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

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Basic information

Entry
Database: PDB / ID: 6frb
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: 1.75 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 1.3Oct 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


Theoretical massNumber of molelcules
Total (without water)49,6462
Polymers49,6462
Non-polymers00
Water1,802100
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4140 Å2
ΔGint-28 kcal/mol
Surface area21160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.160, 115.430, 50.480
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: 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 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 100 / 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: 2.5 Å3/Da / Density % sol: 50.78 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 0.1M SPG Buffer, 25% PEG 1500

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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: 1.75→47.78 Å / Num. obs: 50657 / % possible obs: 99.9 % / Redundancy: 6.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.058 / Rrim(I) all: 0.064 / Net I/σ(I): 18.5
Reflection shellResolution: 1.75→1.8 Å / Redundancy: 6.8 % / Rmerge(I) obs: 1.161 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 3716 / CC1/2: 0.711 / Rrim(I) all: 1.258 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
xia2data reduction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6EH6

6eh6


Resolution: 1.75→47.78 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.937 / SU B: 6.358 / SU ML: 0.095 / Cross valid method: THROUGHOUT / ESU R: 0.123 / ESU R Free: 0.119 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24314 2569 5.1 %RANDOM
Rwork0.20988 ---
obs0.21153 48036 99.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 32.091 Å2
Baniso -1Baniso -2Baniso -3
1-2.79 Å20 Å2-0 Å2
2--0.17 Å2-0 Å2
3----2.96 Å2
Refinement stepCycle: 1 / Resolution: 1.75→47.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3495 0 0 100 3595
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0193619
X-RAY DIFFRACTIONr_bond_other_d0.0020.023293
X-RAY DIFFRACTIONr_angle_refined_deg2.0861.9414931
X-RAY DIFFRACTIONr_angle_other_deg0.9633.0047592
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.825452
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.01224.419172
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.94315590
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.4951519
X-RAY DIFFRACTIONr_chiral_restr0.1290.2534
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0214168
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02861
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: 1.754→1.799 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.342 196 -
Rwork0.308 3511 -
obs--99.89 %
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)
15.01960.028-0.99551.085-0.30131.54410.1214-0.1406-0.0670.0513-0.0803-0.1463-0.09120.124-0.04110.0248-0.0477-0.03090.11650.0120.1987-17.64395.4317-3.6832
22.17061.0127-0.39484.3458-0.63213.4692-0.08750.169-0.1012-0.30270.14710.1233-0.0231-0.2468-0.05950.0241-0.00350.00980.12050.00150.2144-50.59511.6747-9.8239
33.66290.30631.72241.07310.23611.9230.05270.0391-0.0074-0.1108-0.0438-0.1126-0.10590.0876-0.00890.0292-0.01410.02720.11520.00350.1907-12.670116.2574-24.5148
41.43590.178-1.86871.4669-0.92415.95540.07910.0236-0.01520.2582-0.0406-0.0236-0.4601-0.0297-0.03850.07-0.0059-0.02940.05780.01320.1734-42.379324.3699-17.8326
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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