.2160.24030.00590.1110.05860.0876-0.0845-0.0225-0.1972-41.5036-8.5393-29.921
22.4439-0.74731.2260.6191-0.44420.34980.1209-0.21420.0662-0.3519-0.0613-0.06340.213-0.184-0.05960.0366-0.07340.0527-0.0157-0.0802-0.088-37.6818-18.5813-13.7938
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ D|* }D5 - 401
2X-RAY DIFFRACTION2{ G|* }G10 - 238

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