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- PDB-6eh8: HA1.7 Human T-Cell Receptor specific for Influenza virus epitope ... -

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Basic information

Entry
Database: PDB / ID: 6eh8
TitleHA1.7 Human T-Cell Receptor specific for Influenza virus epitope PKYVKQNTLKLAT presented by Human Leukocyte Antigen HLA-DR0101
Components
  • Human T Cell Receptor Alpha Chain
  • Human T Cell Receptor Beta Chain
KeywordsIMMUNE SYSTEM / Human T Cell Receptor / Human Leukocute Antigen / Influenza Haemagglutinin epitope / 3D structure
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.51 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 / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
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 9, 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 Beta Chain


Theoretical massNumber of molelcules
Total (without water)49,7672
Polymers49,7672
Non-polymers00
Water45025
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4050 Å2
ΔGint-23 kcal/mol
Surface area21130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.210, 49.500, 72.590
Angle α, β, γ (deg.)90.000, 94.660, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Human T Cell Receptor Alpha Chain


Mass: 22231.758 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 Beta Chain


Mass: 27534.910 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)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 25 / Source method: isolated from a natural source / Formula: H2O
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: 50.61 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 15% PEG 4K, 15% Glycerol, 100mM MES pH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.917 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 9, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.917 Å / Relative weight: 1
ReflectionResolution: 2.51→52.084 Å / Num. obs: 16674 / % possible obs: 98.2 % / Redundancy: 3.8 % / Rpim(I) all: 0.073 / Rrim(I) all: 0.147 / Rsym value: 0.116 / Net I/av σ(I): 4.7 / Net I/σ(I): 12.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsRpim(I) allRrim(I) allRsym value% possible all
2.51-2.583.91.3880.40.8341.7061.38897.9
2.58-2.653.91.0810.50.6511.3241.08197.8
2.65-2.723.80.9340.50.5721.1560.93498.3
2.72-2.813.60.8030.70.5131.0020.80397.7
2.81-2.93.60.5970.90.3880.7630.59797.3
2.9-340.4511.20.2650.5510.45199.2
3-3.113.90.331.60.1970.4060.3398.9
3.11-3.243.90.2582.10.1560.3210.25899.3
3.24-3.383.90.18330.1090.2260.18398.6
3.38-3.553.80.13840.0860.1730.13899.2
3.55-3.743.80.115.10.0690.140.1198.1
3.74-3.973.60.096.30.0590.1160.0997.6
3.97-4.243.40.0610.10.0420.0790.0695.9
4.24-4.583.90.04712.60.030.0620.04799
4.58-5.023.90.04513.30.0290.0590.04598.8
5.02-5.613.90.04812.90.030.0620.04899.2
5.61-6.483.70.05311.60.0330.0670.05399
6.48-7.943.50.04115.40.0280.0540.04196.3
7.94-11.233.60.03120.60.0220.0420.03197.3
11.23-52.0843.60.0320.70.0210.040.0397.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
SCALA3.3.20data scaling
PHASERphasing
REFMAC5.7.0032refinement
PDB_EXTRACT3.22data extraction
xia2data reduction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4GKZ

4gkz


Resolution: 2.51→52.08 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.893 / SU B: 32.303 / SU ML: 0.325 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.861 / ESU R Free: 0.362
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2959 837 5.1 %RANDOM
Rwork0.2228 ---
obs0.2266 15735 97.41 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 142.98 Å2 / Biso mean: 63.314 Å2 / Biso min: 24.47 Å2
Baniso -1Baniso -2Baniso -3
1-1.7 Å20 Å2-0.08 Å2
2--3.32 Å20 Å2
3----4.95 Å2
Refinement stepCycle: final / Resolution: 2.51→52.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3497 0 0 25 3522
Biso mean---51.6 -
Num. residues----442
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0193609
X-RAY DIFFRACTIONr_bond_other_d0.0010.023305
X-RAY DIFFRACTIONr_angle_refined_deg1.5521.9414903
X-RAY DIFFRACTIONr_angle_other_deg0.8143.0037618
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.6655444
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.42424.235170
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.96415596
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3891519
X-RAY DIFFRACTIONr_chiral_restr0.0960.2532
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214116
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02861
LS refinement shellResolution: 2.51→2.575 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.458 50 -
Rwork0.307 1102 -
all-1152 -
obs--94.12 %
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)
12.1026-0.2738-0.2084.14081.007411.4954-0.12840.11140.11280.1810.00640.0881-0.2843-0.29050.1220.2146-0.0030.01040.01340.00430.3598-8.10515.8921107.3553
212.8246-1.3135-1.37786.8348-0.10615.87090.00620.2582-0.7601-0.3442-0.0398-0.45310.70010.72390.03360.6783-0.07650.00770.73530.00320.215412.43223.977578.7655
34.512-2.2096-1.11413.47421.51326.1548-0.3228-0.25260.07830.15270.3553-0.3046-0.14021.8179-0.03250.3137-0.0725-0.03120.6440.04860.246612.127910.2441119.3047
42.9049-0.12231.64751.3754-0.39674.8991-0.1219-0.21990.1687-0.27890.0376-0.255-0.03870.71540.08430.4313-0.19930.04520.918-0.01150.304719.612614.335589.5051
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 117
2X-RAY DIFFRACTION2A118 - 203
3X-RAY DIFFRACTION3B1 - 117
4X-RAY DIFFRACTION4B118 - 246

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