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

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Basic information

Entry
Database: PDB / ID: 2cde
TitleStructure and binding kinetics of three different human CD1d-alpha- Galactosylceramide specific T cell receptors - iNKT-TCR
Components(INKT-TCR) x 2
KeywordsCELL RECEPTOR / T CELL RECEPTOR / TCR / NATURAL KILLER T CELL / CD1D / ALPHA- GALACTOSYLCERAMIDE / MHC CLASS I
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 / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Downstream TCR signaling / T cell receptor signaling pathway / adaptive immune response ...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 / 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
: / 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 ...: / 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 beta constant 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 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 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 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 1.4Nov 20, 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: INKT-TCR
B: INKT-TCR
C: INKT-TCR
D: INKT-TCR
E: INKT-TCR
F: INKT-TCR


Theoretical massNumber of molelcules
Total (without water)147,1456
Polymers147,1456
Non-polymers00
Water00
1
A: INKT-TCR
B: INKT-TCR


Theoretical massNumber of molelcules
Total (without water)49,0482
Polymers49,0482
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
C: INKT-TCR
D: INKT-TCR


Theoretical massNumber of molelcules
Total (without water)49,0482
Polymers49,0482
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
E: INKT-TCR
F: INKT-TCR


Theoretical massNumber of molelcules
Total (without water)49,0482
Polymers49,0482
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)289.360, 84.950, 78.860
Angle α, β, γ (deg.)90.00, 103.30, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.844404, 0.535675, -0.005903), (-0.5355, -0.843719, 0.037117), (0.014903, 0.034503, 0.999293)262.5757, 214.3092, 14.4407
2given(0.839673, -0.542482, -0.025737), (-0.541724, -0.839979, 0.031155), (-0.038519, -0.012217, -0.999183)10.334, 215.7126, 65.4295

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Components

#1: Antibody INKT-TCR


Mass: 21345.570 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: HUMAN INVARIANT NATURAL KILLER T CELL RECEPTOR VALPHA 24 AND VBETA11
Source: (gene. exp.) HOMO SAPIENS (human) / Cell: NATURAL KILLER T CELL / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
#2: Protein INKT-TCR


Mass: 27702.627 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: HUMAN INVARIANT NATURAL KILLER T CELL RECEPTOR VALPHA 24 AND VBETA11
Source: (gene. exp.) HOMO SAPIENS (human) / Cell: NATURAL KILLER T CELL / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P01850*PLUS
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: 3.26 Å3/Da / Density % sol: 61.99 %
Crystal growDetails: 0.5 M NACL, 11 % PEG 8000, 50 MM HEPES PH7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
DetectorType: ADSC CCD / Detector: CCD / Date: Aug 2, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 3.5→30 Å / Num. obs: 23622 / % possible obs: 98.1 % / Observed criterion σ(I): 0.5 / Redundancy: 3.2 % / Rmerge(I) obs: 0.18 / Net I/σ(I): 6.4
Reflection shellResolution: 3.5→3.62 Å / Rmerge(I) obs: 0.88 / Mean I/σ(I) obs: 1.4 / % possible all: 90.9

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1MI5

1mi5


Resolution: 3.5→30 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0.5 / Stereochemistry target values: RESIDUAL
RfactorNum. reflection% reflectionSelection details
Rfree0.3504 1193 5 %RANDOM
Rwork0.283 ---
obs0.283 23435 98.9 %-
Solvent computationBsol: 80 Å2 / ksol: 0.34 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-2.291 Å20 Å2-7.262 Å2
2---17.073 Å20 Å2
3---14.782 Å2
Refinement stepCycle: LAST / Resolution: 3.5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10330 0 0 0 10330
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005938
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.19976
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 3.5→3.66 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.375 142 5.2 %
Rwork0.347 2905 -
obs--34.66 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1PROTEIN_REP.PARAM
X-RAY DIFFRACTION2WATER_REP.PARAM

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