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- PDB-5ivx: Crystal Structure of B4.2.3 T-Cell Receptor and H2-Dd P18-I10 Complex -

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Basic information

Entry
Database: PDB / ID: 5ivx
TitleCrystal Structure of B4.2.3 T-Cell Receptor and H2-Dd P18-I10 Complex
Components
  • (T-CELL RECEPTOR ...) x 2
  • Beta-2-microglobulin
  • H-2 class I histocompatibility antigen, D-D alpha chain
  • P18-I10
KeywordsIMMUNE SYSTEM / MAJOR HISTOMPATIBILITY COMPLEX CLASS I / MHC-I / H2-Dd / H-2DD / T-Cell Receptor / TCR / B4.2.3 / B423 / IMMUNE RESPONSE / VIRAL IMMUNOEVASION / HUMAN IMMUNODEFICIENCY VIRUS / MOLECULAR RECOGNITION
Function / homology
Function and homology information


Synthesis and processing of ENV and VPU / evasion of host immune response / Alpha-defensins / 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 / Dectin-2 family ...Synthesis and processing of ENV and VPU / evasion of host immune response / Alpha-defensins / 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 / Dectin-2 family / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / Binding and entry of HIV virion / beta-2-microglobulin binding / cellular defense response / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / Neutrophil degranulation / host cell endosome membrane / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / lumenal side of endoplasmic reticulum membrane / actin filament organization / peptide binding / Assembly Of The HIV Virion / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / negative regulation of forebrain neuron differentiation / Budding and maturation of HIV virion / regulation of erythrocyte differentiation / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport / response to molecule of bacterial origin / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / MHC class I protein complex / multicellular organismal-level iron ion homeostasis / negative regulation of neurogenesis / peptide antigen assembly with MHC class II protein complex / positive regulation of receptor-mediated endocytosis / MHC class II protein complex / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / phagocytic vesicle membrane / positive regulation of cellular senescence / peptide antigen binding / negative regulation of epithelial cell proliferation / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / sensory perception of smell / positive regulation of T cell activation / negative regulation of neuron projection development / MHC class II protein complex binding / late endosome membrane / iron ion transport / T cell differentiation in thymus / protein refolding / protein homotetramerization / clathrin-dependent endocytosis of virus by host cell / intracellular iron ion homeostasis / amyloid fibril formation / learning or memory / viral protein processing / symbiont entry into host cell / immune response / lysosomal membrane / fusion of virus membrane with host plasma membrane / external side of plasma membrane / signaling receptor binding / virus-mediated perturbation of host defense response / fusion of virus membrane with host endosome membrane / viral envelope / protein-containing complex binding / virion attachment to host cell / host cell plasma membrane / structural molecule activity / virion membrane / Golgi apparatus / protein homodimerization activity / extracellular space / membrane / plasma membrane / cytosol
Similarity search - Function
Envelope glycoprotein Gp160 / Retroviral envelope protein / Retroviral envelope protein GP41-like / Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / 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 ...Envelope glycoprotein Gp160 / Retroviral envelope protein / Retroviral envelope protein GP41-like / Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / 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 / Beta-2-Microglobulin / 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 / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Beta-2-microglobulin / H-2 class I histocompatibility antigen, D-D alpha chain / Envelope glycoprotein gp160
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsNatarajan, K. / Jiang, J. / Margulies, D.
CitationJournal: Nat Commun / Year: 2017
Title: An allosteric site in the T-cell receptor C beta domain plays a critical signalling role.
Authors: Natarajan, K. / McShan, A.C. / Jiang, J. / Kumirov, V.K. / Wang, R. / Zhao, H. / Schuck, P. / Tilahun, M.E. / Boyd, L.F. / Ying, J. / Bax, A. / Margulies, D.H. / Sgourakis, N.G.
History
DepositionMar 21, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 29, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 21, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Sep 27, 2023Group: 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

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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-D alpha chain
B: Beta-2-microglobulin
E: T-CELL RECEPTOR ALPHA CHAIN
F: T-CELL RECEPTOR BETA CHAIN
P: P18-I10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,8779
Polymers93,6295
Non-polymers2484
Water7,963442
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11200 Å2
ΔGint-52 kcal/mol
Surface area38030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)210.107, 51.316, 93.741
Angle α, β, γ (deg.)90.00, 97.14, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11E-354-

HOH

21E-396-

HOH

31E-414-

HOH

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Components

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Protein , 2 types, 2 molecules AB

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


Mass: 32265.902 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: H2-D1 / Plasmid: PET21-B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P01900
#2: Protein Beta-2-microglobulin


Mass: 11791.545 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: B2m / Plasmid: PET3A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P01887

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T-CELL RECEPTOR ... , 2 types, 2 molecules EF

#3: Protein T-CELL RECEPTOR ALPHA CHAIN


Mass: 21658.111 Da / Num. of mol.: 1 / Mutation: T163C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Strain: BALB/C / Cell: T LYMPHOCYTE / Cell line: B4.2.3 T CELL HYBRIDOMA / Gene: TCRAV2S6J38 / Plasmid: PET3A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
#4: Protein T-CELL RECEPTOR BETA CHAIN


Mass: 26838.346 Da / Num. of mol.: 1 / Mutation: F167C, C181A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: PET3A / Production host: Escherichia coli (E. coli)

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Protein/peptide , 1 types, 1 molecules P

#5: Protein/peptide P18-I10


Mass: 1075.265 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: THE PEPTIDE IS CHEMICALLY SYNTHESIZED. FOUND NATURALLY IN HUMAN IMMUNODEFICIENCY VIRUS ENVELOPE SOURCE 26 GLYCOPROTEIN GP120.
Source: (synth.) Homo sapiens (human) / References: UniProt: P04578*PLUS

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Non-polymers , 2 types, 446 molecules

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


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 442 / 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: 2.77 Å3/Da / Density % sol: 55.67 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.2 / Details: 15% PEG 3350, 0.1M HEPES, 0.15M Magnesium Chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.0809 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 15, 2006
RadiationMonochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0809 Å / Relative weight: 1
ReflectionResolution: 2.1→29.8 Å / Num. obs: 57154 / % possible obs: 97.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.2 % / Biso Wilson estimate: 36.3 Å2 / Rmerge(I) obs: 0.082 / Net I/σ(I): 16.3
Reflection shellResolution: 2.1→2.2 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.332 / Mean I/σ(I) obs: 2.2 / % possible all: 80.1

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1LP9

1lp9


Resolution: 2.1→29.799 Å / SU ML: 0.22 / Data cutoff high absF: 10000 / Data cutoff low absF: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 22.95
RfactorNum. reflection% reflectionSelection details
Rfree0.2197 2889 5.05 %Random
Rwork0.18 ---
obs0.182 57154 97.83 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.1→29.799 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6544 0 16 443 7003
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026767
X-RAY DIFFRACTIONf_angle_d0.6559164
X-RAY DIFFRACTIONf_dihedral_angle_d12.7872500
X-RAY DIFFRACTIONf_chiral_restr0.028951
X-RAY DIFFRACTIONf_plane_restr0.0031197
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.13440.29951190.23172116X-RAY DIFFRACTION80
2.1344-2.17120.28981100.21582261X-RAY DIFFRACTION87
2.1712-2.21070.25531140.2162444X-RAY DIFFRACTION93
2.2107-2.25320.23821400.21392519X-RAY DIFFRACTION97
2.2532-2.29920.30131290.21012603X-RAY DIFFRACTION99
2.2992-2.34910.26081390.20712623X-RAY DIFFRACTION100
2.3491-2.40380.26371310.20332636X-RAY DIFFRACTION100
2.4038-2.46380.26091440.19942614X-RAY DIFFRACTION100
2.4638-2.53040.211520.19632612X-RAY DIFFRACTION100
2.5304-2.60480.27151430.20662598X-RAY DIFFRACTION100
2.6048-2.68890.24131390.19442648X-RAY DIFFRACTION100
2.6889-2.78490.24451410.2032613X-RAY DIFFRACTION100
2.7849-2.89630.26371410.20762646X-RAY DIFFRACTION100
2.8963-3.0280.26381350.20522659X-RAY DIFFRACTION100
3.028-3.18750.2581430.20122624X-RAY DIFFRACTION100
3.1875-3.38690.22041390.20022649X-RAY DIFFRACTION100
3.3869-3.6480.21031530.17212627X-RAY DIFFRACTION100
3.648-4.01430.17891380.16542661X-RAY DIFFRACTION100
4.0143-4.59340.17231600.1432652X-RAY DIFFRACTION100
4.5934-5.78030.20011400.14542695X-RAY DIFFRACTION100
5.7803-29.8020.20281390.17142765X-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)
11.3020.371-0.11140.96180.34671.9252-0.05560.1708-0.0277-0.00940.0282-0.0208-0.02060.121900.1605-0.00380.01680.2218-0.00140.2593-43.1073-6.769832.3382
20.1834-0.02410.16270.18970.11650.689-0.0820.23870.1229-0.17060.28050.2761-0.34220.04360.04680.4708-0.0623-0.05980.62650.17810.4827-65.1928-1.82493.1968
30.981-0.07550.2820.8083-0.21410.90130.03280.24990.00220.03670.08120.06690.10660.01190.01780.1805-0.0603-0.00250.3224-0.03290.254-64.2275-18.289318.632
41.3507-0.2071-0.01080.8327-0.38020.5796-0.09720.1125-0.0111-0.0148-0.0553-0.0844-0.02970.1496-00.18570.01730.00830.31550.03330.2773-17.61272.272946.8166
50.70560.147-0.12640.1472-0.07730.19040.17040.20590.09920.2764-0.1491-0.1026-0.07390.47320.04060.74240.0469-0.15450.413-0.02880.34690.376810.106875.0127
60.13770.15690.06590.15920.18330.1632-0.0812-0.2820.0540.3593-0.01650.29120.1131-0.43890.00010.44770.05390.05010.35840.02950.3315-29.618-5.773570.5744
70.5648-0.32090.3751.3307-0.01910.8769-0.03750.0167-0.08530.24040.0710.06110.2097-0.0516-0.00060.31690.0575-0.00610.22580.03710.2724-30.101-11.698561.7063
81.44841.34860.65521.49950.27341.9835-0.20850.1967-0.08411.0390.76050.0056-0.47780.23680.56561.0510.2413-0.0046-0.0858-0.01150.2053-14.56556.652681.9217
90.0660.08720.05950.07510.04750.0321-0.00320.0223-0.19720.0516-0.1173-0.050.0121-0.0008-0.00010.24820.0065-0.00670.3290.00280.3189-38.7329-6.315539.2774
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 181 )
2X-RAY DIFFRACTION2chain 'A' and (resid 182 through 274 )
3X-RAY DIFFRACTION3chain 'B' and (resid 1 through 99 )
4X-RAY DIFFRACTION4chain 'E' and (resid 3 through 114 )
5X-RAY DIFFRACTION5chain 'E' and (resid 115 through 192 )
6X-RAY DIFFRACTION6chain 'F' and (resid 1 through 13 )
7X-RAY DIFFRACTION7chain 'F' and (resid 14 through 112 )
8X-RAY DIFFRACTION8chain 'F' and (resid 113 through 234 )
9X-RAY DIFFRACTION9chain 'P' and (resid 1 through 10 )

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