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- PDB-6eh9: HA1.7 Human T-Cell Receptor specific for Influenza virus epitope ... -

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Basic information

Entry
Database: PDB / ID: 6eh9
TitleHA1.7 Human T-Cell Receptor specific for Influenza virus epitope PKYVKQNTLKLAT presented by Human Leukocyte Antigen HLA-DR0101
Components
  • Human T Cell Receptor Alpha Chain
  • Human T Cell Receptor Beta Chain
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: 2.49 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 1.2Jan 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 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)49,8982
Polymers49,8982
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4060 Å2
ΔGint-22 kcal/mol
Surface area20960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.460, 49.960, 72.750
Angle α, β, γ (deg.)90.00, 93.08, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Human T Cell Receptor Alpha Chain


Mass: 22362.955 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: 27534.910 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)
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: 2.53 Å3/Da / Density % sol: 51.31 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 15% PEG 4K, 15% Glycerol, 100mM MES pH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9173 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 9, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9173 Å / Relative weight: 1
ReflectionResolution: 2.49→48.87 Å / Num. obs: 17434 / % possible obs: 98.5 % / Redundancy: 3.7 % / Biso Wilson estimate: 64.5 Å2 / Net I/σ(I): 17.5
Reflection shellResolution: 2.49→2.55 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 2.3 / Num. unique all: 1273 / Rpim(I) all: 0.353 / Rrim(I) all: 0.703 / % possible all: 99.2

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
xia2data reduction
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4GKZ

4gkz


Resolution: 2.49→48.87 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.9 / SU B: 29.803 / SU ML: 0.302 / Cross valid method: THROUGHOUT / ESU R: 0.709 / ESU R Free: 0.349 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29651 881 5.1 %RANDOM
Rwork0.23225 ---
obs0.23539 16545 98.25 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 65.654 Å2
Baniso -1Baniso -2Baniso -3
1--0.31 Å20 Å2-0.58 Å2
2--1.81 Å2-0 Å2
3----1.46 Å2
Refinement stepCycle: 1 / Resolution: 2.49→48.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3505 0 0 0 3505
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0193617
X-RAY DIFFRACTIONr_bond_other_d0.0010.023314
X-RAY DIFFRACTIONr_angle_refined_deg1.6451.9424913
X-RAY DIFFRACTIONr_angle_other_deg0.863.0037639
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5455445
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.7924.235170
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.98615599
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.0641519
X-RAY DIFFRACTIONr_chiral_restr0.0980.2533
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214123
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02862
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_it0.6520.3061777
X-RAY DIFFRACTIONr_mcbond_other0.6520.3061776
X-RAY DIFFRACTIONr_mcangle_it1.0710.4572220
X-RAY DIFFRACTIONr_mcangle_other1.0710.4572221
X-RAY DIFFRACTIONr_scbond_it0.410.3091840
X-RAY DIFFRACTIONr_scbond_other0.410.3091841
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.6440.4582693
X-RAY DIFFRACTIONr_long_range_B_refined2.8992.4163877
X-RAY DIFFRACTIONr_long_range_B_other2.8992.4163878
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.49→2.555 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.479 65 -
Rwork0.336 1205 -
obs--99.06 %
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)
15.01420.80410.66623.6012-0.14548.9441-0.01380.00260.22270.1826-0.16330.119-0.1444-0.05650.17710.31560.00380.03330.0099-0.01560.5146-0.80476.04835.3285
210.4495-3.08710.19386.1992-1.1457.9964-0.20730.4867-0.2934-0.54420.297-0.7170.55150.7688-0.08970.7359-0.04160.08521.2553-0.20950.456318.93313.80736.4402
38.6044-4.0839-2.4166.19972.59285.0246-0.244-0.34490.50370.36820.3468-0.80030.01561.381-0.10280.4359-0.0271-0.11620.64570.08740.424519.65410.021846.7961
44.59290.07533.73582.28250.12498.5951-0.44350.7864-0.0133-0.23370.25-0.3276-0.96971.09370.19350.6063-0.28810.07121.1901-0.13510.489426.561114.066317.0768
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 117
2X-RAY DIFFRACTION2A118 - 201
3X-RAY DIFFRACTION3B2 - 117
4X-RAY DIFFRACTION4B118 - 242

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