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- PDB-6fr5: HA1.7 TCR Study of CDR Loop Flexibility -

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Basic information

Entry
Database: PDB / ID: 6fr5
TitleHA1.7 TCR Study of CDR Loop Flexibility
Components(TCR HA1.7 specific for FLU epitope PKYVKQNTLKLAT, ...) x 2
KeywordsIMMUNE SYSTEM / 003 TCR / CDR Flexibility / 3D Structure / MHC Class II
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / ACETATE ION
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.37 Å
AuthorsRizkallah, P.J. / Cole, D.K.
Citation
Journal: 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.
#1: Journal: To Be Published
Title: Flexibility Study of CDRs in 003 TCR
Authors: Rizkallah, P.J. / 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: TCR HA1.7 specific for FLU epitope PKYVKQNTLKLAT, alpha chain
B: TCR HA1.7 specific for FLU epitope PKYVKQNTLKLAT, beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,20624
Polymers49,6932
Non-polymers1,51322
Water6,828379
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8990 Å2
ΔGint18 kcal/mol
Surface area21150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.080, 81.180, 64.790
Angle α, β, γ (deg.)90.00, 90.37, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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TCR HA1.7 specific for FLU epitope PKYVKQNTLKLAT, ... , 2 types, 2 molecules AB

#1: Protein TCR HA1.7 specific for FLU epitope PKYVKQNTLKLAT, alpha chain


Mass: 22241.654 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 TCR HA1.7 specific for FLU epitope PKYVKQNTLKLAT, beta chain


Mass: 27451.434 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, 401 molecules

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


Mass: 62.068 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 379 / 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: 2.28 Å3/Da / Density % sol: 46.05 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.2M Na Citrate, 0.1M TrisHCl, 30% PEG 400

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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 6M / Detector: PIXEL / Date: Mar 16, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.37→40.59 Å / Num. obs: 91903 / % possible obs: 98.4 % / Redundancy: 3.8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.049 / Rrim(I) all: 0.057 / Net I/σ(I): 13.7
Reflection shellResolution: 1.37→1.41 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.545 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 6599 / CC1/2: 0.736 / Rrim(I) all: 0.638 / % possible all: 95.8

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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: 6EH4

6eh4


Resolution: 1.37→40.59 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.96 / SU B: 1.976 / SU ML: 0.04 / Cross valid method: THROUGHOUT / ESU R: 0.057 / ESU R Free: 0.059 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19069 4602 5 %RANDOM
Rwork0.16769 ---
obs0.16887 87273 98.31 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 19.183 Å2
Baniso -1Baniso -2Baniso -3
1-0.14 Å20 Å2-0.16 Å2
2---0.12 Å20 Å2
3----0.02 Å2
Refinement stepCycle: 1 / Resolution: 1.37→40.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3497 0 98 379 3974
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0193918
X-RAY DIFFRACTIONr_bond_other_d0.0020.023445
X-RAY DIFFRACTIONr_angle_refined_deg1.8421.9475324
X-RAY DIFFRACTIONr_angle_other_deg1.0338070
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8845504
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.57924.555191
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.52315630
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.1641525
X-RAY DIFFRACTIONr_chiral_restr0.1180.2567
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0214463
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02818
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_it0.8241.1221904
X-RAY DIFFRACTIONr_mcbond_other0.8181.1191902
X-RAY DIFFRACTIONr_mcangle_it1.3681.6762413
X-RAY DIFFRACTIONr_mcangle_other1.3691.6782414
X-RAY DIFFRACTIONr_scbond_it1.3241.332014
X-RAY DIFFRACTIONr_scbond_other1.3231.332014
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.9191.8982901
X-RAY DIFFRACTIONr_long_range_B_refined4.60714.2054121
X-RAY DIFFRACTIONr_long_range_B_other4.55913.6944043
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.37→1.406 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.27 315 -
Rwork0.246 6273 -
obs--95.64 %
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)
11.1122-0.0439-0.33630.89990.44532.2034-0.01120.07960.0465-0.0951-0.0435-0.0105-0.0083-0.01910.05470.01910.0069-0.01460.0089-0.00120.037315.4802-47.9896113.5394
22.16971.52820.45733.54890.77481.91450.0347-0.1331-0.11660.08340.0292-0.14580.05870.0884-0.06390.00310.002-0.00580.04820.01120.0214-0.3885-65.3143138.86
31.56140.7391-0.10752.6453-0.31291.4206-0.04970.09590.14340.0190.0093-0.031-0.06230.08860.04040.0207-0.0032-0.0140.01380.01120.0207-2.1338-53.2309100.3984
41.00830.34210.54921.2360.86983.3666-0.0092-0.0699-0.0702-0.09920.0069-0.01390.12130.01970.00240.02120.00080.00230.00660.0060.0059-12.8412-62.142127.0225
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 113
2X-RAY DIFFRACTION2A114 - 203
3X-RAY DIFFRACTION3B1 - 114
4X-RAY DIFFRACTION4B115 - 244

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