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- PDB-6fr9: F11 T-Cell Receptor Recognising PKYVKQNTLKLAT Peptide Presented b... -

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Basic information

Entry
Database: PDB / ID: 6fr9
TitleF11 T-Cell Receptor Recognising PKYVKQNTLKLAT Peptide Presented by HLA-DR*0101
Components(T-Cell Receptor F11 ...) x 2
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: 1.62 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 16, 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 F11 alpha chain
B: T-Cell Receptor F11 beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,33112
Polymers49,6462
Non-polymers68510
Water7,692427
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6330 Å2
ΔGint-19 kcal/mol
Surface area20940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.490, 115.360, 50.860
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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T-Cell Receptor F11 ... , 2 types, 2 molecules AB

#1: Protein 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 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)

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Non-polymers , 4 types, 437 molecules

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


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 427 / 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: 2.53 Å3/Da / Density % sol: 51.3 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 20% PEG 4K, 20% 2-Propanol, 0.1M HEPES

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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: 1.62→47.81 Å / Num. obs: 64727 / % possible obs: 99.9 % / Redundancy: 6.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.049 / Rrim(I) all: 0.053 / Net I/σ(I): 20.6
Reflection shellResolution: 1.62→1.66 Å / Redundancy: 7 % / Rmerge(I) obs: 0.768 / Num. unique obs: 4734 / CC1/2: 0.801 / Rrim(I) all: 0.833 / % possible all: 100

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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: 1.62→47.81 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.954 / SU B: 3.621 / SU ML: 0.064 / Cross valid method: THROUGHOUT / ESU R: 0.088 / ESU R Free: 0.09 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21144 3280 5.1 %RANDOM
Rwork0.17854 ---
obs0.18022 61390 99.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 26.873 Å2
Baniso -1Baniso -2Baniso -3
1-0.38 Å2-0 Å2-0 Å2
2--0.5 Å2-0 Å2
3----0.88 Å2
Refinement stepCycle: 1 / Resolution: 1.62→47.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3493 0 43 427 3963
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0193734
X-RAY DIFFRACTIONr_bond_other_d0.0020.023305
X-RAY DIFFRACTIONr_angle_refined_deg1.9021.9455082
X-RAY DIFFRACTIONr_angle_other_deg1.0633.0027713
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1175.021472
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.2324.576177
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.46115608
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8881519
X-RAY DIFFRACTIONr_chiral_restr0.1210.2551
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0214200
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02771
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_it1.0111.4931825
X-RAY DIFFRACTIONr_mcbond_other1.0081.4921824
X-RAY DIFFRACTIONr_mcangle_it1.6582.2322296
X-RAY DIFFRACTIONr_mcangle_other1.6582.2342297
X-RAY DIFFRACTIONr_scbond_it1.4851.6991907
X-RAY DIFFRACTIONr_scbond_other1.4811.6941903
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.2232.4562774
X-RAY DIFFRACTIONr_long_range_B_refined5.92619.0444025
X-RAY DIFFRACTIONr_long_range_B_other5.82618.3093937
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.62→1.662 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.267 243 -
Rwork0.252 4484 -
obs--100 %
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)
15.31890.0146-0.7931.14850.3721.29630.07440.1333-0.0799-0.0719-0.06610.1661-0.0752-0.0786-0.00830.03920.0218-0.0270.0172-0.01070.0591-25.12465.3584-21.7997
22.2047-1.148-0.50373.76290.86593.1268-0.0642-0.1774-0.09190.18670.1533-0.16670.00240.2316-0.08910.0196-0.00330.00220.0345-0.00790.07818.014511.745-15.5565
33.8623-0.82292.01080.811-0.452.09520.025-0.0573-0.02730.0982-0.03640.1236-0.0674-0.0250.01140.06160.00290.01060.0242-0.00980.0604-29.924416.269-0.7321
41.3685-0.3071-1.96531.37781.31636.03580.1142-0.0577-0.0242-0.2896-0.0645-0.0055-0.5602-0.0301-0.04970.10110.0214-0.020.0099-0.0040.0379-0.125524.296-7.4255
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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