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- PDB-5nmk: HLA A02 presenting SLFNTIAVL -

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Basic information

Entry
Database: PDB / ID: 5nmk
TitleHLA A02 presenting SLFNTIAVL
Components
  • Beta-2-microglobulinBeta-2 microglobulin
  • Gag proteinHIV-1 protease
  • HLA class I histocompatibility antigen, A-2 alpha chain
KeywordsIMMUNE SYSTEM / MHC / TCR / CD8+
Function / homology
Function and homology information


host cellular component / Synthesis And Processing Of GAG, GAGPOL Polyproteins / host cell nuclear membrane / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / T cell mediated cytotoxicity directed against tumor cell target / positive regulation of memory T cell activation / Minus-strand DNA synthesis / Plus-strand DNA synthesis / Uncoating of the HIV Virion ...host cellular component / Synthesis And Processing Of GAG, GAGPOL Polyproteins / host cell nuclear membrane / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / T cell mediated cytotoxicity directed against tumor cell target / positive regulation of memory T cell activation / Minus-strand DNA synthesis / Plus-strand DNA synthesis / Uncoating of the HIV Virion / 2-LTR circle formation / Vpr-mediated nuclear import of PICs / viral budding via host ESCRT complex / Early Phase of HIV Life Cycle / antigen processing and presentation of exogenous peptide antigen via MHC class I / Integration of provirus / APOBEC3G mediated resistance to HIV-1 infection / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / 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 / Binding and entry of HIV virion / endoplasmic reticulum exit site / beta-2-microglobulin binding / detection of bacterium / TAP binding / protection from natural killer cell mediated cytotoxicity / Membrane binding and targetting of GAG proteins / 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 / viral process / T cell receptor binding / 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 / 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 / ER to Golgi transport vesicle membrane / Budding and maturation of HIV virion / response to molecule of bacterial origin / regulation of erythrocyte differentiation / regulation of iron ion transport / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / cellular response to iron ion / 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 / positive regulation of receptor-mediated endocytosis / MHC class II protein complex / cellular response to nicotine / recycling endosome membrane / phagocytic vesicle membrane / specific granule lumen / peptide antigen binding / positive regulation of type II interferon production / 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 / positive regulation of immune response / Interferon gamma signaling / negative regulation of epithelial cell proliferation / Modulation by Mtb of host immune system / positive regulation of T cell activation / Interferon alpha/beta signaling / sensory perception of smell / negative regulation of neuron projection development / E3 ubiquitin ligases ubiquitinate target proteins / tertiary granule lumen / DAP12 signaling / MHC class II protein complex binding / T cell differentiation in thymus / late endosome membrane / T cell receptor signaling pathway / positive regulation of protein binding / ER-Phagosome pathway / iron ion transport / antibacterial humoral response / protein refolding / early endosome membrane / protein homotetramerization / viral nucleocapsid
Similarity search - Function
Gag protein p6 / Gag protein p6 / gag protein p24 N-terminal 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 / Beta-2-Microglobulin ...Gag protein p6 / Gag protein p6 / gag protein p24 N-terminal 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 / Beta-2-Microglobulin / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / Immunodeficiency lentiviral matrix, N-terminal / gag gene protein p17 (matrix protein) / MHC classes I/II-like antigen recognition protein / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / 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 / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
HLA class I histocompatibility antigen, A alpha chain / HLA class I histocompatibility antigen, A alpha chain / Gag polyprotein / Beta-2-microglobulin / Gag protein
Similarity search - Component
Biological speciesHomo sapiens (human)
Human immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.66 Å
AuthorsRizkallah, P.J. / Cole, D.K. / Fuller, A. / Sewell, A.K.
CitationJournal: Front Immunol / Year: 2017
Title: Dual Molecular Mechanisms Govern Escape at Immunodominant HLA A2-Restricted HIV Epitope.
Authors: Cole, D.K. / Fuller, A. / Dolton, G. / Zervoudi, E. / Legut, M. / Miles, K. / Blanchfield, L. / Madura, F. / Holland, C.J. / Bulek, A.M. / Bridgeman, J.S. / Miles, J.J. / Schauenburg, A.J.A. ...Authors: Cole, D.K. / Fuller, A. / Dolton, G. / Zervoudi, E. / Legut, M. / Miles, K. / Blanchfield, L. / Madura, F. / Holland, C.J. / Bulek, A.M. / Bridgeman, J.S. / Miles, J.J. / Schauenburg, A.J.A. / Beck, K. / Evavold, B.D. / Rizkallah, P.J. / Sewell, A.K.
History
DepositionApr 6, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 15, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Dec 20, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HLA class I histocompatibility antigen, A-2 alpha chain
B: Beta-2-microglobulin
C: Gag protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,65115
Polymers44,8083
Non-polymers84312
Water5,278293
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6800 Å2
ΔGint-14 kcal/mol
Surface area18980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.840, 79.030, 58.370
Angle α, β, γ (deg.)90.00, 116.11, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein HLA class I histocompatibility antigen, A-2 alpha chain / MHC class I antigen A*2


Mass: 31951.316 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-A, HLAA / Production host: Escherichia coli (E. coli) / References: UniProt: P01892, UniProt: P04439*PLUS
#2: Protein Beta-2-microglobulin / 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

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Protein/peptide , 1 types, 1 molecules C

#3: Protein/peptide Gag protein / HIV-1 protease


Mass: 977.155 Da / Num. of mol.: 1 / Fragment: UNP Residues 67-75 / Source method: obtained synthetically / Source: (synth.) Human immunodeficiency virus 1 / References: UniProt: W0GUW4, UniProt: P04591*PLUS

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Non-polymers , 4 types, 305 molecules

#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 293 / 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: 2.58 Å3/Da / Density % sol: 52.34 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Sodium Cacodylate, pH 6.0, 25% PEG 4000, 0.2 M Ammonium Sulphate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9778 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 27, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9778 Å / Relative weight: 1
ReflectionResolution: 1.655→48.4 Å / Num. obs: 53961 / % possible obs: 98.9 % / Redundancy: 3.6 % / Biso Wilson estimate: 22.5 Å2 / Rmerge(I) obs: 0.074 / Net I/σ(I): 9.5
Reflection shellResolution: 1.655→1.7 Å / Redundancy: 3.7 % / Rmerge(I) obs: 1.3 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 4000 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
xia2data reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.66→48.4 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.952 / SU B: 4.288 / SU ML: 0.07 / Cross valid method: THROUGHOUT / ESU R: 0.092 / ESU R Free: 0.094 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20979 2724 5.1 %RANDOM
Rwork0.17533 ---
obs0.17707 50896 98.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.242 Å2
Baniso -1Baniso -2Baniso -3
1-0.78 Å2-0 Å2-0.29 Å2
2--0.5 Å20 Å2
3----0.67 Å2
Refinement stepCycle: 1 / Resolution: 1.66→48.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3160 0 52 293 3505
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0193327
X-RAY DIFFRACTIONr_bond_other_d0.0020.022919
X-RAY DIFFRACTIONr_angle_refined_deg1.8311.9314502
X-RAY DIFFRACTIONr_angle_other_deg1.03236762
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5675390
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.53723.086175
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.50615535
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7971529
X-RAY DIFFRACTIONr_chiral_restr0.1120.2459
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0213709
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02744
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0191.3141557
X-RAY DIFFRACTIONr_mcbond_other1.0141.3131556
X-RAY DIFFRACTIONr_mcangle_it1.6841.9631948
X-RAY DIFFRACTIONr_mcangle_other1.6841.9641949
X-RAY DIFFRACTIONr_scbond_it1.5971.6131770
X-RAY DIFFRACTIONr_scbond_other1.591.5721762
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.4722.262543
X-RAY DIFFRACTIONr_long_range_B_refined6.92816.5193704
X-RAY DIFFRACTIONr_long_range_B_other6.82816.0863660
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.655→1.698 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.284 210 -
Rwork0.27 3748 -
obs--98.83 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.983-0.37060.20881.79-0.19750.7274-0.016-0.00270.02190.01770.0024-0.1541-0.05010.10810.01360.0094-0.0057-0.02420.018-0.00690.101654.73687.839665.9233
23.65151.51212.15010.90050.8531.61520.05890.1049-0.178-0.0293-0.0093-0.03070.0832-0.015-0.04960.0195-0.0032-0.02010.0422-0.00140.110929.5139-18.370264.744
32.02841.0227-1.20213.4689-1.78333.04570.0722-0.0380.1580.22960.06930.3589-0.2676-0.2186-0.14150.03270.0257-0.00180.0382-0.00780.13130.690.987577.2812
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 180
2X-RAY DIFFRACTION1C1 - 9
3X-RAY DIFFRACTION2A181 - 276
4X-RAY DIFFRACTION3B0 - 99

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