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

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Basic information

Entry
Database: PDB / ID: 6fun
TitleF11 T-Cell Receptor Recognising PKYVKQNTLKLAT Peptide Presented by HLA-DR*0101
Components(Human F11 T-Cell Receptor ...) 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: 1.58 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: Derived calculations / Structure summary / Category: entity / pdbx_struct_special_symmetry / 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 1.4Nov 6, 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)50,73718
Polymers49,6462
Non-polymers1,09116
Water7,008389
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7320 Å2
ΔGint-23 kcal/mol
Surface area20740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.080, 115.300, 50.650
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-310-

GOL

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Components

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Human F11 T-Cell Receptor ... , 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 , 4 types, 405 molecules

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


Mass: 62.068 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 389 / 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: 2.5 Å3/Da / Density % sol: 50.84 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.2M Na Malonate, 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: 1.58→46.37 Å / Num. obs: 69019 / % possible obs: 99 % / Redundancy: 6.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.041 / Rrim(I) all: 0.045 / Net I/σ(I): 23.6
Reflection shellResolution: 1.58→1.62 Å / Redundancy: 7 % / Rmerge(I) obs: 0.654 / Mean I/σ(I) obs: 3.1 / Num. unique obs: 5006 / CC1/2: 0.841 / Rrim(I) all: 0.707 / % possible all: 100

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Processing

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

6eh6


Resolution: 1.58→46.37 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.952 / SU B: 3.085 / SU ML: 0.055 / Cross valid method: THROUGHOUT / ESU R: 0.08 / ESU R Free: 0.083 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20743 3488 5.1 %RANDOM
Rwork0.17375 ---
obs0.17542 65474 99.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 26.652 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å20 Å20 Å2
2--0.3 Å2-0 Å2
3----0.36 Å2
Refinement stepCycle: 1 / Resolution: 1.58→46.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3493 0 68 389 3950
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0193783
X-RAY DIFFRACTIONr_bond_other_d0.0020.023366
X-RAY DIFFRACTIONr_angle_refined_deg1.9041.9475135
X-RAY DIFFRACTIONr_angle_other_deg1.0583.0027849
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7035.021473
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.11124.407177
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.07115616
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.9851520
X-RAY DIFFRACTIONr_chiral_restr0.1220.2553
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0214231
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02785
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_it1.1121.5741837
X-RAY DIFFRACTIONr_mcbond_other1.1091.5721836
X-RAY DIFFRACTIONr_mcangle_it1.7962.3542314
X-RAY DIFFRACTIONr_mcangle_other1.7962.3562315
X-RAY DIFFRACTIONr_scbond_it1.6381.8261942
X-RAY DIFFRACTIONr_scbond_other1.6371.8261942
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.4242.6372817
X-RAY DIFFRACTIONr_long_range_B_refined6.8719.7254055
X-RAY DIFFRACTIONr_long_range_B_other6.8719.7384056
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.58→1.621 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.274 246 -
Rwork0.239 4752 -
obs--99.98 %
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)
15.08410.0788-1.01381.01320.25021.35340.07240.1737-0.0628-0.0502-0.03890.1407-0.0483-0.0705-0.03350.02370.0262-0.01420.0308-0.01430.03-25.02835.3357-21.7048
22.5776-1.5327-0.11123.90150.28033.4778-0.104-0.2019-0.04350.2430.1589-0.2116-0.08110.1822-0.05490.0190.0022-0.00680.0469-0.00540.05468.045511.7305-15.5822
33.6715-0.44391.62810.904-0.33531.77870.0659-0.02870.06310.1032-0.07710.0919-0.0583-0.02050.01120.04390.00540.01520.0266-0.01380.0152-29.79216.258-0.7161
41.3957-0.2538-1.7741.56120.73845.30720.0777-0.0543-0.0266-0.2056-0.0136-0.0072-0.3690.0237-0.0640.06170.009-0.00770.0053-0.0030.0162-0.140624.2921-7.4829
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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