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

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Basic information

Entry
Database: PDB / ID: 6fra
TitleF11 T-Cell Receptor Recognising PKYVKQNTLKLAT Peptide Presented by HLA-DR*0101
Components
  • Human T-Cell Receptor F11 alpha Chain
  • Human T-Cell Receptor F11 beta Chain
KeywordsIMMUNE SYSTEM / T Cell Receptor / Human Leukocyte Antigen / Influenza Epitope / Haemagglutinin / 3D Structure
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.73 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 1.3Oct 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 T-Cell Receptor F11 alpha Chain
B: Human T-Cell Receptor F11 beta Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,63417
Polymers49,5332
Non-polymers1,10115
Water2,378132
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7050 Å2
ΔGint-62 kcal/mol
Surface area21220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.710, 114.630, 50.660
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 F11 alpha Chain


Mass: 22324.887 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 F11 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.: 10 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 132 / 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: 51.04 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 30% PEG 8K, 0.1M MES, 0.2M Na Acetate

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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: 1.73→47.64 Å / Num. obs: 52808 / % possible obs: 99.9 % / Redundancy: 6.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.06 / Rrim(I) all: 0.065 / Net I/σ(I): 19.2
Reflection shellResolution: 1.73→1.78 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.783 / Num. unique obs: 3853 / Rrim(I) all: 0.847 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
XDSdata reduction
UCSD-systemdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6EH6

6eh6


Resolution: 1.73→47.64 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.933 / SU B: 5.081 / SU ML: 0.082 / Cross valid method: THROUGHOUT / ESU R: 0.116 / ESU R Free: 0.117 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24339 2690 5.1 %RANDOM
Rwork0.2034 ---
obs0.20545 50066 99.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 29.76 Å2
Baniso -1Baniso -2Baniso -3
1-0.52 Å2-0 Å2-0 Å2
2--1.6 Å20 Å2
3----2.12 Å2
Refinement stepCycle: 1 / Resolution: 1.73→47.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3487 0 65 132 3684
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0193664
X-RAY DIFFRACTIONr_bond_other_d0.0020.023338
X-RAY DIFFRACTIONr_angle_refined_deg2.0381.9514974
X-RAY DIFFRACTIONr_angle_other_deg0.9553.0037695
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9145452
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.45224.335173
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.39915591
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3871520
X-RAY DIFFRACTIONr_chiral_restr0.1360.2538
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0214152
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.731→1.776 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.29 211 -
Rwork0.264 3631 -
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)
15.42770.157-0.94671.07260.30491.34610.01430.0878-0.05910.0066-0.02380.0982-0.1111-0.14740.00950.05050.0335-0.02050.0279-0.00410.1351-24.93415.3475-21.8653
23.0699-1.6204-0.41054.21911.03924.384-0.157-0.28460.00910.23570.2255-0.1773-0.20630.2366-0.06840.0503-0.00350.00840.0413-0.01650.17818.040111.5736-15.3847
33.7735-0.19821.76580.7686-0.17071.73830.0563-0.00740.01940.0793-0.05250.0943-0.0948-0.0707-0.00390.10560.02460.0220.03650.00050.1512-30.135916.0594-0.7856
41.5817-0.5109-2.29462.07591.75746.63850.1890.02590.0128-0.4027-0.0526-0.0334-0.694-0.0002-0.13640.13750.0031-0.02870.0047-0.01040.1534-0.253824.2544-7.4198
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 113
2X-RAY DIFFRACTION2A114 - 206
3X-RAY DIFFRACTION3B1 - 114
4X-RAY DIFFRACTION4B115 - 242

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