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- PDB-6eh5: 003 Human T-Cell Receptor specific for HIV GAG epitope SLYNTVATL ... -

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Basic information

Entry
Database: PDB / ID: 6eh5
Title003 Human T-Cell Receptor specific for HIV GAG epitope SLYNTVATL carried by Human Leukocyte Antigen HLA-A*0201
Components(Human T Cell Receptor ...) x 2
KeywordsIMMUNE SYSTEM / Human T Cell Receptor / Human Leukocute Antigen / Influenza Haemagglutinin epitope / 3D structure
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.29 Å
AuthorsRizkallah, P.J. / Cole, D.K.
CitationJournal: Front Immunol / Year: 2018
Title: In Silicoand Structural Analyses Demonstrate That Intrinsic Protein Motions Guide T Cell Receptor Complementarity Determining Region Loop Flexibility.
Authors: Holland, C.J. / MacLachlan, B.J. / Bianchi, V. / Hesketh, S.J. / Morgan, R. / Vickery, O. / Bulek, A.M. / Fuller, A. / Godkin, A. / Sewell, A.K. / Rizkallah, P.J. / Wells, S. / Cole, D.K.
History
DepositionSep 12, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 18, 2018Provider: repository / Type: Initial release
Revision 1.1May 9, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Dec 19, 2018Group: Advisory / Data collection / Derived calculations
Category: pdbx_validate_close_contact / struct_conn / struct_conn_type
Revision 1.3Oct 16, 2019Group: Data collection / Category: reflns_shell
Revision 1.4Jan 17, 2024Group: 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
Revision 1.5Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Human T Cell Receptor Alpha Chain
B: Human T Cell Receptor Beta Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,83933
Polymers49,6932
Non-polymers2,14631
Water8,755486
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10530 Å2
ΔGint56 kcal/mol
Surface area21280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.150, 81.170, 64.900
Angle α, β, γ (deg.)90.00, 90.33, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Human T Cell Receptor ... , 2 types, 2 molecules AB

#1: Protein Human T Cell Receptor Alpha Chain


Mass: 22241.654 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 Human T Cell Receptor Beta Chain


Mass: 27451.434 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)

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Non-polymers , 4 types, 517 molecules

#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 27 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 486 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.29 Å3/Da / Density % sol: 46.22 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 20% PEG 4K, 200mM Ammonium sulfate, 100mM Sodium cacodylate pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 17, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.29→50.69 Å / Num. obs: 106513 / % possible obs: 94.9 % / Redundancy: 3.7 % / Biso Wilson estimate: 13.4 Å2 / Net I/σ(I): 16.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
xia2data reduction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4GKZ

4gkz


Resolution: 1.29→50.69 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.96 / SU B: 1.677 / SU ML: 0.036 / Cross valid method: THROUGHOUT / ESU R: 0.051 / ESU R Free: 0.054 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19503 5313 5 %RANDOM
Rwork0.16821 ---
obs0.16957 101171 94.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 18.944 Å2
Baniso -1Baniso -2Baniso -3
1-0.12 Å2-0 Å20.16 Å2
2---0.27 Å2-0 Å2
3---0.15 Å2
Refinement stepCycle: 1 / Resolution: 1.29→50.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3497 0 139 486 4122
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0350.0193916
X-RAY DIFFRACTIONr_bond_other_d0.0060.023623
X-RAY DIFFRACTIONr_angle_refined_deg2.6921.9525288
X-RAY DIFFRACTIONr_angle_other_deg1.37638367
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0875496
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.48824.346191
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.17515628
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8721527
X-RAY DIFFRACTIONr_chiral_restr0.170.2560
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.0214509
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02946
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0140.8791877
X-RAY DIFFRACTIONr_mcbond_other1.0010.8781876
X-RAY DIFFRACTIONr_mcangle_it1.5731.3172371
X-RAY DIFFRACTIONr_mcangle_other1.5751.3182372
X-RAY DIFFRACTIONr_scbond_it2.3331.1822039
X-RAY DIFFRACTIONr_scbond_other2.3331.1822039
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.9571.6252905
X-RAY DIFFRACTIONr_long_range_B_refined6.6489.4774628
X-RAY DIFFRACTIONr_long_range_B_other6.6479.4834629
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.29→1.324 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.267 274 -
Rwork0.25 5151 -
obs--65.31 %
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)
11.11570.1093-0.10150.956-0.45021.9374-0.0484-0.07330.0070.1248-0.04270.0002-0.00290.02560.09120.0251-0.0018-0.00750.05220.00230.0481-16.6978-7.722481.0042
22.1944-1.53840.36913.1038-0.68151.54870.02720.1153-0.1285-0.09220.03270.16620.0446-0.1013-0.05990.0056-0.0004-0.00950.1075-0.01510.026-0.7891-25.079655.5555
31.3569-0.6359-0.31312.69320.34791.1846-0.0283-0.04590.0935-0.04930.0010.0323-0.0354-0.07180.02730.03440.0041-0.00810.0577-0.00180.01130.9467-13.119694.0537
40.9591-0.23680.46271.2925-0.78092.9598-0.01410.073-0.04930.1056-0.01270.01890.11980.00450.02680.0227-0.00040.00490.0463-0.01390.006111.6703-21.726567.2638
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 113
2X-RAY DIFFRACTION2A114 - 203
3X-RAY DIFFRACTION3B1 - 115
4X-RAY DIFFRACTION4B116 - 244

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