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- PDB-6fr7: HA1.7 Human T-Cell Receptor specific for Influenza virus epitope ... -

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Basic information

Entry
Database: PDB / ID: 6fr7
TitleHA1.7 Human T-Cell Receptor specific for Influenza virus epitope PKYVKQNTLKLAT presented by Human Leukocyte Antigen HLA-DR0101
Components
  • T-Cell Receptor alpha chain
  • T-cell Rceceptor 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: 2.31 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
DepositionFeb 15, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 18, 2018Provider: repository / Type: Initial release
Revision 1.1May 9, 2018Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / citation ...chem_comp / citation / entity / pdbx_entity_nonpoly
Item: _chem_comp.name / _citation.journal_volume ..._chem_comp.name / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _entity.pdbx_description / _pdbx_entity_nonpoly.name
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 20, 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: T-Cell Receptor alpha chain
B: T-cell Rceceptor beta Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,2995
Polymers50,0452
Non-polymers2543
Water1,06359
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4550 Å2
ΔGint-51 kcal/mol
Surface area21900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.350, 49.850, 72.750
Angle α, β, γ (deg.)90.00, 94.45, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein T-Cell Receptor alpha chain


Mass: 22510.129 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 T-cell Rceceptor 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)
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 59 / 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: 2.51 Å3/Da / Density % sol: 50.9 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.2M KSCN, 0.1M Bis-Tris, 20% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 8, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.31→72.53 Å / Num. obs: 21302 / % possible obs: 97.1 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.077 / Rrim(I) all: 0.108 / Net I/σ(I): 9.2
Reflection shellResolution: 2.31→2.37 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.862 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 1562 / Rrim(I) all: 1.077 / % possible all: 97.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
XDSdata reduction
xia2data reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6EH8

6eh8


Resolution: 2.31→72.53 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.912 / SU B: 22.135 / SU ML: 0.25 / Cross valid method: THROUGHOUT / ESU R: 0.414 / ESU R Free: 0.279 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27707 1094 5.1 %RANDOM
Rwork0.21917 ---
obs0.2222 20191 96.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 58.711 Å2
Baniso -1Baniso -2Baniso -3
1-1.33 Å2-0 Å2-0.63 Å2
2--3.28 Å2-0 Å2
3----4.46 Å2
Refinement stepCycle: 1 / Resolution: 2.31→72.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3516 0 14 59 3589
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0193649
X-RAY DIFFRACTIONr_bond_other_d0.0020.023222
X-RAY DIFFRACTIONr_angle_refined_deg1.9381.9434956
X-RAY DIFFRACTIONr_angle_other_deg1.10237512
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.6785448
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.23124.244172
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.19515601
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.5851519
X-RAY DIFFRACTIONr_chiral_restr0.1140.2537
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0214069
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02770
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_it0.3070.951786
X-RAY DIFFRACTIONr_mcbond_other0.3070.951785
X-RAY DIFFRACTIONr_mcangle_it0.5571.4222233
X-RAY DIFFRACTIONr_mcangle_other0.5571.4232234
X-RAY DIFFRACTIONr_scbond_it0.5721.0011863
X-RAY DIFFRACTIONr_scbond_other0.2630.9681855
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.4471.4392711
X-RAY DIFFRACTIONr_long_range_B_refined5.99410.8353766
X-RAY DIFFRACTIONr_long_range_B_other5.92310.7663763
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.31→2.37 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.416 75 -
Rwork0.316 1482 -
obs--96.71 %
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)
13.05880.0821-0.04443.15140.23558.7757-0.06850.09070.04390.1822-0.03680.1344-0.2189-0.19170.10530.2925-0.01470.00880.0081-0.00090.5488-7.73755.7698108.7021
27.4439-0.4036-0.84.0517-0.0294.9301-0.02460.1936-0.286-0.27120.0165-0.35760.21220.49960.00810.6205-0.0502-0.00930.6646-0.01550.531911.98193.74378.7268
35.2909-2.9528-1.33354.98231.7633.1825-0.1847-0.06940.26540.22820.1596-0.4541-0.19991.12840.02510.3263-0.0785-0.08380.52350.10180.510212.28519.9178119.9129
42.965-0.52912.09431.5771-0.22144.4914-0.2168-0.19880.1441-0.23690.0486-0.2482-0.28260.38690.16820.4679-0.17770.02130.8247-0.02070.585520.490413.543190.1248
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 113
2X-RAY DIFFRACTION2A114 - 202
3X-RAY DIFFRACTION3B2 - 114
4X-RAY DIFFRACTION4B115 - 242

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