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- PDB-8d5q: TCR TG6 in complex with Ld-HF10 -

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Basic information

Entry
Database: PDB / ID: 8d5q
TitleTCR TG6 in complex with Ld-HF10
Components
  • Dense granule protein 6, HF10 peptide
  • H-2 class I histocompatibility antigen, L-D alpha chain
  • TCR-alpha
  • TCR-beta
KeywordsIMMUNE SYSTEM / MHCI / CD8 T cell
Function / homology
Function and homology information


antigen processing and presentation of peptide antigen via MHC class I / lumenal side of endoplasmic reticulum membrane / defense response / MHC class I protein complex / phagocytic vesicle membrane / immune response
Similarity search - Function
MHC class I, alpha chain, C-terminal / MHC_I C-terminus / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / : / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / MHC classes I/II-like antigen recognition protein / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. ...MHC class I, alpha chain, C-terminal / MHC_I C-terminus / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / : / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / MHC classes I/II-like antigen recognition protein / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
H-2 class I histocompatibility antigen, L-D alpha chain
Similarity search - Component
Biological speciesMus musculus (house mouse)
Toxoplasma gondii (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.501 Å
AuthorsWang, Y. / Dai, S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS) United States
CitationJournal: Front Immunol / Year: 2022
Title: Peptide Centric V beta Specific Germline Contacts Shape a Specialist T Cell Response.
Authors: Wang, Y. / Tsitsiklis, A. / Devoe, S. / Gao, W. / Chu, H.H. / Zhang, Y. / Li, W. / Wong, W.K. / Deane, C.M. / Neau, D. / Slansky, J.E. / Thomas, P.G. / Robey, E.A. / Dai, S.
History
DepositionJun 5, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 14, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TCR-alpha
B: TCR-beta
C: H-2 class I histocompatibility antigen, L-D alpha chain
E: Dense granule protein 6, HF10 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,7297
Polymers73,3414
Non-polymers3873
Water3,747208
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)89.963, 89.963, 105.982
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41

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Components

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Protein , 3 types, 3 molecules ABC

#1: Protein TCR-alpha


Mass: 23161.312 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Variant: Transgenic mouse line TG6 / Production host: Escherichia coli (E. coli)
#2: Protein TCR-beta


Mass: 27929.439 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Variant: Transgenic mouse line TG6 / Production host: Escherichia coli (E. coli)
#3: Protein H-2 class I histocompatibility antigen, L-D alpha chain


Mass: 21101.275 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: H2-L / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P01897

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Protein/peptide , 1 types, 1 molecules E

#4: Protein/peptide Dense granule protein 6, HF10 peptide


Mass: 1149.189 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Toxoplasma gondii (eukaryote)

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Non-polymers , 3 types, 211 molecules

#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 208 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
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: 2.92 Å3/Da / Density % sol: 57.93 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 11 % w/v PEG 8000, 0.1 M MES 6.0, 0.24 M Ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 2, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.5→90 Å / Num. obs: 29168 / % possible obs: 99.8 % / Redundancy: 6.4 % / Rpim(I) all: 0.03 / Net I/σ(I): 26.6
Reflection shellResolution: 2.5→2.54 Å / Num. unique obs: 2864 / Rpim(I) all: 0.29

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1LD9, 3TO4

1ld9

3to4


Resolution: 2.501→45.022 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.944 / SU B: 15.549 / SU ML: 0.18 / Cross valid method: NONE / ESU R: 0.397 / ESU R Free: 0.248
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.222 1493 5.119 %
Rwork0.1688 27675 -
all0.172 --
obs-29168 99.839 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 65.211 Å2
Baniso -1Baniso -2Baniso -3
1--0.251 Å20 Å20 Å2
2---0.251 Å2-0 Å2
3---0.501 Å2
Refinement stepCycle: LAST / Resolution: 2.501→45.022 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5108 0 22 208 5338
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0135283
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174553
X-RAY DIFFRACTIONr_angle_refined_deg1.8921.657181
X-RAY DIFFRACTIONr_angle_other_deg1.3721.57610582
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.5575633
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.11422.125320
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.36115829
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.231540
X-RAY DIFFRACTIONr_chiral_restr0.0870.2645
X-RAY DIFFRACTIONr_gen_planes_refined0.010.026021
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021211
X-RAY DIFFRACTIONr_nbd_refined0.210.21009
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2050.24298
X-RAY DIFFRACTIONr_nbtor_refined0.1810.22376
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0880.22540
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1680.2225
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0630.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2620.215
X-RAY DIFFRACTIONr_nbd_other0.1920.247
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2350.26
X-RAY DIFFRACTIONr_mcbond_it4.1675.7652541
X-RAY DIFFRACTIONr_mcbond_other4.1665.7652540
X-RAY DIFFRACTIONr_mcangle_it6.1848.6323171
X-RAY DIFFRACTIONr_mcangle_other6.1838.6323172
X-RAY DIFFRACTIONr_scbond_it4.9966.2242742
X-RAY DIFFRACTIONr_scbond_other4.8546.2192740
X-RAY DIFFRACTIONr_scangle_it7.369.1314010
X-RAY DIFFRACTIONr_scangle_other7.3599.1344011
X-RAY DIFFRACTIONr_lrange_it10.02265.4515798
X-RAY DIFFRACTIONr_lrange_other10.02165.4685799
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.501-2.5650.39970.32002X-RAY DIFFRACTION98.6372
2.565-2.6350.3341340.2431956X-RAY DIFFRACTION99.809
2.635-2.7120.271880.2071962X-RAY DIFFRACTION100
2.712-2.7950.2871090.1881836X-RAY DIFFRACTION100
2.795-2.8860.291030.1921827X-RAY DIFFRACTION100
2.886-2.9870.214990.1661762X-RAY DIFFRACTION100
2.987-3.0990.249770.1781720X-RAY DIFFRACTION100
3.099-3.2250.232900.1681627X-RAY DIFFRACTION100
3.225-3.3680.191600.1761585X-RAY DIFFRACTION100
3.368-3.5310.232900.1861515X-RAY DIFFRACTION100
3.531-3.7210.232870.1841411X-RAY DIFFRACTION99.8667
3.721-3.9450.244680.1731370X-RAY DIFFRACTION100
3.945-4.2150.2590.1451266X-RAY DIFFRACTION99.9246
4.215-4.550.156580.1321200X-RAY DIFFRACTION100
4.55-4.9790.175650.1181085X-RAY DIFFRACTION99.6534
4.979-5.5580.215560.149997X-RAY DIFFRACTION100
5.558-6.4020.261490.179873X-RAY DIFFRACTION100
6.402-7.8030.211400.168746X-RAY DIFFRACTION99.8729
7.803-10.8780.188390.14586X-RAY DIFFRACTION100
10.878-45.0220.234250.249349X-RAY DIFFRACTION99.4681
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)
11.0189-0.08450.75120.6865-0.6791.1210.1985-0.0539-0.2344-0.0315-0.1539-0.10660.15420.0805-0.04450.07110.0028-0.07810.0847-0.01110.150928.3932-103.34325.5415
21.7483-0.69380.6050.7174-0.34930.23970.0473-0.20150.01040.0157-0.03930.01630.0041-0.0192-0.00790.014-0.02920.00130.1876-0.06430.031936.1728-88.08615.2565
31.1624-0.45010.14530.79120.13770.35640.10440.04480.1106-0.0687-0.0136-0.0945-0.0533-0.0273-0.09080.0646-0.01710.06420.0252-0.00620.07238.2427-68.7207-17.4619
43.7884-0.4050.79960.19610.33251.32310.1907-0.15320.1586-0.0264-0.0231-0.0921-0.0083-0.1319-0.16750.0895-0.055-0.00050.05130.01010.105113.3186-71.9171-12.2034
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLA0 - 204
2X-RAY DIFFRACTION2ALLB0 - 243
3X-RAY DIFFRACTION3ALLC1 - 176
4X-RAY DIFFRACTION4ALLE1 - 10

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