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- PDB-7wt4: Crystal structure of HLA-A*2402 complexed with 8-mer Influenza PB... -

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Basic information

Entry
Database: PDB / ID: 7wt4
TitleCrystal structure of HLA-A*2402 complexed with 8-mer Influenza PB1 peptide
Components
  • Beta-2-microglobulin
  • MHC class I antigen
  • PB1 peptide
KeywordsIMMUNE SYSTEM / MHC class I / antigen presentation
Function / homology
Function and homology information


viral transcription / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / : / : / 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 / cellular response to iron ion ...viral transcription / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / : / : / 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 / 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 / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / MHC class II protein complex / negative regulation of forebrain neuron differentiation / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of erythrocyte differentiation / regulation of iron ion transport / MHC class I peptide loading complex / response to molecule of bacterial origin / HFE-transferrin receptor complex / T cell mediated cytotoxicity / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / antigen processing and presentation of exogenous peptide antigen via MHC class II / MHC class I protein complex / positive regulation of immune response / peptide antigen binding / negative regulation of neurogenesis / positive regulation of T cell mediated cytotoxicity / positive regulation of receptor-mediated endocytosis / multicellular organismal-level iron ion homeostasis / positive regulation of T cell activation / cellular response to nicotine / specific granule lumen / recycling endosome membrane / phagocytic vesicle membrane / positive regulation of cellular senescence / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / negative regulation of epithelial cell proliferation / Interferon gamma signaling / MHC class II protein complex binding / positive regulation of protein binding / Modulation by Mtb of host immune system / late endosome membrane / sensory perception of smell / tertiary granule lumen / DAP12 signaling / negative regulation of neuron projection development / iron ion transport / T cell differentiation in thymus / ER-Phagosome pathway / protein refolding / early endosome membrane / protein homotetramerization / amyloid fibril formation / intracellular iron ion homeostasis / host cell cytoplasm / learning or memory / symbiont-mediated suppression of host gene expression / Amyloid fiber formation / endoplasmic reticulum lumen / Golgi membrane / external side of plasma membrane / lysosomal membrane / RNA-directed RNA polymerase / viral RNA genome replication / focal adhesion / RNA-directed RNA polymerase activity / nucleotide binding / 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-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 / : ...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-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
ACETATE ION / 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: 1.89459140677 Å
AuthorsAsa, M. / Morita, D. / Sugita, M.
Funding support Japan, 8items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)18K07172 Japan
Japan Society for the Promotion of Science (JSPS)21K07078 Japan
Japan Society for the Promotion of Science (JSPS)20J23335 Japan
Japan Society for the Promotion of Science (JSPS)21H02968 Japan
Japan Society for the Promotion of Science (JSPS)20K21615 Japan
Japan Society for the Promotion of Science (JSPS)19H04805 Japan
Japan Society for the Promotion of Science (JSPS)18K19563 Japan
Japan Society for the Promotion of Science (JSPS)18H02852 Japan
CitationJournal: J.Biol.Chem. / Year: 2022
Title: Crystal structures of N-myristoylated lipopeptide-bound HLA class I complexes indicate reorganization of B-pocket architecture upon ligand binding.
Authors: Asa, M. / Morita, D. / Kuroha, J. / Mizutani, T. / Mori, N. / Mikami, B. / Sugita, M.
History
DepositionFeb 3, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 22, 2022Provider: repository / Type: Initial release
Revision 1.1Jul 6, 2022Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 16, 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
B: Beta-2-microglobulin
C: PB1 peptide
D: MHC class I antigen
E: Beta-2-microglobulin
F: PB1 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,64058
Polymers89,2856
Non-polymers3,35552
Water7,620423
1
A: MHC class I antigen
B: Beta-2-microglobulin
C: PB1 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,12541
Polymers44,6433
Non-polymers2,48238
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: MHC class I antigen
E: Beta-2-microglobulin
F: PB1 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,51517
Polymers44,6433
Non-polymers87214
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)86.122, 46.434, 141.529
Angle α, β, γ (deg.)90.0, 103.97, 90.0
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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Protein , 2 types, 4 molecules ADBE

#1: Protein MHC class I antigen


Mass: 31849.191 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-A / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosseta2 / References: UniProt: A0A411J078
#2: Protein Beta-2-microglobulin / hB2m


Mass: 11819.238 Da / Num. of mol.: 2
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) / Variant (production host): Rosseta2 / References: UniProt: P61769

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Protein/peptide , 1 types, 2 molecules CF

#3: Protein/peptide PB1 peptide


Mass: 974.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Influenza A virus / References: UniProt: Q9WLS3

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Non-polymers , 5 types, 475 molecules

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


Mass: 62.068 Da / Num. of mol.: 46 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#6: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C4H12NO3 / Comment: pH buffer*YM
#7: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 423 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.08 Å3/Da / Density % sol: 60.01 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.8 / Details: 100mM Tris, 20% PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Oct 24, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.89→50 Å / Num. obs: 85081 / % possible obs: 97.6 % / Redundancy: 2.9 % / CC1/2: 0.997 / Rmerge(I) obs: 0.078 / Net I/σ(I): 11.56
Reflection shellResolution: 1.89→2.01 Å / Rmerge(I) obs: 0.472 / Num. unique obs: 13627 / CC1/2: 0.795

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Processing

Software
NameVersionClassification
PHENIX1.9_1692+SVNrefinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4F7T

4f7t


Resolution: 1.89459140677→47.7082686372 Å / SU ML: 0.222593445076 / Cross valid method: FREE R-VALUE / σ(F): 1.33788422941 / Phase error: 23.0945270358
RfactorNum. reflection% reflection
Rfree0.23177370325 4254 5.00052896992 %
Rwork0.199843944753 80817 -
obs0.201452304898 85071 97.5853445903 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.1207177542 Å2
Refinement stepCycle: LAST / Resolution: 1.89459140677→47.7082686372 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5839 0 207 423 6469
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008138664729996286
X-RAY DIFFRACTIONf_angle_d1.020115202518414
X-RAY DIFFRACTIONf_chiral_restr0.0465139237592832
X-RAY DIFFRACTIONf_plane_restr0.004451019320471102
X-RAY DIFFRACTIONf_dihedral_angle_d14.35556485362345
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8946-1.91610.3412195715581360.3109212449442570X-RAY DIFFRACTION93.3103448276
1.9161-1.93870.2941348168311380.2757240006442620X-RAY DIFFRACTION96.670171749
1.9387-1.96230.2740117989131430.2489299313192715X-RAY DIFFRACTION98.6537797722
1.9623-1.98710.3013821169621420.2499690313122707X-RAY DIFFRACTION99.2682926829
1.9871-2.01330.2640606307971440.2307616951972736X-RAY DIFFRACTION99.173553719
2.0133-2.04090.3179591244031420.2358208701542699X-RAY DIFFRACTION99.370409234
2.0409-2.070.2389503244071440.2291075797282725X-RAY DIFFRACTION99.2733564014
2.07-2.10090.2660210560741440.2247538725842748X-RAY DIFFRACTION99.5524956971
2.1009-2.13380.2189868683021420.220195284452690X-RAY DIFFRACTION98.9172196996
2.1338-2.16870.2684024420861420.2090604419072696X-RAY DIFFRACTION99.2654774397
2.1687-2.20610.2310413026621440.2070385108932752X-RAY DIFFRACTION99.2120589243
2.2061-2.24630.2647462385151410.2036276796032685X-RAY DIFFRACTION99.0189208129
2.2463-2.28950.2597798063081430.2024007227922725X-RAY DIFFRACTION99.1701244813
2.2895-2.33620.231943628871440.2093777392772731X-RAY DIFFRACTION98.9672977625
2.3362-2.3870.2529025716351440.2020737309342728X-RAY DIFFRACTION99.0686443601
2.387-2.44250.2184930427121450.2014837260442756X-RAY DIFFRACTION98.7742594484
2.4425-2.50360.2422665215731380.2069088583582633X-RAY DIFFRACTION98.6823361823
2.5036-2.57130.2626204869091460.2012921137672765X-RAY DIFFRACTION98.5777175753
2.5713-2.64690.229826251981410.2009911788492688X-RAY DIFFRACTION98.7434554974
2.6469-2.73240.2387899295891440.1947336055062738X-RAY DIFFRACTION98.4289617486
2.7324-2.830.2253339665381410.2002702168432668X-RAY DIFFRACTION98.2167832168
2.83-2.94330.2562910175861430.1979566904952715X-RAY DIFFRACTION97.4096796183
2.9433-3.07720.212967043081420.2021969026852701X-RAY DIFFRACTION97.1633629528
3.0772-3.23940.232010815221370.1984632032722614X-RAY DIFFRACTION95.5540118097
3.2394-3.44230.2409222056931370.2000620912482592X-RAY DIFFRACTION93.6513383665
3.4423-3.7080.2258566115131380.1798362094782628X-RAY DIFFRACTION94.3383356071
3.708-4.0810.2057406132241430.1706484084552713X-RAY DIFFRACTION96.6170500677
4.081-4.67110.1783842401041420.1636537482872701X-RAY DIFFRACTION95.9824442944
4.6711-5.88340.2006425304081410.177441780232670X-RAY DIFFRACTION94.9983102399
5.8834-47.708260.2051612150541430.2104639284792708X-RAY DIFFRACTION92.3849643552

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