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- PDB-2cdf: Structure and binding kinetics of three different human CD1d-alph... -

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Basic information

Entry
Database: PDB / ID: 2cdf
TitleStructure and binding kinetics of three different human CD1d-alpha- Galactosylceramide-specific T cell receptors (TCR 5E)
Components(TCR 5E) x 2
KeywordsCELL RECEPTOR / CD1D / ALPHA-GALACTOSYLCERAMIDE / NON-CANONICAL TCR / TCR / T CELL RECEPTOR / MHC CLASS I / NATURAL KILLER T CELL / TCR 5E
Function / homology
Function and homology information


alpha-beta T cell receptor complex / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / alpha-beta T cell activation / Generation of second messenger molecules / Co-inhibition by PD-1 / response to bacterium / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Downstream TCR signaling / T cell receptor signaling pathway ...alpha-beta T cell receptor complex / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / alpha-beta T cell activation / Generation of second messenger molecules / Co-inhibition by PD-1 / response to bacterium / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Downstream TCR signaling / T cell receptor signaling pathway / adaptive immune response / immune response / membrane / plasma membrane
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 constant 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsGadola, S.D. / Koch, M. / Marles-Wright, J. / Lissin, N.M. / Sheperd, D. / Matulis, G. / Harlos, K. / Villiger, P.M. / Stuart, D.I. / Jakobsen, B.K. ...Gadola, S.D. / Koch, M. / Marles-Wright, J. / Lissin, N.M. / Sheperd, D. / Matulis, G. / Harlos, K. / Villiger, P.M. / Stuart, D.I. / Jakobsen, B.K. / Cerundolo, V. / Jones, E.Y.
CitationJournal: J.Exp.Med. / Year: 2006
Title: Structrue and Binding Kinetics of Three Different Human Cd1D-Alpha-Galactosylceramide-Specific T Cell Receptors
Authors: Gadola, S.D. / Koch, M. / Marles-Wright, J. / Lissin, N.M. / Sheperd, D. / Matulis, G. / Harlos, K. / Villiger, P.M. / Stuart, D.I. / Jakobsen, B.K. / Cerundolo, V. / Jones, E.Y.
History
DepositionJan 23, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 7, 2006Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TCR 5E
B: TCR 5E


Theoretical massNumber of molelcules
Total (without water)48,8322
Polymers48,8322
Non-polymers00
Water5,116284
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)64.451, 64.451, 184.977
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Antibody TCR 5E


Mass: 21085.320 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: NON CANONICAL HUMAN NATURAL KILLER (NK) T CELL RECEPTOR 5E NON-VALPHA24 AND VBETA11
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P01848*PLUS
#2: Protein TCR 5E


Mass: 27746.768 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: NON CANONICAL HUMAN NATURAL KILLER (NK) T CELL RECEPTOR 5E NON-VALPHA24 AND VBETA11
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P01850*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 284 / Source method: isolated from a natural source / Formula: H2O
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: 2.27 Å3/Da / Density % sol: 44 %
Crystal growDetails: 200 MM MAGNESIUM SULPHATE, 20 % PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.976
DetectorType: ADSC CCD / Detector: CCD / Date: Sep 14, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.25→30 Å / Num. obs: 21795 / % possible obs: 98.8 % / Observed criterion σ(I): 0.5 / Redundancy: 12.4 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 31
Reflection shellResolution: 2.25→2.3 Å / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 7.9 / % possible all: 89.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1OGA

1oga


Resolution: 2.25→30 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.916 / SU B: 14.596 / SU ML: 0.197 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.351 / ESU R Free: 0.263 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.269 1098 5.1 %RANDOM
Rwork0.188 ---
obs0.192 20555 98.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.59 Å2
Baniso -1Baniso -2Baniso -3
1--0.08 Å2-0.04 Å20 Å2
2---0.08 Å20 Å2
3---0.13 Å2
Refinement stepCycle: LAST / Resolution: 2.25→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3436 0 0 284 3720
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0223523
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4181.944788
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9975433
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.75124.54174
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.34415573
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.5631520
X-RAY DIFFRACTIONr_chiral_restr0.10.2515
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022734
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2060.21399
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2980.22309
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1850.2263
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1960.260
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1870.217
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.94272228
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.96393503
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.56671487
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.85891285
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.25→2.31 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.464 82
Rwork0.296 1260
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)
14.7729-0.26521.127.08230.26643.94350.042-0.0072-0.28360.34140.1258-0.2950.21920.3794-0.1678-0.11750.0256-0.0226-0.2358-0.0358-0.2473113.3673-4.8942-71.7045
28.84921.8669-1.18056.3867-0.07454.59620.2821-0.35830.49980.5864-0.20780.5897-0.3872-0.2639-0.07430.05330.1090.0368-0.2458-0.0554-0.085483.43397.9416-80.4552
39.9837-0.3031-0.08513.33841.14613.6670.126-0.09160.06920.51570.1269-0.17270.24260.16-0.25290.09490.0874-0.0237-0.2825-0.0065-0.1734105.1721-25.8042-74.5043
42.45350.14660.10553.9506-0.85843.521-0.1395-0.0665-0.00250.35510.11250.3149-0.1278-0.41470.027-0.17290.06080.0429-0.2111-0.0553-0.194382.0501-8.1747-85.0906
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 111
2X-RAY DIFFRACTION2A112 - 193
3X-RAY DIFFRACTION3B3 - 105
4X-RAY DIFFRACTION4B106 - 245

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