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- PDB-7dzm: Crystal Structure of the cross-restricted T18A TCR and HLAB8101 b... -

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Basic information

Entry
Database: PDB / ID: 7dzm
TitleCrystal Structure of the cross-restricted T18A TCR and HLAB8101 bound to HIV-1 Gag TL9 peptide
Components
  • Beta-2-microglobulin
  • Gag-Pol polyprotein
  • MHC class I antigen
  • alpha chain T18A TCR
  • beta chain T18A TCR
KeywordsIMMUNE SYSTEM / TCR and p-MHC complex / HIV epitope TL9
Function / homology
Function and homology information


antigen processing and presentation / negative regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / transferrin transport / cellular response to iron ion / Endosomal/Vacuolar pathway / lumenal side of endoplasmic reticulum membrane / HIV-1 retropepsin ...antigen processing and presentation / negative regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / transferrin transport / cellular response to iron ion / Endosomal/Vacuolar pathway / lumenal side of endoplasmic reticulum membrane / HIV-1 retropepsin / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / symbiont-mediated activation of host apoptosis / peptide antigen assembly with MHC class II protein complex / retroviral ribonuclease H / exoribonuclease H / cellular response to iron(III) ion / MHC class II protein complex / exoribonuclease H activity / negative regulation of forebrain neuron differentiation / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / ER to Golgi transport vesicle membrane / 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 / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / MHC class I protein complex / DNA integration / positive regulation of T cell activation / peptide antigen binding / positive regulation of receptor-mediated endocytosis / negative regulation of neurogenesis / host multivesicular body / cellular response to nicotine / viral genome integration into host DNA / positive regulation of T cell mediated cytotoxicity / multicellular organismal-level iron ion homeostasis / RNA-directed DNA polymerase / establishment of integrated proviral latency / RNA stem-loop binding / specific granule lumen / viral penetration into host nucleus / phagocytic vesicle membrane / recycling endosome membrane / RNA-directed DNA polymerase activity / Interferon gamma signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / RNA-DNA hybrid ribonuclease activity / negative regulation of epithelial cell proliferation / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / MHC class II protein complex binding / Modulation by Mtb of host immune system / late endosome membrane / sensory perception of smell / positive regulation of cellular senescence / tertiary granule lumen / DAP12 signaling / T cell differentiation in thymus / host cell / negative regulation of neuron projection development / ER-Phagosome pathway / protein refolding / viral nucleocapsid / early endosome membrane / DNA recombination / protein homotetramerization / amyloid fibril formation / DNA-directed DNA polymerase / aspartic-type endopeptidase activity / Hydrolases; Acting on ester bonds / intracellular iron ion homeostasis / DNA-directed DNA polymerase activity / learning or memory / immune response / endoplasmic reticulum lumen / Amyloid fiber formation / symbiont-mediated suppression of host gene expression / Golgi membrane / viral translational frameshifting / lysosomal membrane / external side of plasma membrane / focal adhesion / lipid binding / Neutrophil degranulation / symbiont entry into host cell / host cell nucleus / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / virion membrane / structural molecule activity / cell surface / endoplasmic reticulum / Golgi apparatus / protein homodimerization activity
Similarity search - Function
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 / Reverse transcriptase connection / Reverse transcriptase connection domain / Beta-2-Microglobulin / : ...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 / Reverse transcriptase connection / Reverse transcriptase connection domain / Beta-2-Microglobulin / : / Reverse transcriptase thumb / Reverse transcriptase thumb domain / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / Integrase Zinc binding domain / Zinc finger integrase-type profile. / Integrase-like, N-terminal / Integrase DNA binding domain / Integrase, C-terminal domain superfamily, retroviral / Integrase, N-terminal zinc-binding domain / Integrase, C-terminal, retroviral / Integrase DNA binding domain profile. / Immunodeficiency lentiviral matrix, N-terminal / gag gene protein p17 (matrix protein) / RNase H / Integrase core domain / Integrase, catalytic core / Integrase catalytic domain profile. / Retropepsin-like catalytic domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / MHC classes I/II-like antigen recognition protein / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / RNase H type-1 domain profile. / Ribonuclease H domain / : / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Retrovirus capsid, C-terminal / Reverse transcriptase domain / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase (RT) catalytic domain profile. / Retroviral matrix protein / Retrovirus capsid, N-terminal / zinc finger / Zinc knuckle / Zinc finger, CCHC-type superfamily / Zinc finger, CCHC-type / Zinc finger CCHC-type profile. / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily / Ribonuclease H superfamily / Ribonuclease H-like superfamily / Reverse transcriptase/Diguanylate cyclase domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / DNA/RNA polymerase superfamily / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
MHC class I antigen / Gag-Pol polyprotein / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
Human immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsLiu, Y. / Yin, L.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31870728 China
National Natural Science Foundation of China (NSFC)31470738 China
CitationJournal: Biorxiv / Year: 2021
Title: Cross-reactive TCR with alloreactivity for immunodominant HIV-1 epitope Gag TL9 with enhanced control of viral infection
Authors: Liu, Y. / San, D. / Yin, L.
History
DepositionJan 25, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 26, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / pdbx_initial_refinement_model
Item: _citation.journal_id_ISSN
Revision 1.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MHC class I antigen
B: Beta-2-microglobulin
C: Gag-Pol polyprotein
D: beta chain T18A TCR
E: alpha chain T18A TCR


Theoretical massNumber of molelcules
Total (without water)95,2555
Polymers95,2555
Non-polymers00
Water7,620423
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10360 Å2
ΔGint-58 kcal/mol
Surface area38340 Å2
Unit cell
Length a, b, c (Å)93.098, 93.098, 263.051
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

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Protein , 4 types, 4 molecules ABDE

#1: Protein MHC class I antigen / MHC class I histocompatibility antigen / B-81 alpha chain / MHC class I protein


Mass: 32071.203 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-B / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: I3ZN85
#2: Protein Beta-2-microglobulin


Mass: 11879.356 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P61769
#4: Protein beta chain T18A TCR


Mass: 27263.512 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
#5: Protein alpha chain T18A TCR


Mass: 23008.664 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)

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Protein/peptide / Non-polymers , 2 types, 424 molecules C

#3: Protein/peptide Gag-Pol polyprotein


Mass: 1032.168 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P03367
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 423 / 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: 2.99 Å3/Da / Density % sol: 58.88 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Potassium chloride, 0.05 M HEPES pH 7.5, 35% v/v Pentaerythritol propoxylate (5/4 PO/OH)

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Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 31, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.25→46.55 Å / Num. obs: 56526 / % possible obs: 100 % / Redundancy: 6.9 % / Biso Wilson estimate: 38.63 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.03414 / Rrim(I) all: 0.04828 / Net I/σ(I): 15.84
Reflection shellResolution: 2.242→2.322 Å / Rmerge(I) obs: 0.3732 / Num. unique obs: 5547 / CC1/2: 0.865 / CC star: 0.963 / Rrim(I) all: 0.5277

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4u1i, 4GG6, 4UDT

4u1i

4gg6

4udt


Resolution: 2.25→46.55 Å / SU ML: 0.3044 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.6803
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2399 1999 3.54 %
Rwork0.1958 54500 -
obs0.1974 56499 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 47.5 Å2
Refinement stepCycle: LAST / Resolution: 2.25→46.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6656 0 0 423 7079
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00626827
X-RAY DIFFRACTIONf_angle_d0.82199277
X-RAY DIFFRACTIONf_chiral_restr0.0504976
X-RAY DIFFRACTIONf_plane_restr0.00711229
X-RAY DIFFRACTIONf_dihedral_angle_d6.6188915
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.24-2.30.38511390.30213816X-RAY DIFFRACTION99.57
2.3-2.360.32871400.28133808X-RAY DIFFRACTION99.77
2.36-2.430.32851410.25323826X-RAY DIFFRACTION99.85
2.43-2.510.28271410.23573837X-RAY DIFFRACTION99.9
2.51-2.60.2971400.2273847X-RAY DIFFRACTION99.9
2.6-2.70.25081410.22533831X-RAY DIFFRACTION99.95
2.7-2.820.27031420.21993856X-RAY DIFFRACTION99.85
2.82-2.970.28241400.22153842X-RAY DIFFRACTION99.77
2.97-3.160.2661430.19943875X-RAY DIFFRACTION100
3.16-3.40.25841420.19673878X-RAY DIFFRACTION100
3.4-3.750.24761440.18543921X-RAY DIFFRACTION99.95
3.75-4.290.20951440.16743934X-RAY DIFFRACTION100
4.29-5.40.16921470.15254002X-RAY DIFFRACTION99.93
5.4-46.550.22041550.18564227X-RAY DIFFRACTION99.84
Refinement TLS params.Method: refined / Origin x: 44.5675649105 Å / Origin y: 97.3127616472 Å / Origin z: 4.73058954554 Å
111213212223313233
T0.224071245512 Å20.0287864493352 Å2-0.019237730323 Å2-0.265607026154 Å2-0.012518499615 Å2--0.268377028593 Å2
L0.180502557195 °20.0350837719473 °20.00543369170469 °2-0.534743180333 °20.585629237171 °2--1.02690140256 °2
S0.0252183646964 Å °-0.0152143113806 Å °-0.00575302077561 Å °0.0532239486426 Å °0.0976028190521 Å °-0.122295500322 Å °0.139144195569 Å °0.144566397282 Å °-0.102712659709 Å °
Refinement TLS groupSelection details: all

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