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- PDB-6eh7: F11 Human T-Cell Receptor specific for influenza virus haaemagglu... -

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Basic information

Entry
Database: PDB / ID: 6eh7
TitleF11 Human T-Cell Receptor specific for influenza virus haaemagglutinin epitope PKYVKQNTLKLAT carried 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 / DI(HYDROXYETHYL)ETHER
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 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 ...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 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: Human T Cell Receptor Alpha Chain
B: Human T Cell Receptor Beta Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,60316
Polymers49,6462
Non-polymers95714
Water3,063170
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7450 Å2
ΔGint22 kcal/mol
Surface area20490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.420, 114.480, 50.630
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Human T Cell Receptor Alpha Chain


Mass: 22438.043 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: AQSVTQLGSHVSVSEGALVLLRCNYSSSVPPYLFWYVQYPNQGLQLLLKYTSAATLVKGINGFEAEFKKSETSFHLTKPSAHMSDAAEYFCAVSE QDDKIIFGKGTRLHILPNIQNPDPAVYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWSNKSDFACANAFNNSIIP EDTFFPS
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#2: Protein Human T Cell Receptor Beta Chain


Mass: 27208.246 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.: 12 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 170 / 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: 4.57 Å3/Da / Density % sol: 73.09 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 25% PEG 1.5K, 100mM SPG buffer pH 6.0

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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 S 6M / Detector: PIXEL / Date: Oct 13, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.89→46.3 Å / Num. obs: 37906 / % possible obs: 98.7 % / Redundancy: 6.5 % / Biso Wilson estimate: 28.5 Å2 / Net I/σ(I): 22.3
Reflection shellResolution: 1.89→1.94 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.706 / Mean I/σ(I) obs: 2.8 / Num. unique all: 2005 / CC1/2: 0.852 / Rrim(I) all: 0.765 / % possible all: 98.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
xia2data reduction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4GKZ

4gkz


Resolution: 1.89→46.3 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.943 / SU B: 7.141 / SU ML: 0.103 / Cross valid method: THROUGHOUT / ESU R: 0.144 / ESU R Free: 0.141 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23211 2005 5 %RANDOM
Rwork0.18532 ---
obs0.18763 37906 98.39 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 33.942 Å2
Baniso -1Baniso -2Baniso -3
1-0.52 Å2-0 Å20 Å2
2--0.33 Å2-0 Å2
3----0.86 Å2
Refinement stepCycle: 1 / Resolution: 1.89→46.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3493 0 62 170 3725
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0193631
X-RAY DIFFRACTIONr_bond_other_d0.0020.023337
X-RAY DIFFRACTIONr_angle_refined_deg1.9261.9464903
X-RAY DIFFRACTIONr_angle_other_deg0.88637694
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2385440
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.0324.419172
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.18115584
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.8871519
X-RAY DIFFRACTIONr_chiral_restr0.1230.2528
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0214104
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02853
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_it2.2612.1861766
X-RAY DIFFRACTIONr_mcbond_other2.2612.1851765
X-RAY DIFFRACTIONr_mcangle_it3.3933.2642204
X-RAY DIFFRACTIONr_mcangle_other3.3933.2662205
X-RAY DIFFRACTIONr_scbond_it2.9872.571864
X-RAY DIFFRACTIONr_scbond_other2.9822.571864
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.543.6752699
X-RAY DIFFRACTIONr_long_range_B_refined7.24718.5363929
X-RAY DIFFRACTIONr_long_range_B_other7.24818.5453930
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.89→1.939 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.29 146 -
Rwork0.244 2763 -
obs--98.34 %
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)
12.81570.0742-0.42740.4292-0.28740.25080.1557-0.0958-0.10340.0663-0.13760.0052-0.06120.0888-0.0180.049-0.0568-0.01340.09930.02060.0983-17.71575.3423-3.5384
20.30830.6597-0.4081.4218-0.9151.4699-0.04940.0615-0.025-0.08690.1441-0.0283-0.0237-0.2296-0.09480.0403-0.00180.02940.11060.00850.0917-50.734411.6464-9.7663
31.26250.03940.41110.1768-0.16860.50510.0909-0.0902-0.0514-0.059-0.0555-0.0426-0.0195-0.0019-0.03540.11310.00480.03730.0930.00370.0826-12.703416.0367-24.5376
40.40690.1899-1.08350.9926-0.97073.17140.1050.0725-0.01840.2552-0.1193-0.0363-0.4235-0.09620.01420.1323-0.01940.00520.0635-0.00770.0639-42.403224.2945-17.8937
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 113
2X-RAY DIFFRACTION2A114 - 202
3X-RAY DIFFRACTION3B1 - 114
4X-RAY DIFFRACTION4B115 - 240

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