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- PDB-6vqe: HLA-B*27:05 presenting an HIV-1 13mer peptide -

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Basic information

Entry
Database: PDB / ID: 6vqe
TitleHLA-B*27:05 presenting an HIV-1 13mer peptide
Components
  • 13-mer peptide
  • Beta-2-microglobulin
  • MHC class I antigen
KeywordsIMMUNE SYSTEM / Human Leukocyte Antigen / Human Immunodeficiency Virus
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 / 2-LTR circle formation / Uncoating of the HIV Virion / Early Phase of HIV Life Cycle / Vpr-mediated nuclear import of PICs / 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 / 2-LTR circle formation / Uncoating of the HIV Virion / Early Phase of HIV Life Cycle / Vpr-mediated nuclear import of PICs / Integration of provirus / APOBEC3G mediated resistance to HIV-1 infection / Binding and entry of HIV virion / viral life cycle / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / negative regulation of receptor binding / DAP12 interactions / 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 / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / lumenal side of endoplasmic reticulum membrane / HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / cellular response to iron(III) ion / Assembly Of The HIV Virion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / retroviral ribonuclease H / negative regulation of forebrain neuron differentiation / exoribonuclease H / regulation of erythrocyte differentiation / peptide antigen assembly with MHC class I protein complex / ER to Golgi transport vesicle membrane / regulation of iron ion transport / exoribonuclease H activity / response to molecule of bacterial origin / Budding and maturation of HIV virion / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / host multivesicular body / MHC class I protein complex / protein processing / negative regulation of neurogenesis / positive regulation of receptor-mediated endocytosis / viral genome integration into host DNA / peptide antigen assembly with MHC class II protein complex / multicellular organismal-level iron ion homeostasis / RNA-directed DNA polymerase / establishment of integrated proviral latency / MHC class II protein complex / cellular response to nicotine / specific granule lumen / symbiont-mediated suppression of host gene expression / viral penetration into host nucleus / positive regulation of cellular senescence / positive regulation of T cell mediated cytotoxicity / RNA stem-loop binding / recycling endosome membrane / phagocytic vesicle membrane / peptide antigen binding / antigen processing and presentation of exogenous peptide antigen via MHC class II / RNA-directed DNA polymerase activity / negative regulation of epithelial cell proliferation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / positive regulation of immune response / Interferon gamma signaling / RNA-DNA hybrid ribonuclease activity / Modulation by Mtb of host immune system / positive regulation of T cell activation / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / sensory perception of smell / host cell / negative regulation of neuron projection development / positive regulation of protein binding / tertiary granule lumen / DAP12 signaling / MHC class II protein complex binding / late endosome membrane / peptidase activity / iron ion transport / ER-Phagosome pathway / T cell differentiation in thymus / early endosome membrane / protein refolding / viral nucleocapsid / DNA recombination / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / DNA-directed DNA polymerase / Hydrolases; Acting on ester bonds / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity
Similarity search - Function
MHC class I, alpha chain, C-terminal / MHC_I C-terminus / 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-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily ...MHC class I, alpha chain, C-terminal / MHC_I C-terminus / 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-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 / Integrase core domain / Integrase, catalytic core / Integrase catalytic domain profile. / MHC classes I/II-like antigen recognition protein / Retropepsin-like catalytic domain / RNase H type-1 domain profile. / Ribonuclease H domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Reverse transcriptase domain / Reverse transcriptase (RT) catalytic domain profile. / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Reverse transcriptase (RNA-dependent DNA polymerase) / Retroviral matrix protein / Retrovirus capsid, C-terminal / 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. / Ribonuclease H superfamily / Aspartic peptidase domain superfamily / Ribonuclease H-like superfamily / Reverse transcriptase/Diguanylate cyclase domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / DNA/RNA polymerase superfamily
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: 1.77 Å
AuthorsPymm, P. / Tenzer, S. / Wee, E. / Weimershaus, M. / Burgevin, A. / Kollnberger, S. / Gerstoft, J. / Josephs, T.M. / Ladell, K. / Mclaren, J.E. ...Pymm, P. / Tenzer, S. / Wee, E. / Weimershaus, M. / Burgevin, A. / Kollnberger, S. / Gerstoft, J. / Josephs, T.M. / Ladell, K. / Mclaren, J.E. / Appay, V. / Price, D.A. / Fugger, L. / Bell, J.I. / Hansjorg, S. / Van Endert, P. / Harkiolaki, M. / Iversen, A.K.N.
CitationJournal: Cell Rep / Year: 2022
Title: Epitope length variants balance protective immune responses and viral escape in HIV-1 infection
Authors: Pymm, P. / Tenzer, S. / Wee, E. / Weimershaus, M. / Burgevin, A. / Kollnberger, S. / Gerstoft, J. / Josephs, T.M. / Ladell, K. / McLaren, J.E. / Appay, V. / Price, D.A. / Fugger, L. / Bell, ...Authors: Pymm, P. / Tenzer, S. / Wee, E. / Weimershaus, M. / Burgevin, A. / Kollnberger, S. / Gerstoft, J. / Josephs, T.M. / Ladell, K. / McLaren, J.E. / Appay, V. / Price, D.A. / Fugger, L. / Bell, J.I. / Schild, H. / van Endert, P. / Harkiolaki, M. / Iversen, A.K.
History
DepositionFeb 5, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 10, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 9, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _citation_author.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 11, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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: 13-mer peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,6055
Polymers45,4213
Non-polymers1842
Water6,882382
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5210 Å2
ΔGint-15 kcal/mol
Surface area19060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.940, 82.782, 109.426
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein MHC class I antigen


Mass: 31928.160 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 (E. coli) / References: UniProt: O78189
#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 (E. coli) / References: UniProt: P61769
#3: Protein/peptide 13-mer peptide


Mass: 1613.047 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Human immunodeficiency virus 1 / References: UniProt: P04585*PLUS
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 382 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.54 Å3/Da / Density % sol: 51.57 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.8
Details: 20 %w/v Polyethylene Glycol 3350, 0.2 M Potassium di-Hydrogen Phosphate

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Data collection

DiffractionMean temperature: 105 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9778 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 25, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9778 Å / Relative weight: 1
ReflectionResolution: 1.77→46.181 Å / Num. obs: 45852 / % possible obs: 99.8 % / Redundancy: 6.1 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 13.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsDiffraction-ID% possible all
1.77-1.814.90.4472489196.7
9.03-46.185.50.038421199.7

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Processing

Software
NameVersionClassification
xia2data scaling
PHENIX1.16_3549refinement
PDB_EXTRACT3.25data extraction
xia2data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1W0V

1w0v


Resolution: 1.77→46.181 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 17.93
RfactorNum. reflection% reflection
Rfree0.1861 2000 4.37 %
Rwork0.1613 --
obs0.1625 45760 99.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 93.27 Å2 / Biso mean: 26.0754 Å2 / Biso min: 5.5 Å2
Refinement stepCycle: final / Resolution: 1.77→46.181 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3182 0 12 383 3577
Biso mean--42.43 37.19 -
Num. residues----386
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.77-1.81430.24411370.198298497
1.8143-1.86330.23791390.18463065100
1.8633-1.91820.21721420.16873088100
1.9182-1.98010.21271410.16543111100
1.9801-2.05090.21141420.16743092100
2.0509-2.1330.19551410.16373087100
2.133-2.230.19831430.16413127100
2.23-2.34760.21021410.16773085100
2.3476-2.49470.20351430.16933134100
2.4947-2.68730.23291430.17593139100
2.6873-2.95770.2041440.17873131100
2.9577-3.38550.17261440.16033162100
3.3855-4.2650.14831460.13823209100
4.265-46.1810.15391540.1513346100
Refinement TLS params.Method: refined / Origin x: -12.0182 Å / Origin y: -9.4204 Å / Origin z: 18.9159 Å
111213212223313233
T0.0565 Å20.0012 Å20.0006 Å2-0.0294 Å2-0.0124 Å2--0.0377 Å2
L0.9354 °20.1118 °20.1015 °2-0.409 °2-0.063 °2--0.3442 °2
S-0.0569 Å °-0.0026 Å °0.0675 Å °-0.0295 Å °0.0198 Å °-0.0235 Å °-0.0101 Å °-0.0399 Å °-0.0981 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1 - 276
2X-RAY DIFFRACTION1allB0 - 99
3X-RAY DIFFRACTION1allC1 - 13
4X-RAY DIFFRACTION1allE1 - 421
5X-RAY DIFFRACTION1allD1 - 2

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