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- PDB-6fr8: HA1.7 Human T-Cell Receptor specific for Influenza virus epitope ... -

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Basic information

Entry
Database: PDB / ID: 6fr8
TitleHA1.7 Human T-Cell Receptor specific for Influenza virus epitope PKYVKQNTLKLAT presented by Human Leukocyte Antigen HLA-DR0101
Components
  • T-Cell Receptor HA1.7 alpha Chain
  • T-Cell Receptor HA1.7 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: 2.38 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 / 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 13, 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 HA1.7 alpha Chain
B: T-Cell Receptor HA1.7 beta Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,9943
Polymers49,8982
Non-polymers961
Water55831
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4100 Å2
ΔGint-40 kcal/mol
Surface area21220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.530, 49.880, 72.890
Angle α, β, γ (deg.)90.00, 94.26, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein T-Cell Receptor HA1.7 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 T-Cell Receptor HA1.7 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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 31 / 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: 2.53 Å3/Da / Density % sol: 51.31 %
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: I02 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jan 29, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.38→69.34 Å / Num. obs: 19994 / % possible obs: 98.8 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.065 / Rrim(I) all: 0.098 / Net I/σ(I): 9.9
Reflection shellResolution: 2.38→2.44 Å / Redundancy: 3.7 % / Rmerge(I) obs: 1.101 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 1444 / Rrim(I) all: 1.638 / % possible all: 99.6

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Processing

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

6eh8


Resolution: 2.38→69.34 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.912 / SU B: 27.531 / SU ML: 0.287 / Cross valid method: THROUGHOUT / ESU R: 0.472 / ESU R Free: 0.294 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27844 1019 5.1 %RANDOM
Rwork0.22195 ---
obs0.22493 18937 98.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 67.137 Å2
Baniso -1Baniso -2Baniso -3
1--0.49 Å20 Å2-0.91 Å2
2--3.37 Å20 Å2
3----2.72 Å2
Refinement stepCycle: 1 / Resolution: 2.38→69.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3505 0 5 31 3541
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0193631
X-RAY DIFFRACTIONr_bond_other_d0.0020.023217
X-RAY DIFFRACTIONr_angle_refined_deg1.9391.9424932
X-RAY DIFFRACTIONr_angle_other_deg1.08737502
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.5965447
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.0724.235170
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.00515603
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.51519
X-RAY DIFFRACTIONr_chiral_restr0.1140.2535
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0214051
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02764
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_it0.5981.5251782
X-RAY DIFFRACTIONr_mcbond_other0.5981.5251781
X-RAY DIFFRACTIONr_mcangle_it1.0782.2852228
X-RAY DIFFRACTIONr_mcangle_other1.0782.2852229
X-RAY DIFFRACTIONr_scbond_it0.7511.5611849
X-RAY DIFFRACTIONr_scbond_other0.5551.5481846
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.9072.3022698
X-RAY DIFFRACTIONr_long_range_B_refined4.7617.1833778
X-RAY DIFFRACTIONr_long_range_B_other4.75917.1883779
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.38→2.442 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.372 76 -
Rwork0.328 1352 -
obs--98.62 %
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)
13.9365-0.0081-0.52553.8362-0.26617.9531-0.09750.07640.0460.21760.01150.0478-0.1167-0.06650.0860.323-0.01610.08170.0027-0.00170.58767.57154.293936.2862
28.28-1.3172-0.07234.3836-0.16746.0647-0.08740.236-0.3634-0.2430.1057-0.16180.34310.4226-0.01830.7567-0.04970.08650.6213-0.04090.531787.45041.93686.5604
36.9645-2.7006-1.42554.79892.12683.7043-0.1444-0.11210.2270.21870.2048-0.3601-0.01020.9833-0.06040.38710.00820.05840.41180.04580.494287.78958.475547.3693
42.9009-0.61213.111.8466-0.58717.0812-0.28360.03940.1245-0.21390.1259-0.2484-0.43420.82030.15770.5798-0.1630.1830.7569-0.04210.654695.982111.956317.6248
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 113
2X-RAY DIFFRACTION2A114 - 201
3X-RAY DIFFRACTION3B2 - 114
4X-RAY DIFFRACTION4B115 - 242

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