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- PDB-2vlm: The Structural Dynamics and Energetics of an Immunodominant T-cel... -

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Basic information

Entry
Database: PDB / ID: 2vlm
TitleThe Structural Dynamics and Energetics of an Immunodominant T-cell Receptor are Programmed by its Vbeta Domain
Components
  • JM22 TCR ALPHA CHAIN
  • JM22 TCR BETA CHAIN
KeywordsIMMUNE SYSTEM / HOST-VIRUS INTERACTION / IMMUNE SYSTEM-RECEPTOR-COMPLEX / IMMUNODOMINANCE / IMMUNOGLOBULIN DOMAIN / TCR / MHC / FLU / MHC I / T-CELL / COMPLEX / MEMBRANE / RECEPTOR / IMMUNE RESPONSE
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 Å
AuthorsIshizuka, J. / Stewart-Jones, G. / Van der Merwe, A. / Bell, J. / McMichael, A. / Jones, Y.
CitationJournal: Immunity / Year: 2008
Title: The Structural Dynamics and Energetics of an Immunodominant T-Cell Receptor are Programmed by its Vbeta Domain
Authors: Ishizuka, J. / Stewart-Jones, G. / Van Der Merwe, A. / Bell, J. / Mcmichael, A. / Jones, Y.
History
DepositionJan 15, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 22, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
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
D: JM22 TCR ALPHA CHAIN
E: JM22 TCR BETA CHAIN


Theoretical massNumber of molelcules
Total (without water)49,8102
Polymers49,8102
Non-polymers00
Water6,071337
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3840 Å2
ΔGint-27.4 kcal/mol
Surface area24810 Å2
MethodPQS
Unit cell
Length a, b, c (Å)87.371, 87.371, 110.397
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein JM22 TCR ALPHA CHAIN


Mass: 22040.574 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli)
#2: Protein JM22 TCR BETA CHAIN


Mass: 27769.723 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 337 / 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

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Sample preparation

CrystalDensity Matthews: 2.36 Å3/Da / Density % sol: 47.52 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.98→30 Å / Num. obs: 31111 / % possible obs: 93.3 % / Observed criterion σ(I): 1.9 / Redundancy: 30.1 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 36.1
Reflection shellResolution: 1.98→2.03 Å / Rmerge(I) obs: 0.68 / Mean I/σ(I) obs: 3.9 / % possible all: 99.4

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Processing

SoftwareName: REFMAC / Version: 5.2.0019 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.98→28.15 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.912 / SU B: 9.275 / SU ML: 0.138 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.227 / ESU R Free: 0.213 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.279 1486 5.1 %RANDOM
Rwork0.204 ---
obs0.208 27792 88.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.3 Å2
Baniso -1Baniso -2Baniso -3
1-0.1 Å20.05 Å20 Å2
2--0.1 Å20 Å2
3----0.14 Å2
Refinement stepCycle: LAST / Resolution: 1.98→28.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3341 0 0 337 3678
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0223425
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4921.9414654
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3155420
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.50324.852169
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.91315550
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.361517
X-RAY DIFFRACTIONr_chiral_restr0.1140.2500
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022659
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2250.21457
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3070.22281
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1630.2284
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1970.249
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.180.216
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8551.52172
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.41123414
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.17931447
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.264.51240
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: 1.98→2.03 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.375 145
Rwork0.236 2261
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)
13.35410.847-0.44561.0683-0.28462.23430.14040.0795-0.00430.0323-0.043-0.05980.01050.0768-0.0974-0.08780.03010.0064-0.04530.0084-0.039810.859740.177551.4349
28.00513.06544.5175.2991.97325.2042-0.3228-0.19880.8869-0.3563-0.07810.5446-0.3843-0.49670.4009-0.13810.026-0.040.03240.0050.0602-3.403236.676381.431
31.67610.0617-2.50481.79021.49928.17840.1639-0.06010.03110.0098-0.0767-0.0438-0.49070.3262-0.0872-0.0945-0.0250.0132-0.026-0.0065-0.038628.525652.607561.3869
40.8580.3459-0.2031.29850.34711.27370.0551-0.1479-0.0419-0.06580.0271-0.10920.00150.0767-0.0822-0.08060.0273-0.0115-0.0198-0.0144-0.010814.44437.699685.2181
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1D3 - 115
2X-RAY DIFFRACTION2D116 - 201
3X-RAY DIFFRACTION3E5 - 115
4X-RAY DIFFRACTION4E116 - 244

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