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- PDB-6j1v: The structure of HLA-A*3003/RT313 -

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Basic information

Entry
Database: PDB / ID: 6j1v
TitleThe structure of HLA-A*3003/RT313
Components
  • Beta-2-microglobulin
  • HLA-A*3003
  • RT313
KeywordsIMMUNE SYSTEM / The structure of HLA-A*3003/RT313
Function / homology
Function and homology information


integrase activity / 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 ...integrase activity / 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 / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / viral life cycle / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / Endosomal/Vacuolar pathway / T cell mediated cytotoxicity / HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / retroviral ribonuclease H / exoribonuclease H / lumenal side of endoplasmic reticulum membrane / regulation of iron ion transport / cellular response to iron(III) ion / negative regulation of iron ion transport / negative regulation of forebrain neuron differentiation / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / exoribonuclease H activity / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of erythrocyte differentiation / Assembly Of The HIV Virion / response to molecule of bacterial origin / MHC class I peptide loading complex / HFE-transferrin receptor complex / transferrin transport / cellular response to iron ion / negative regulation of receptor-mediated endocytosis / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / Budding and maturation of HIV virion / protein processing / MHC class I protein complex / peptide antigen assembly with MHC class II protein complex / negative regulation of neurogenesis / viral genome integration into host DNA / cellular response to nicotine / positive regulation of receptor-mediated endocytosis / MHC class II protein complex / positive regulation of T cell mediated cytotoxicity / establishment of integrated proviral latency / RNA-directed DNA polymerase / multicellular organismal-level iron ion homeostasis / RNA stem-loop binding / specific granule lumen / peptide antigen binding / viral penetration into host nucleus / antigen processing and presentation of exogenous peptide antigen via MHC class II / host multivesicular body / phagocytic vesicle membrane / positive regulation of immune response / RNA-directed DNA polymerase activity / recycling endosome membrane / RNA-DNA hybrid ribonuclease activity / Interferon gamma signaling / positive regulation of T cell activation / negative regulation of epithelial cell proliferation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / Modulation by Mtb of host immune system / sensory perception of smell / positive regulation of cellular senescence / tertiary granule lumen / DAP12 signaling / MHC class II protein complex binding / T cell differentiation in thymus / peptidase activity / late endosome membrane / host cell / negative regulation of neuron projection development / ER-Phagosome pathway / protein refolding / viral nucleocapsid / early endosome membrane / DNA recombination / amyloid fibril formation / DNA-directed DNA polymerase / protein homotetramerization / 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
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 / Reverse transcriptase thumb / Reverse transcriptase thumb domain ...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 / Reverse transcriptase thumb / Reverse transcriptase thumb domain / Beta-2-Microglobulin / Integrase Zinc binding domain / : / Zinc finger integrase-type profile. / MHC class I-like antigen recognition-like / Integrase DNA binding domain / Integrase, C-terminal domain superfamily, retroviral / MHC class I-like antigen recognition-like superfamily / Integrase, N-terminal zinc-binding domain / Integrase-like, N-terminal / 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 / RNase H type-1 domain profile. / Ribonuclease H domain / MHC classes I/II-like antigen recognition protein / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / : / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Reverse transcriptase (RNA-dependent DNA polymerase) / Retrovirus capsid, C-terminal / Reverse transcriptase domain / 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 / Resolution: 2 Å
AuthorsZhu, S.Y. / Liu, K.F. / Chai, Y. / Ding, C.M. / Lv, J.X. / Gao, G.F. / Lou, Y.L. / Liu, W.J.
CitationJournal: Front Immunol / Year: 2019
Title: Divergent Peptide Presentations of HLA-A*30 Alleles Revealed by Structures With Pathogen Peptides.
Authors: Zhu, S. / Liu, K. / Chai, Y. / Wu, Y. / Lu, D. / Xiao, W. / Cheng, H. / Zhao, Y. / Ding, C. / Lyu, J. / Lou, Y. / Gao, G.F. / Liu, W.J.
History
DepositionDec 29, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 25, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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: HLA-A*3003
B: Beta-2-microglobulin
C: RT313


Theoretical massNumber of molelcules
Total (without water)44,3543
Polymers44,3543
Non-polymers00
Water5,296294
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4190 Å2
ΔGint-17 kcal/mol
Surface area18750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.263, 72.129, 124.679
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein HLA-A*3003


Mass: 31592.729 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): K-12 / References: UniProt: A0A173ADK6*PLUS
#2: Protein Beta-2-microglobulin / hB2m / FcRn light chain


Mass: 11748.160 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): K-12 / References: UniProt: P61769
#3: Protein/peptide RT313


Mass: 1013.188 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Human immunodeficiency virus 1 / References: UniProt: P04585*PLUS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 294 / Source method: isolated from a natural source / Formula: H2O
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: 2.65 Å3/Da / Density % sol: 53.57 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M HEPES (pH 7.5), 25% (w/v) polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å
DetectorType: SDMS / Detector: IMAGE PLATE / Date: Jan 10, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 32751 / % possible obs: 99.8 % / Redundancy: 7.3 % / Net I/σ(I): 0.2
Reflection shellResolution: 2→2.07 Å

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementResolution: 2→48.2 Å / SU ML: 0.2 / Cross valid method: NONE / σ(F): 1.34 / Phase error: 20.94
RfactorNum. reflection% reflection
Rfree0.217 1624 5.01 %
Rwork0.2013 --
obs0.2021 32428 98.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2→48.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3125 0 0 294 3419
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073211
X-RAY DIFFRACTIONf_angle_d0.8034356
X-RAY DIFFRACTIONf_dihedral_angle_d27.9671195
X-RAY DIFFRACTIONf_chiral_restr0.06443
X-RAY DIFFRACTIONf_plane_restr0.005575
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9966-2.05540.25941420.24712336X-RAY DIFFRACTION93
2.0554-2.12170.28311280.23622516X-RAY DIFFRACTION97
2.1217-2.19750.27211280.23062525X-RAY DIFFRACTION99
2.1975-2.28550.2591150.23212582X-RAY DIFFRACTION100
2.2855-2.38950.24711470.23062542X-RAY DIFFRACTION100
2.3895-2.51550.24321500.23032532X-RAY DIFFRACTION100
2.5155-2.67310.23131590.21922551X-RAY DIFFRACTION100
2.6731-2.87950.21261340.22642592X-RAY DIFFRACTION100
2.8795-3.16920.24011260.2182595X-RAY DIFFRACTION100
3.1692-3.62770.21321290.19882622X-RAY DIFFRACTION100
3.6277-4.56990.15461320.16082649X-RAY DIFFRACTION100
4.5699-48.21370.19781340.16912762X-RAY DIFFRACTION99

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