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- PDB-5xot: Crystal structure of pHLA-B35 in complex with TU55 T cell receptor -

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Basic information

Entry
Database: PDB / ID: 5xot
TitleCrystal structure of pHLA-B35 in complex with TU55 T cell receptor
Components
  • An HIV reverse transcriptase epitope
  • Beta-2-microglobulinBeta-2 microglobulin
  • HLA class I histocompatibility antigen, B-35 alpha chain
  • The Delta chain of TU55 TCR
  • The beta chain of TU55 TCR
KeywordsIMMUNE SYSTEM / antigen presentation / MHC / peptide antigen / T cell activation
Function / homology
Function and homology information


regulation of interleukin-12 production / regulation of dendritic cell differentiation / integrase activity / regulation of T cell anergy / regulation of interleukin-6 production / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / Minus-strand DNA synthesis / Plus-strand DNA synthesis / Uncoating of the HIV Virion ...regulation of interleukin-12 production / regulation of dendritic cell differentiation / integrase activity / regulation of T cell anergy / regulation of interleukin-6 production / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / Minus-strand DNA synthesis / Plus-strand DNA synthesis / Uncoating of the HIV Virion / 2-LTR circle formation / Vpr-mediated nuclear import of PICs / Early Phase of HIV Life Cycle / Integration of provirus / APOBEC3G mediated resistance to HIV-1 infection / Binding and entry of HIV virion / TAP binding / protection from natural killer cell mediated cytotoxicity / viral life cycle / 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 / detection of bacterium / secretory granule membrane / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / early endosome lumen / positive regulation of receptor binding / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / negative regulation of receptor binding / lumenal side of endoplasmic reticulum membrane / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / Assembly Of The HIV Virion / HIV-1 retropepsin / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / cellular response to iron(III) ion / : / negative regulation of forebrain neuron differentiation / defense response / Budding and maturation of HIV virion / ER to Golgi transport vesicle membrane / retroviral ribonuclease H / exoribonuclease H / peptide antigen assembly with MHC class I protein complex / response to molecule of bacterial origin / regulation of erythrocyte differentiation / regulation of iron ion transport / MHC class I peptide loading complex / : / exoribonuclease H activity / HFE-transferrin receptor complex / T cell mediated cytotoxicity / cellular response to iron ion / protein processing / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / MHC class I protein complex / host multivesicular body / multicellular organismal-level iron ion homeostasis / positive regulation of T cell mediated cytotoxicity / peptide antigen assembly with MHC class II protein complex / negative regulation of neurogenesis / MHC class II protein complex / positive regulation of receptor-mediated endocytosis / cellular response to nicotine / RNA-directed DNA polymerase / recycling endosome membrane / phagocytic vesicle membrane / specific granule lumen / peptide antigen binding / viral genome integration into host DNA / viral penetration into host nucleus / establishment of integrated proviral latency / positive regulation of cellular senescence / antigen processing and presentation of exogenous peptide antigen via MHC class II / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / RNA-directed DNA polymerase activity / Interferon gamma signaling / positive regulation of immune response / negative regulation of epithelial cell proliferation / Modulation by Mtb of host immune system / positive regulation of T cell activation / Interferon alpha/beta signaling / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / sensory perception of smell / RNA-DNA hybrid ribonuclease activity / negative regulation of neuron projection development / tertiary granule lumen / DAP12 signaling / MHC class II protein complex binding / late endosome membrane / T cell differentiation in thymus / positive regulation of protein binding / peptidase activity / ER-Phagosome pathway / iron ion transport / protein-folding chaperone binding / protein refolding / early endosome membrane
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 / Beta-2-Microglobulin / Reverse transcriptase connection / Reverse transcriptase connection domain / MHC class I-like antigen recognition-like ...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 / Reverse transcriptase connection / Reverse transcriptase connection domain / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / Reverse transcriptase thumb / Reverse transcriptase thumb domain / 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 / MHC classes I/II-like antigen recognition protein / Integrase core domain / Integrase, catalytic core / Integrase catalytic domain profile. / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Retropepsin-like catalytic domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Ribonuclease H domain / RNase H type-1 domain profile. / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase domain / Reverse transcriptase (RT) catalytic domain profile. / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Retrovirus capsid, C-terminal / 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 / Ribonuclease H superfamily / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily / Ribonuclease H-like superfamily / Reverse transcriptase/Diguanylate cyclase domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / DNA/RNA polymerase superfamily / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
HLA class I histocompatibility antigen, B alpha chain / Gag-Pol polyprotein / HLA class I histocompatibility antigen, B alpha chain / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
Human immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.787 Å
AuthorsShi, Y. / Qi, J. / Gao, G.F.
CitationJournal: J. Virol. / Year: 2017
Title: Conserved V delta 1 Binding Geometry in a Setting of Locus-Disparate pHLA Recognition by delta / alpha beta T Cell Receptors (TCRs): Insight into Recognition of HIV Peptides by TCRs.
Authors: Shi, Y. / Kawana-Tachikawa, A. / Gao, F. / Qi, J. / Liu, C. / Gao, J. / Cheng, H. / Ueno, T. / Iwamoto, A. / Gao, G.F.
History
DepositionMay 31, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 14, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 30, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.2Nov 22, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_DOI ..._citation.journal_abbrev / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Apr 17, 2019Group: Data collection / Database references / Category: citation / Item: _citation.journal_volume / _citation.title
Revision 1.4Mar 20, 2024Group: Data collection / Database references / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_src_gen
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HLA class I histocompatibility antigen, B-35 alpha chain
B: Beta-2-microglobulin
C: An HIV reverse transcriptase epitope
D: The Delta chain of TU55 TCR
E: The beta chain of TU55 TCR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,1828
Polymers94,9065
Non-polymers2763
Water59433
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11930 Å2
ΔGint-58 kcal/mol
Surface area37520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)195.687, 59.596, 92.808
Angle α, β, γ (deg.)90.00, 105.98, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 3 types, 3 molecules ABE

#1: Protein HLA class I histocompatibility antigen, B-35 alpha chain / MHC class I antigen B*35


Mass: 31956.203 Da / Num. of mol.: 1 / Fragment: UNP residues 25-300 / Mutation: V34D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-B, HLAB
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P30685, UniProt: P01889*PLUS
#2: Protein Beta-2-microglobulin / Beta-2 microglobulin


Mass: 11748.160 Da / Num. of mol.: 1 / Fragment: UNP residues 21-119
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P61769
#5: Protein The beta chain of TU55 TCR


Mass: 27342.471 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)

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Protein/peptide / Antibody , 2 types, 2 molecules CD

#3: Protein/peptide An HIV reverse transcriptase epitope


Mass: 1014.126 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Human immunodeficiency virus 1 / References: UniProt: P04585*PLUS
#4: Antibody The Delta chain of TU55 TCR


Mass: 22844.660 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)

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Non-polymers , 2 types, 36 molecules

#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C3H8O3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 33 / 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: 2.73 Å3/Da / Density % sol: 55.02 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 5% v/v Tacsimate pH 7.0, 0.1 M HEPES, pH 7.3, 10% w/v polyethylene glycol monomethyl either 5000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jul 20, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.787→50 Å / Num. obs: 24542 / % possible obs: 94.4 % / Redundancy: 5.9 % / Net I/σ(I): 17.762
Reflection shellResolution: 2.787→2.9 Å / Redundancy: 5.7 % / Mean I/σ(I) obs: 4.976 / % possible all: 75.8

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Processing

Software
NameVersionClassification
PHENIX1.5_2refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.787→36.596 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 0.11 / Phase error: 27.94
RfactorNum. reflection% reflection
Rfree0.254 1227 5.2 %
Rwork0.1988 --
obs0.2017 23597 90.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Bsol: 40.129 Å2 / ksol: 0.386 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-31.0111 Å20 Å2-17.0188 Å2
2---11.1735 Å20 Å2
3----19.8375 Å2
Refinement stepCycle: LAST / Resolution: 2.787→36.596 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6695 0 0 33 6728
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0056871
X-RAY DIFFRACTIONf_angle_d0.6959313
X-RAY DIFFRACTIONf_dihedral_angle_d18.5542491
X-RAY DIFFRACTIONf_chiral_restr0.05977
X-RAY DIFFRACTIONf_plane_restr0.0031223
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7867-2.89820.3004980.23991829X-RAY DIFFRACTION67
2.8982-3.030.30821360.23172070X-RAY DIFFRACTION77
3.03-3.18970.29361310.222339X-RAY DIFFRACTION86
3.1897-3.38940.27471450.20452532X-RAY DIFFRACTION93
3.3894-3.65090.27091360.19772641X-RAY DIFFRACTION97
3.6509-4.01790.26011450.18182687X-RAY DIFFRACTION98
4.0179-4.59830.19611360.16852739X-RAY DIFFRACTION99
4.5983-5.78970.24031470.17842727X-RAY DIFFRACTION99
5.7897-36.5990.2321530.20412806X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -37.537 Å / Origin y: -0.0097 Å / Origin z: -16.2187 Å
111213212223313233
T0.3128 Å2-0.0119 Å20.0137 Å2-0.3067 Å2-0.014 Å2--0.3158 Å2
L0.2202 °2-0.173 °20.2918 °2-0.1739 °2-0.1836 °2--0.4821 °2
S0.0643 Å °-0.0038 Å °-0.0116 Å °0.0188 Å °-0.0252 Å °0.0248 Å °0.013 Å °0.0013 Å °0 Å °
Refinement TLS groupSelection details: all

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