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- PDB-4onh: Crystal Structure of DN6 TCR -

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Basic information

Entry
Database: PDB / ID: 4onh
TitleCrystal Structure of DN6 TCR
Components(T-cell receptor ...) x 2
KeywordsIMMUNE SYSTEM / Ig fold / TCR / Antigen recognition / MHC like
Function / homology
Function and homology information


alpha-beta T cell receptor complex / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / alpha-beta T cell activation / Generation of second messenger molecules / PD-1 signaling / immunoglobulin complex, circulating / immunoglobulin receptor binding / complement activation, classical pathway / antigen binding ...alpha-beta T cell receptor complex / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / alpha-beta T cell activation / Generation of second messenger molecules / PD-1 signaling / immunoglobulin complex, circulating / immunoglobulin receptor binding / complement activation, classical pathway / antigen binding / response to bacterium / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Downstream TCR signaling / T cell receptor signaling pathway / antibacterial humoral response / adaptive immune response / blood microparticle / extracellular exosome / plasma membrane
Similarity search - Function
T-cell receptor alpha chain, constant domain / Domain of unknown function (DUF1968) / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold ...T-cell receptor alpha chain, constant domain / Domain of unknown function (DUF1968) / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
T cell receptor beta constant 2 / T cell receptor alpha chain constant
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.008 Å
AuthorsRoy, S. / Adams, E.J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: Molecular basis of mycobacterial lipid antigen presentation by CD1c and its recognition by alpha beta T cells.
Authors: Roy, S. / Ly, D. / Li, N.S. / Altman, J.D. / Piccirilli, J.A. / Moody, D.B. / Adams, E.J.
History
DepositionJan 28, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 8, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 18, 2015Group: Database references
Revision 1.2Jul 29, 2020Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: T-cell receptor alpha
A: T-cell receptor beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,8609
Polymers50,1272
Non-polymers7337
Water724
1
B: T-cell receptor alpha
A: T-cell receptor beta
hetero molecules

B: T-cell receptor alpha
A: T-cell receptor beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,72018
Polymers100,2544
Non-polymers1,46614
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area10350 Å2
ΔGint-102 kcal/mol
Surface area41620 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4390 Å2
ΔGint-46 kcal/mol
Surface area21590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)143.825, 64.063, 69.534
Angle α, β, γ (deg.)90.00, 115.88, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-401-

HOH

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Components

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T-cell receptor ... , 2 types, 2 molecules BA

#1: Protein T-cell receptor alpha


Mass: 27485.672 Da / Num. of mol.: 1 / Mutation: S169C, C188A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRAV,TRAC,TRAB / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Insect cells, Hi5 cells / References: UniProt: A0A5B9*PLUS
#2: Protein T-cell receptor beta


Mass: 22641.426 Da / Num. of mol.: 1 / Mutation: T157C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P01848*PLUS

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Sugars , 1 types, 2 molecules

#3: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 9 molecules

#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O

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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: 2.87 Å3/Da / Density % sol: 57.21 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M Mes, pH-6.5, 20% PEG 4000, 0.6 M NaCl, VAPOR DIFFUSION, SITTING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.03321 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Nov 20, 2011
RadiationMonochromator: Si(111) double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03321 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 11289 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Rmerge(I) obs: 0.122 / Χ2: 1.657 / Net I/σ(I): 18.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
3-3.052.80.5615221.634193.4
3.05-3.113.10.5135501.489198.4
3.11-3.173.40.4465571.663198.6
3.17-3.233.70.365821.6091100
3.23-3.33.90.3435491.832198.9
3.3-3.3840.3055691.7981100
3.38-3.4640.2415561.907199.5
3.46-3.564.10.2095881.827199.8
3.56-3.6640.1935531.717199.5
3.66-3.784.10.1725621.7171100
3.78-3.9140.1595831.728199.3
3.91-4.0740.1295511.524199.5
4.07-4.2640.1245761.636199.7
4.26-4.483.90.1085631.513199.6
4.48-4.763.90.1095611.377198.1
4.76-5.133.90.15701.324199.3
5.13-5.643.90.0945771.4711100
5.64-6.463.90.1075761.681100
6.46-8.133.90.1025841.65199.8
8.13-503.70.1075601.995192.7

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 51.56 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3.01 Å38.73 Å
Translation3.01 Å38.73 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.1.4phasing
PHENIX1.7_650refinement
PDB_EXTRACT3.14data extraction
HKL-2000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.008→24.674 Å / SU ML: 0.58 / σ(F): 1.34 / Phase error: 36.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3165 542 4.81 %
Rwork0.2571 --
obs0.2598 11276 98.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.008→24.674 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3170 0 43 4 3217
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033293
X-RAY DIFFRACTIONf_angle_d0.924506
X-RAY DIFFRACTIONf_dihedral_angle_d13.0081083
X-RAY DIFFRACTIONf_chiral_restr0.034517
X-RAY DIFFRACTIONf_plane_restr0.003587
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0081-3.31020.44481370.37032595X-RAY DIFFRACTION96
3.3102-3.78770.34611400.3292682X-RAY DIFFRACTION100
3.7877-4.76640.30191350.24532703X-RAY DIFFRACTION99
4.7664-24.67510.28711300.22092754X-RAY DIFFRACTION99
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)
12.90360.3232.03079.54050.71034.78610.12680.45450.61540.1072-0.49430.75120.4311-0.93310.24270.4639-0.16150.22051.0218-0.08350.8392-27.97869.52550.3931
25.81274.96872.14840.70671.7912.64140.5614-0.21120.32620.1523-0.2312-0.50810.4585-0.3166-0.17540.6513-0.04160.14170.6472-0.03010.7254-15.197114.93128.8487
36.0281-0.3201-3.64212.78670.48384.55140.2663-0.37840.8086-0.0692-0.1552-0.0295-0.22850.4432-0.09150.4051-0.0261-0.03490.4326-0.07140.6324-2.040224.16099.9528
46.16516.17745.60546.05323.86695.43911.1403-2.6182-0.79890.6842-1.2023-0.3160.7469-1.2071-0.36540.91310.0977-0.00250.76110.13020.6249-20.5386-5.558422.0047
51.7106-1.14391.40382.0387-1.96273.07831.41272.2118-0.5739-3.8108-2.011-1.21571.99770.5715-0.25481.0157-0.2011-0.24181.3454-0.55250.9083-17.567-6.226212.1899
69.81974.04114.0917.7577-0.13894.46-0.6040.3401-1.35620.45640.6913-0.4911-0.54520.53150.0080.73550.113-0.08280.7232-0.04040.4511-19.5557-6.463617.3559
73.4621.4489-0.85458.45092.9072.3020.1409-0.40720.13350.6098-0.140.1297-0.25730.3023-0.18340.7329-0.0538-0.15681.3149-0.1320.697-0.516319.777727.5994
89.5808-3.5523-5.4175.51413.79773.95390.83942.11360.3399-2.2217-0.8096-0.433-1.1230.0770.2961.0123-0.0442-0.17251.17390.43710.95967.23717.850120.141
97.32876.56050.96016.07112.64959.8783-0.09551.14140.03223.22151.90540.8812-1.3471.8539-1.61451.79990.0383-0.13491.1758-0.04590.5908-1.053828.682428.6305
104.49215.7123-4.48011.9379-4.71954.95481.45573.3658-0.23964.5115-0.57670.4873-0.98122.7582-1.05971.78550.2523-0.35091.76690.17651.16873.885421.985137.8744
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resseq 2:83)
2X-RAY DIFFRACTION2chain 'B' and (resseq 84:136)
3X-RAY DIFFRACTION3chain 'B' and (resseq 141:244)
4X-RAY DIFFRACTION4chain 'A' and (resseq 2:35)
5X-RAY DIFFRACTION5chain 'A' and (resseq 36:53)
6X-RAY DIFFRACTION6chain 'A' and (resseq 54:105)
7X-RAY DIFFRACTION7chain 'A' and (resseq 106:158)
8X-RAY DIFFRACTION8chain 'A' and (resseq 159:169)
9X-RAY DIFFRACTION9chain 'A' and (resseq 170:187)
10X-RAY DIFFRACTION10chain 'A' and (resseq 188:200)

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