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

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Basic information

Entry
Database: PDB / ID: 6fum
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 / 1-ETHOXY-2-(2-ETHOXYETHOXY)ETHANE
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.76 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 beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,1538
Polymers49,6462
Non-polymers5076
Water6,233346
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5820 Å2
ΔGint-24 kcal/mol
Surface area20940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.610, 114.180, 50.630
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 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, 352 molecules

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


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-P4G / 1-ETHOXY-2-(2-ETHOXYETHOXY)ETHANE


Mass: 162.227 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O3
#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.: 346 / 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: 2.49 Å3/Da / Density % sol: 50.65 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.2M Na/K PO4, 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: 1.76→46.28 Å / Num. obs: 49905 / % possible obs: 99.7 % / Redundancy: 6.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.058 / Rrim(I) all: 0.063 / Net I/σ(I): 17.4
Reflection shellResolution: 1.76→1.81 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.694 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 3658 / CC1/2: 0.854 / Rrim(I) all: 0.752 / % possible all: 99.9

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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: 1.76→46.28 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.95 / SU B: 5.608 / SU ML: 0.087 / Cross valid method: THROUGHOUT / ESU R: 0.115 / ESU R Free: 0.115 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22266 2530 5.1 %RANDOM
Rwork0.18132 ---
obs0.18341 47326 99.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 31.17 Å2
Baniso -1Baniso -2Baniso -3
1-0.4 Å20 Å20 Å2
2--1.03 Å2-0 Å2
3----1.44 Å2
Refinement stepCycle: 1 / Resolution: 1.76→46.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3493 0 32 346 3871
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0193694
X-RAY DIFFRACTIONr_bond_other_d0.0020.023280
X-RAY DIFFRACTIONr_angle_refined_deg1.881.9435027
X-RAY DIFFRACTIONr_angle_other_deg1.0533.0027653
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6125.021467
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.13824.432176
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.93415605
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.2611520
X-RAY DIFFRACTIONr_chiral_restr0.1190.2545
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0214137
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02767
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_it1.141.7461801
X-RAY DIFFRACTIONr_mcbond_other1.1391.7441800
X-RAY DIFFRACTIONr_mcangle_it1.8682.612258
X-RAY DIFFRACTIONr_mcangle_other1.8682.6122259
X-RAY DIFFRACTIONr_scbond_it1.4741.9571889
X-RAY DIFFRACTIONr_scbond_other1.4741.9581890
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.3222.8522759
X-RAY DIFFRACTIONr_long_range_B_refined6.29321.6553983
X-RAY DIFFRACTIONr_long_range_B_other6.29421.6663984
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.76→1.806 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.278 197 -
Rwork0.265 3450 -
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)
16.17290.0215-1.00311.17810.29671.2220.11160.154-0.095-0.06-0.08450.1808-0.113-0.129-0.02710.05740.0561-0.02560.0672-0.00970.078-25.0825.2812-21.8513
22.6039-1.4344-0.37344.66350.93454.018-0.12-0.2078-0.13560.26110.2089-0.1489-0.00890.3137-0.08890.02550.00270.0190.0447-0.01530.08217.966111.7021-15.4223
34.5428-0.31781.81680.9248-0.27342.14870.086-0.0022-0.03630.1245-0.06220.1705-0.1002-0.0838-0.02380.06080.02830.02930.0391-0.0070.0769-30.107415.949-0.7698
41.5266-0.2857-2.10451.63691.06326.50960.0946-0.0526-0.0206-0.2716-0.03160.0021-0.56220.0466-0.0630.09760.0089-0.02130.0041-0.00620.0465-0.350124.2112-7.3717
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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