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- PDB-6eh6: F11 T-Cell Receptor Recognising PKYVKQNTLKLAT Peptide Presented b... -

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Basic information

Entry
Database: PDB / ID: 6eh6
TitleF11 T-Cell Receptor Recognising PKYVKQNTLKLAT Peptide Presented by HLA-DR*0101
Components(Human 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 / DI(HYDROXYETHYL)ETHER
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 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
DepositionSep 12, 2017Deposition 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 T Cell Receptor Alpha Chain
B: Human T Cell Receptor BetaChain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,46514
Polymers49,6462
Non-polymers81912
Water2,756153
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6880 Å2
ΔGint7 kcal/mol
Surface area21130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.780, 114.080, 50.720
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-441-

HOH

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Components

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Human T Cell Receptor ... , 2 types, 2 molecules AB

#1: Protein Human 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 T Cell Receptor BetaChain


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, 165 molecules

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


Mass: 62.068 Da / Num. of mol.: 10 / 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-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 153 / 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: 50.79 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 25% PEG 1.5K, 100mM MMT pH 6.0

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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: 1.78→50.72 Å / Num. obs: 48509 / % possible obs: 99.9 % / Redundancy: 6.5 % / Biso Wilson estimate: 26.7 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.049 / Rpim(I) all: 0.021 / Rrim(I) all: 0.053 / Net I/σ(I): 22.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Rpim(I) allRrim(I) all% possible all
1.78-1.836.80.8080.8180.3340.875100
7.96-50.726.10.0210.9990.010.02499.8

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Processing

Software
NameVersionClassification
Aimless0.1.16data scaling
REFMAC5.8.0049refinement
PDB_EXTRACT3.22data extraction
xia2data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4GKZ

4gkz


Resolution: 1.78→50.72 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.947 / SU B: 6.244 / SU ML: 0.094 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.121 / ESU R Free: 0.115
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2236 2450 5.1 %RANDOM
Rwork0.1937 ---
obs0.1953 46009 99.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 97.34 Å2 / Biso mean: 32.953 Å2 / Biso min: 16.19 Å2
Baniso -1Baniso -2Baniso -3
1-1.7 Å2-0 Å20 Å2
2---0.06 Å20 Å2
3----1.64 Å2
Refinement stepCycle: final / Resolution: 1.78→50.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3493 0 53 153 3699
Biso mean--47.32 33.6 -
Num. residues----442
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0193624
X-RAY DIFFRACTIONr_bond_other_d0.0010.023324
X-RAY DIFFRACTIONr_angle_refined_deg2.0081.9454899
X-RAY DIFFRACTIONr_angle_other_deg0.91537665
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9515440
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.13324.419172
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.75415584
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.6251519
X-RAY DIFFRACTIONr_chiral_restr0.1290.2529
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0214104
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02853
LS refinement shellResolution: 1.78→1.826 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.346 171 -
Rwork0.283 3350 -
all-3521 -
obs--99.91 %
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)
15.76-0.31630.98281.29470.30991.40190.0938-0.09990.04610.0313-0.07690.14810.1383-0.1603-0.01690.0313-0.05220.01910.1152-0.00370.1355-25.0542-5.361721.8238
22.3731.34250.42174.75181.12113.5151-0.08850.19650.1226-0.22830.2023-0.15480.04070.2305-0.11380.01850.0088-0.01390.1091-0.01170.15027.959-11.622515.5151
34.23230.3446-1.77310.9802-0.35032.24480.04710.00640.0335-0.1065-0.02710.15510.1228-0.0784-0.020.0301-0.0206-0.0260.0811-0.00690.1406-30.1224-15.93530.7756
41.57640.38912.1071.91941.31626.29820.14210.00250.02420.3696-0.03930.02860.6244-0.006-0.10290.113-0.00260.02370.0411-0.01490.0976-0.3069-24.26667.4618
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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