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- PDB-8rnh: Crystal structure of HLA B*18:01 in complex with EEIEITTHF, an 9-... -

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Basic information

Entry
Database: PDB / ID: 8rnh
TitleCrystal structure of HLA B*18:01 in complex with EEIEITTHF, an 9-mer epitope from Influenza A
Components
  • Beta-2-microglobulin
  • MHC class I antigen
  • RNA-directed RNA polymerase catalytic subunit
KeywordsIMMUNE SYSTEM / human leukocyte antigen / major histocompatibility complex / HLA-B*18:01 / Influenza A
Function / homology
Function and homology information


viral transcription / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / 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 / Antigen Presentation: Folding, assembly and peptide loading of class I MHC ...viral transcription / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / 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 / 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 / positive regulation of T cell mediated cytotoxicity / multicellular organismal-level iron ion homeostasis / specific granule lumen / 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 / Modulation by Mtb of host immune system / late endosome membrane / sensory perception of smell / positive regulation of cellular senescence / tertiary granule lumen / DAP12 signaling / T cell differentiation in thymus / negative regulation of neuron projection development / ER-Phagosome pathway / protein refolding / early endosome membrane / protein homotetramerization / amyloid fibril formation / intracellular iron ion homeostasis / host cell cytoplasm / learning or memory / endoplasmic reticulum lumen / Amyloid fiber formation / Golgi membrane / lysosomal membrane / external side of plasma membrane / RNA-directed RNA polymerase / viral RNA genome replication / focal adhesion / nucleotide binding / RNA-directed RNA polymerase activity / DNA-templated transcription / Neutrophil degranulation / host cell nucleus / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / endoplasmic reticulum / Golgi apparatus / protein homodimerization activity / extracellular space / RNA binding / extracellular exosome / extracellular region / identical protein binding / membrane / plasma membrane / cytosol
Similarity search - Function
Influenza RNA-dependent RNA polymerase subunit PB1 / Influenza RNA-dependent RNA polymerase subunit PB1 / RNA-directed RNA polymerase, negative-strand RNA virus / RdRp of negative ssRNA viruses with segmented genomes catalytic domain profile. / 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 ...Influenza RNA-dependent RNA polymerase subunit PB1 / Influenza RNA-dependent RNA polymerase subunit PB1 / RNA-directed RNA polymerase, negative-strand RNA virus / RdRp of negative ssRNA viruses with segmented genomes catalytic domain profile. / 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
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / MHC class I antigen / Beta-2-microglobulin / RNA-directed RNA polymerase catalytic subunit
Similarity search - Component
Biological speciesHomo sapiens (human)
Influenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsMurdolo, L.D. / Maddumaage, J. / Gras, S.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia) Australia
CitationJournal: Clin Transl Immunology / Year: 2024
Title: Characterisation of novel influenza-derived HLA-B*18:01-restricted epitopes.
Authors: Leong, S.L. / Murdolo, L. / Maddumage, J.C. / Koutsakos, M. / Kedzierska, K. / Purcell, A.W. / Gras, S. / Grant, E.J.
History
DepositionJan 10, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 8, 2024Provider: repository / Type: Initial release
Revision 1.1Jul 24, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 20, 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

Downloads & links

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Assembly

Deposited unit
A: MHC class I antigen
C: RNA-directed RNA polymerase catalytic subunit
B: Beta-2-microglobulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,9776
Polymers44,7463
Non-polymers2303
Water4,342241
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5050 Å2
ΔGint-11 kcal/mol
Surface area18930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.750, 81.627, 110.556
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein MHC class I antigen


Mass: 31747.891 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 BL21(DE3) (bacteria) / References: UniProt: A0A167RQK8
#3: Protein Beta-2-microglobulin


Mass: 11879.356 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(DE3) (bacteria) / References: UniProt: P61769

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Protein/peptide , 1 types, 1 molecules C

#2: Protein/peptide RNA-directed RNA polymerase catalytic subunit / Polymerase basic protein 1 / PB1 / RNA-directed RNA polymerase subunit P1


Mass: 1119.200 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Influenza A virus (A/Memphis/18/1978(H3N2))
References: UniProt: Q2VNC5, RNA-directed RNA polymerase

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Non-polymers , 3 types, 244 molecules

#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 241 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 2.56 Å3/Da / Density % sol: 51.93 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Lithium Acetate, 20% w/v PEG 3350, and 10 mM MgCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.953732 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 30, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953732 Å / Relative weight: 1
ReflectionResolution: 1.6→46.12 Å / Num. obs: 59129 / % possible obs: 97 % / Redundancy: 4.7 % / Biso Wilson estimate: 19.27 Å2 / CC1/2: 0.997 / Net I/σ(I): 10.3
Reflection shellResolution: 1.6→1.63 Å / Mean I/σ(I) obs: 1.6 / Num. unique obs: 3078 / CC1/2: 0.63

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→46.12 Å / SU ML: 0.1912 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.1879
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2345 2982 5.05 %
Rwork0.2016 56089 -
obs0.2033 59071 96.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.48 Å2
Refinement stepCycle: LAST / Resolution: 1.6→46.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3156 0 15 241 3412
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073370
X-RAY DIFFRACTIONf_angle_d0.91644597
X-RAY DIFFRACTIONf_chiral_restr0.0534473
X-RAY DIFFRACTIONf_plane_restr0.0091613
X-RAY DIFFRACTIONf_dihedral_angle_d6.6982475
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.630.28271340.26922710X-RAY DIFFRACTION98.17
1.63-1.650.29521620.26572661X-RAY DIFFRACTION99.23
1.65-1.680.29451640.25632680X-RAY DIFFRACTION98.07
1.68-1.720.2741350.25272657X-RAY DIFFRACTION97.62
1.72-1.750.33331370.27232748X-RAY DIFFRACTION99.52
1.75-1.790.31441390.27982733X-RAY DIFFRACTION99.51
1.79-1.830.2591450.24712722X-RAY DIFFRACTION99.34
1.83-1.880.26571380.22962766X-RAY DIFFRACTION99.18
1.88-1.930.2491370.21522697X-RAY DIFFRACTION98.75
1.93-1.980.26431530.21882671X-RAY DIFFRACTION97.95
1.98-2.050.28891380.21372705X-RAY DIFFRACTION97.13
2.05-2.120.28511380.23272650X-RAY DIFFRACTION96.37
2.12-2.210.30731660.22512626X-RAY DIFFRACTION95.49
2.21-2.310.22821500.20572607X-RAY DIFFRACTION94.42
2.31-2.430.22561310.20372566X-RAY DIFFRACTION92.87
2.43-2.580.25821300.21232621X-RAY DIFFRACTION94.05
2.58-2.780.26171470.2132602X-RAY DIFFRACTION93.57
2.78-3.060.24111380.20512641X-RAY DIFFRACTION93.92
3.06-3.50.21081200.19372693X-RAY DIFFRACTION94.94
3.5-4.410.19281360.16162668X-RAY DIFFRACTION93.13
4.41-46.120.14511440.14042665X-RAY DIFFRACTION88.92

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