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- PDB-5m00: Crystal structure of murine P14 TCR complex with H-2Db and Y4A, m... -

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Basic information

Entry
Database: PDB / ID: 5m00
TitleCrystal structure of murine P14 TCR complex with H-2Db and Y4A, modified gp33 peptide from LCMV
Components
  • Beta-2-microglobulin
  • H-2 class I histocompatibility antigen, D-B alpha chain
  • LCMV-DERIVED GP33 ALTERED PEPTIDE LIGAND Y4A
  • Protein Trav14-1,Uncharacterized protein
  • T-cell receptor beta chain V region C5,Uncharacterized protein
KeywordsIMMUNE SYSTEM / MHC class I / TCR / H-2Db / gp33 / LCMV
Function / homology
Function and homology information


Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / DAP12 signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / T cell receptor complex / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / cellular defense response / Neutrophil degranulation ...Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / DAP12 signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / T cell receptor complex / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / cellular defense response / Neutrophil degranulation / lumenal side of endoplasmic reticulum membrane / cellular response to iron(III) ion / negative regulation of forebrain neuron differentiation / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / iron ion transport / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport / regulation of erythrocyte differentiation / HFE-transferrin receptor complex / response to molecule of bacterial origin / MHC class I peptide loading complex / T cell mediated cytotoxicity / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / MHC class I protein complex / peptide antigen binding / positive regulation of receptor-mediated endocytosis / negative regulation of neurogenesis / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / multicellular organismal-level iron ion homeostasis / phagocytic vesicle membrane / negative regulation of epithelial cell proliferation / sensory perception of smell / positive regulation of cellular senescence / T cell differentiation in thymus / negative regulation of neuron projection development / protein refolding / protein homotetramerization / amyloid fibril formation / adaptive immune response / intracellular iron ion homeostasis / learning or memory / cell surface receptor signaling pathway / external side of plasma membrane / structural molecule activity / Golgi apparatus / protein homodimerization activity / extracellular space / plasma membrane / cytosol
Similarity search - Function
: / : / : / T-cell receptor alpha chain, constant domain / Domain of unknown function (DUF1968) / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / MHC class I alpha chain, alpha1 alpha2 domains ...: / : / : / T-cell receptor alpha chain, constant domain / Domain of unknown function (DUF1968) / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / Immunoglobulin V-Type / Beta-2-Microglobulin / : / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / Immunoglobulin V-set domain / MHC classes I/II-like antigen recognition protein / Immunoglobulin V-set domain / : / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin / 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 / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
T cell receptor alpha variable 14-1 / Beta-2-microglobulin / H-2 class I histocompatibility antigen, D-B alpha chain / T-cell receptor beta chain V region C5 / Ig-like domain-containing protein / Ig-like domain-containing protein
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsAchour, A. / Sandalova, T. / Sun, R. / Han, X.
CitationJournal: To Be Published
Title: Thernary complexes of TCR P14 give insights into the mechanisms behind reestablishment of CTL responses against a viral escape mutant
Authors: Allerbring, E. / Duru, A. / Sun, R. / Han, X. / Uchtenhagen, H. / Madhurantakam, C. / Popov, A. / Markova, N. / Talyzina, A. / Nygren, P.A. / Sandalova, T. / Achour, A.
History
DepositionOct 3, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 20, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 14, 2018Group: Database references / Category: struct_ref_seq_dif / Item: _struct_ref_seq_dif.details
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 6, 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: H-2 class I histocompatibility antigen, D-B alpha chain
B: Beta-2-microglobulin
G: Protein Trav14-1,Uncharacterized protein
H: T-cell receptor beta chain V region C5,Uncharacterized protein
P: LCMV-DERIVED GP33 ALTERED PEPTIDE LIGAND Y4A


Theoretical massNumber of molelcules
Total (without water)96,5565
Polymers96,5565
Non-polymers00
Water6,864381
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10690 Å2
ΔGint-46 kcal/mol
Surface area38030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)258.455, 46.941, 90.253
Angle α, β, γ (deg.)90.00, 94.24, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 3 types, 3 molecules ABH

#1: Protein H-2 class I histocompatibility antigen, D-B alpha chain / H-2D(B)


Mass: 32087.703 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: H2-D1 / Production host: Escherichia coli (E. coli) / References: UniProt: P01899
#2: Protein Beta-2-microglobulin


Mass: 13794.978 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: B2m / Production host: Escherichia coli (E. coli) / References: UniProt: P01887
#4: Protein T-cell receptor beta chain V region C5,Uncharacterized protein


Mass: 26647.633 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) / References: UniProt: P04213, UniProt: Q7TND8

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Antibody / Protein/peptide / Non-polymers , 3 types, 383 molecules GP

#3: Antibody Protein Trav14-1,Uncharacterized protein


Mass: 23072.697 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Trav14-1 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0G2JF94, UniProt: Q6PIR9
#5: Protein/peptide LCMV-DERIVED GP33 ALTERED PEPTIDE LIGAND Y4A


Mass: 953.135 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli)
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 381 / 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: 2.75 Å3/Da / Density % sol: 55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 19% PEG 6000, 0.1M Tris HCl pH 8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.972 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 3, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.972 Å / Relative weight: 1
ReflectionResolution: 1.95→128.9 Å / Num. obs: 77777 / % possible obs: 97.9 % / Redundancy: 3 % / Rmerge(I) obs: 0.043 / Net I/σ(I): 13.1
Reflection shellResolution: 1.95→1.99 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.548 / Num. unique all: 4274 / % possible all: 96

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1s7u

1s7u


Resolution: 1.95→128.87 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.937 / SU B: 7.914 / SU ML: 0.114 / Cross valid method: THROUGHOUT / ESU R: 0.154 / ESU R Free: 0.145 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23715 3894 5 %RANDOM
Rwork0.19958 ---
obs0.20148 73882 97.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 42.426 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å2-0.12 Å2
2---0.34 Å20 Å2
3---0.35 Å2
Refinement stepCycle: 1 / Resolution: 1.95→128.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6504 0 0 381 6885
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0196716
X-RAY DIFFRACTIONr_bond_other_d0.0020.026094
X-RAY DIFFRACTIONr_angle_refined_deg1.6671.9369116
X-RAY DIFFRACTIONr_angle_other_deg0.988314069
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.115809
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.36724.073329
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.253151096
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1011539
X-RAY DIFFRACTIONr_chiral_restr0.0990.2950
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0217634
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021615
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_it1.1122.1733251
X-RAY DIFFRACTIONr_mcbond_other1.1122.1723250
X-RAY DIFFRACTIONr_mcangle_it1.8263.2494054
X-RAY DIFFRACTIONr_mcangle_other1.8263.2494055
X-RAY DIFFRACTIONr_scbond_it1.3382.3293465
X-RAY DIFFRACTIONr_scbond_other1.3382.3293465
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.1653.4285063
X-RAY DIFFRACTIONr_long_range_B_refined6.1717.6857423
X-RAY DIFFRACTIONr_long_range_B_other6.16917.6847423
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.949→1.999 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.314 265 -
Rwork0.285 5299 -
obs--95.96 %
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)
12.1154-0.0569-0.39431.89290.43061.5619-0.0489-0.01040.05210.0370.0463-0.12060.0402-0.04890.00260.1280.02150.02720.16360.0290.0999263.006-19.902114.442
24.2681.09-1.14111.6441-0.38993.09870.03150.042-0.13370.0698-0.03510.0329-0.1501-0.38970.00360.07680.0770.00710.3195-0.02070.065226.848-14.438122.632
33.6049-0.68030.64631.58230.02972.6478-0.03490.35930.0887-0.1655-0.09120.1297-0.0889-0.55660.12610.06030.01110.00770.35190.00230.0448236.702-17.191102.549
43.28470.1349-0.61141.6935-0.26861.9345-0.0322-0.67470.14380.0456-0.0731-0.20510.10450.63510.10530.02490.06530.02440.43230.01360.091292.1-17.315121.971
52.7554-0.22850.76632.52440.84924.0304-0.2152-0.62610.25330.35260.3968-0.0405-0.4085-0.0814-0.18160.1470.1664-0.01970.398-0.14780.0854325.125-23.322116.723
62.64610.2180.708910.51830.05030.20670.10060.24131.28410.0374-0.4363-1.3829-0.01760.17770.33570.3186-0.13240.00970.863-0.08630.9404334.957-17.152111.341
72.88910.0429-1.69590.17030.42562.3142-0.12550.22530.08410.0150.08230.06820.0668-0.05720.04320.03110.04830.04840.2360.09030.1391290.285-20.08398.821
81.7269-0.78721.66861.4996-1.17993.5961-0.0854-0.2470.08650.23360.2688-0.0538-0.03360.0185-0.18330.05510.0946-0.0120.3104-0.02890.0636320.426-28.829106.933
93.3774-3.42593.54036.5589-4.73146.99360.13880.0296-0.0654-0.19590.0789-0.03150.34230.053-0.21770.08060.0116-0.00460.3028-0.02450.1248316.958-34.29496.378
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 175
2X-RAY DIFFRACTION2A176 - 276
3X-RAY DIFFRACTION3B2 - 99
4X-RAY DIFFRACTION4G9 - 116
5X-RAY DIFFRACTION5G117 - 184
6X-RAY DIFFRACTION6G185 - 196
7X-RAY DIFFRACTION7H1 - 112
8X-RAY DIFFRACTION8H113 - 195
9X-RAY DIFFRACTION9H196 - 237

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