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- PDB-6fup: F11 T-Cell Receptor Recognising PKYVKQNTLKLAT Peptide Presented b... -

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Basic information

Entry
Database: PDB / ID: 6fup
TitleF11 T-Cell Receptor Recognising PKYVKQNTLKLAT Peptide Presented by HLA-DR*0101
Components
  • Human F11 T-Cell Receptor beta chain
  • Human F11 T-cell Receptor alpha Chain
KeywordsIMMUNE SYSTEM / T Cell Receptor / Human Leukocyte Antigen / Influenza Epitope / Haemagglutinin / 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: 1.72 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 27, 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 1.2Nov 18, 2020Group: Structure summary / Category: entity / Item: _entity.pdbx_description
Revision 1.3Jan 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 1.4Oct 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 F11 T-cell Receptor alpha Chain
B: Human F11 T-Cell Receptor beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,79733
Polymers49,6462
Non-polymers2,15031
Water4,846269
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10450 Å2
ΔGint45 kcal/mol
Surface area20850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.280, 115.160, 50.710
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-425-

HOH

21A-498-

HOH

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Human F11 T-cell Receptor alpha Chain


Mass: 22438.043 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 F11 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)

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Non-polymers , 5 types, 300 molecules

#3: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 25 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 269 / 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: 2.51 Å3/Da / Density % sol: 50.95 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: PACT Premier E08: 0.2 M Na SO4, 20% PEG 3350

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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: 1.72→46.41 Å / Num. obs: 53476 / % possible obs: 98.6 % / Redundancy: 6.6 % / CC1/2: 1 / Rmerge(I) obs: 0.041 / Rrim(I) all: 0.045 / Net I/σ(I): 23.6
Reflection shellResolution: 1.72→1.77 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.741 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 3936 / CC1/2: 0.814 / Rrim(I) all: 0.802 / % possible all: 99.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
XDSdata reduction
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6EH6

6eh6


Resolution: 1.72→46.41 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.948 / SU B: 4.681 / SU ML: 0.075 / Cross valid method: THROUGHOUT / ESU R: 0.105 / ESU R Free: 0.106 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21484 2715 5.1 %RANDOM
Rwork0.17613 ---
obs0.17802 50709 99.38 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 33.454 Å2
Baniso -1Baniso -2Baniso -3
1--0.37 Å2-0 Å2-0 Å2
2--0.9 Å2-0 Å2
3----0.53 Å2
Refinement stepCycle: 1 / Resolution: 1.72→46.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3493 0 138 269 3900
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0193795
X-RAY DIFFRACTIONr_bond_other_d0.0020.023415
X-RAY DIFFRACTIONr_angle_refined_deg1.8471.9545117
X-RAY DIFFRACTIONr_angle_other_deg1.04837969
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7265470
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.23824.489176
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.82415609
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.7081519
X-RAY DIFFRACTIONr_chiral_restr0.1160.2550
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0214163
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02772
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_it1.3662.0261808
X-RAY DIFFRACTIONr_mcbond_other1.3582.0241807
X-RAY DIFFRACTIONr_mcangle_it2.1543.0282269
X-RAY DIFFRACTIONr_mcangle_other2.1543.032270
X-RAY DIFFRACTIONr_scbond_it1.9422.3771985
X-RAY DIFFRACTIONr_scbond_other1.9322.3651981
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.8263.3622830
X-RAY DIFFRACTIONr_long_range_B_refined6.42224.8534025
X-RAY DIFFRACTIONr_long_range_B_other6.42324.8644026
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.721→1.766 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.285 209 -
Rwork0.25 3717 -
obs--99.97 %
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)
15.6156-0.3134-1.3191.1805-0.2261.96990.0465-0.218-0.08010.0399-0.0202-0.1632-0.05830.0913-0.02630.0173-0.0302-0.00880.05840.01340.0314110.3697120.352321.6969
22.50961.5066-0.4324.5227-0.5484.3989-0.18730.2494-0.0705-0.23530.1780.1315-0.1622-0.20330.00940.0298-0.00180.00220.08570.00140.078377.1336127.141115.6796
34.73270.24491.78490.94290.23942.19310.07360.02190.1432-0.1013-0.1161-0.1167-0.15710.06530.04240.0416-0.0050.01750.02910.01440.0215115.016131.35670.6344
41.86120.2071-2.2061.8003-0.2725.92010.08410.0873-0.05330.2136-0.0335-0.0654-0.4274-0.0731-0.05060.0836-0.0093-0.02660.00660.00420.040285.4171139.57387.5834
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 113
2X-RAY DIFFRACTION2A114 - 215
3X-RAY DIFFRACTION3B0 - 114
4X-RAY DIFFRACTION4B115 - 250

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