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

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Basic information

Entry
Database: PDB / ID: 6fuo
TitleF11 T-Cell Receptor Recognising PKYVKQNTLKLAT Peptide Presented by HLA-DR*0101
Components(Human F11 T-Cell ...) x 2
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: 1.7 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 1.2Jan 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 1.3Nov 20, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,74932
Polymers49,6462
Non-polymers2,10230
Water6,503361
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10720 Å2
ΔGint45 kcal/mol
Surface area20420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.390, 115.190, 50.780
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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Human F11 T-Cell ... , 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


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, 391 molecules

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


Mass: 62.068 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#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: 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.: 361 / 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: 2.52 Å3/Da / Density % sol: 51.1 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.2 M Na Acetate, 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: 1.7→46.47 Å / Num. obs: 55910 / % possible obs: 99.1 % / Redundancy: 6.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.045 / Rrim(I) all: 0.049 / Net I/σ(I): 22.7
Reflection shellResolution: 1.7→1.74 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.627 / Mean I/σ(I) obs: 3.2 / Num. unique obs: 4094 / CC1/2: 0.867 / Rrim(I) all: 0.678 / % possible all: 99.7

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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: 1.7→46.47 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.958 / SU B: 4.193 / SU ML: 0.069 / Cross valid method: THROUGHOUT / ESU R: 0.097 / ESU R Free: 0.096 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19984 2835 5.1 %RANDOM
Rwork0.16836 ---
obs0.16999 53022 99.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 29.631 Å2
Baniso -1Baniso -2Baniso -3
1-0.15 Å2-0 Å2-0 Å2
2--0.19 Å2-0 Å2
3----0.35 Å2
Refinement stepCycle: 1 / Resolution: 1.7→46.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3495 0 135 361 3991
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0193798
X-RAY DIFFRACTIONr_bond_other_d0.0020.023394
X-RAY DIFFRACTIONr_angle_refined_deg1.9221.9555122
X-RAY DIFFRACTIONr_angle_other_deg1.07837923
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2295470
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.28524.514175
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.17615605
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.1591519
X-RAY DIFFRACTIONr_chiral_restr0.1280.2548
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0214203
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02772
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_it1.2471.7431826
X-RAY DIFFRACTIONr_mcbond_other1.2431.741825
X-RAY DIFFRACTIONr_mcangle_it2.0292.6062299
X-RAY DIFFRACTIONr_mcangle_other2.032.6082300
X-RAY DIFFRACTIONr_scbond_it1.8682.1011970
X-RAY DIFFRACTIONr_scbond_other1.8592.0831966
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.7432.9492813
X-RAY DIFFRACTIONr_long_range_B_refined6.98722.4364054
X-RAY DIFFRACTIONr_long_range_B_other6.98622.4474055
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.261 198 -
Rwork0.23 3891 -
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)
16.00640.083-1.21511.2378-0.41321.53580.0847-0.2034-0.09570.0536-0.055-0.1575-0.06980.1106-0.02970.0158-0.0277-0.00940.05080.01370.0315110.4957120.487821.7021
22.4561.4718-0.50654.3645-0.76473.466-0.0810.1734-0.1192-0.21650.15380.22070.0001-0.2534-0.07280.0126-0.0009-0.00640.06010.00240.041177.3396126.976615.6064
34.00750.41381.95270.8160.4492.06650.06620.01020.0596-0.106-0.0934-0.0997-0.08840.0710.02720.0363-0.01160.01750.04710.01070.0176115.2666131.41460.6735
41.52850.3909-2.0471.6236-0.85346.03950.13070.0537-0.00740.2546-0.05130.0211-0.4644-0.0301-0.07950.067-0.0090.00330.00630.00050.008285.5757139.53347.4802
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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