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- PDB-1qvo: STRUCTURES OF HLA-A*1101 IN COMPLEX WITH IMMUNODOMINANT NONAMER A... -

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Entry
Database: PDB / ID: 1qvo
TitleSTRUCTURES OF HLA-A*1101 IN COMPLEX WITH IMMUNODOMINANT NONAMER AND DECAMER HIV-1 EPITOPES CLEARLY REVEAL THE PRESENCE OF A MIDDLE ANCHOR RESIDUE
Components
  • Beta-2-microglobulin
  • HLA class I histocompatibility antigen, A-11 alpha chain
  • Negative factor
KeywordsIMMUNE SYSTEM
Function / homology
Function and homology information


symbiont-mediated suppression of host antigen processing and presentation of peptide antigen via MHC class I / symbiont-mediated suppression of host antigen processing and presentation of peptide antigen via MHC class II / symbiont-mediated suppression of host autophagy / positive regulation of memory T cell activation / T cell mediated cytotoxicity directed against tumor cell target / TAP complex binding / Golgi medial cisterna / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / positive regulation of CD8-positive, alpha-beta T cell proliferation ...symbiont-mediated suppression of host antigen processing and presentation of peptide antigen via MHC class I / symbiont-mediated suppression of host antigen processing and presentation of peptide antigen via MHC class II / symbiont-mediated suppression of host autophagy / positive regulation of memory T cell activation / T cell mediated cytotoxicity directed against tumor cell target / TAP complex binding / Golgi medial cisterna / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / positive regulation of CD8-positive, alpha-beta T cell proliferation / CD8 receptor binding / antigen processing and presentation of exogenous peptide antigen via MHC class I / beta-2-microglobulin binding / endoplasmic reticulum exit site / TAP binding / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / protection from natural killer cell mediated cytotoxicity / host cell Golgi 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 / detection of bacterium / T cell receptor binding / 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 / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / peptide antigen assembly with MHC class II protein complex / cellular response to iron(III) ion / MHC class II protein complex / 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 / positive regulation of T cell activation / peptide antigen binding / positive regulation of receptor-mediated endocytosis / negative regulation of neurogenesis / cellular response to nicotine / SH3 domain binding / positive regulation of T cell mediated cytotoxicity / multicellular organismal-level iron ion homeostasis / virion component / specific granule lumen / positive regulation of type II interferon production / phagocytic vesicle membrane / recycling endosome membrane / Interferon gamma signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / negative regulation of epithelial cell proliferation / MHC class II protein complex binding / Interferon alpha/beta signaling / Modulation by Mtb of host immune system / late endosome membrane / sensory perception of smell / antibacterial humoral response / positive regulation of cellular senescence / tertiary granule lumen / DAP12 signaling / T cell differentiation in thymus / T cell receptor signaling pathway / E3 ubiquitin ligases ubiquitinate target proteins / negative regulation of neuron projection development / ER-Phagosome pathway / protein refolding / early endosome membrane / protein homotetramerization / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / defense response to Gram-positive bacterium / immune response / endoplasmic reticulum lumen / Amyloid fiber formation / signaling receptor binding / Golgi membrane / lysosomal membrane / innate immune response / external side of plasma membrane / focal adhesion / Neutrophil degranulation / endoplasmic reticulum membrane / GTP binding / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane
Similarity search - Function
HIV-1 Nef protein, anchor domain superfamily / HIV negative factor Nef / HIV-1 Nef protein, core domain superfamily / Negative factor, (F-Protein) or Nef / 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 ...HIV-1 Nef protein, anchor domain superfamily / HIV negative factor Nef / HIV-1 Nef protein, core domain superfamily / Negative factor, (F-Protein) or Nef / 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 / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
HLA class I histocompatibility antigen, A alpha chain / Protein Nef / HLA class I histocompatibility antigen, A alpha chain / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
Human immunodeficiency virus 1
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.22 Å
AuthorsLi, L. / McNicholl, J.M. / Bouvier, M.
Citation
Journal: J.Immunol. / Year: 2004
Title: Structures of HLA-A*1101 complexed with immunodominant nonamer and decamer HIV-1 epitopes clearly reveal the presence of a middle, secondary anchor residue.
Authors: Li, L. / Bouvier, M.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2002
Title: Crystallization and preliminary X-ray crystallographic studies of HLA-A*1101 complexed with an HIV-1 decapeptide
Authors: Li, L. / Promadej, N. / McNicholl, J.M. / Bouvier, M.
History
DepositionAug 28, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 1, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Feb 19, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Source and taxonomy
Category: pdbx_entity_src_syn / pdbx_struct_assembly ...pdbx_entity_src_syn / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / struct_biol / struct_ref_seq_dif
Item: _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_scientific / _struct_ref_seq_dif.details
Revision 1.5Oct 30, 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

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Assembly

Deposited unit
A: HLA class I histocompatibility antigen, A-11 alpha chain
B: Beta-2-microglobulin
C: Negative factor
D: HLA class I histocompatibility antigen, A-11 alpha chain
E: Beta-2-microglobulin
F: Negative factor


Theoretical massNumber of molelcules
Total (without water)89,9386
Polymers89,9386
Non-polymers00
Water7,692427
1
A: HLA class I histocompatibility antigen, A-11 alpha chain
B: Beta-2-microglobulin
C: Negative factor


Theoretical massNumber of molelcules
Total (without water)44,9693
Polymers44,9693
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4640 Å2
ΔGint-21 kcal/mol
Surface area18710 Å2
MethodPISA
2
D: HLA class I histocompatibility antigen, A-11 alpha chain
E: Beta-2-microglobulin
F: Negative factor


Theoretical massNumber of molelcules
Total (without water)44,9693
Polymers44,9693
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4610 Å2
ΔGint-22 kcal/mol
Surface area18760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.200, 88.500, 64.800
Angle α, β, γ (deg.)90.00, 90.13, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein HLA class I histocompatibility antigen, A-11 alpha chain / MHC class I antigen A*11


Mass: 31855.051 Da / Num. of mol.: 2 / Fragment: EXTRACELLULAR DOMAINS ALPHA 1,ALPHA 2 AND ALPHA 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: from 1 major histocompatibility complex / Gene: HLA-A OR HLAA / Plasmid: PLM1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)PLYsS / References: UniProt: P13746, UniProt: P04439*PLUS
#2: Protein Beta-2-microglobulin / HDCMA22P


Mass: 11879.356 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M / Plasmid: PHN1 / Production host: Escherichia coli (E. coli) / Strain (production host): XA90 / References: UniProt: P61769
#3: Protein/peptide Negative factor / F-protein / 27 kDa protein / 3'ORF


Mass: 1234.509 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: THE PEPTIDE WAS OBTAINED THROUGH STANDARD SOLID-PHASE PEPTIDE SYNTHESIS. The sequence of the peptide is naturally found in Human Immunodeficiency Virus Type 1.
Source: (synth.) Human immunodeficiency virus 1 / References: UniProt: P04602
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 427 / 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: 2.43 Å3/Da / Density % sol: 49.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: PEG 4000, ammonium acetate, sodium citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: SIEMENS HI-STAR / Detector: AREA DETECTOR / Date: Jun 14, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→49.3 Å / Num. all: 43166 / Num. obs: 40704 / % possible obs: 94.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.063 / Net I/σ(I): 10.6
Reflection shellResolution: 2.22→2.34 Å / Mean I/σ(I) obs: 2.4 / % possible all: 51.3

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Processing

Software
NameClassification
X-GENdata scaling
X-GENdata reduction
AMoREphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.22→49.3 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.255 1988 -RANDOM
Rwork0.212 ---
all0.216 42732 --
obs0.216 39698 92.9 %-
Solvent computationBsol: 53.0261 Å2 / ksol: 0.453517 e/Å3
Displacement parameters
Baniso -1Baniso -3Baniso -2
1-2.862 Å2-0.516 Å2-
2----0.943 Å2
3---1.919 Å2-
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.32 Å0.3 Å
Refinement stepCycle: LAST / Resolution: 2.22→49.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6336 0 0 427 6763
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.3391.5
X-RAY DIFFRACTIONc_mcangle_it2.142
X-RAY DIFFRACTIONc_scbond_it2.1532
X-RAY DIFFRACTIONc_scangle_it3.0882.5
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_dihedral_angle_d25.2
X-RAY DIFFRACTIONc_improper_angle_d0.77
LS refinement shellResolution: 2.22→2.34 Å / Rfactor Rfree error: 0.025
RfactorNum. reflection% reflection
Rfree0.324 170 -
Rwork0.307 --
obs-3734 51.3 %

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