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- PDB-7s8s: Crystal Structure of HLA A*1101 in complex with RVLVNGTFLK, an 10... -

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Basic information

Entry
Database: PDB / ID: 7s8s
TitleCrystal Structure of HLA A*1101 in complex with RVLVNGTFLK, an 10-mer epitope from Influenza B
Components
  • Beta-2-microglobulin
  • HLA class I histocompatibility antigen, A alpha chain
  • Non-structural protein 1 peptide RVLVNGTFLK
KeywordsIMMUNE SYSTEM / HLA A*1101 / influenza B / TCR / T cell
Function / homology
Function and homology information


symbiont-mediated suppression of host PKR/eIFalpha signaling / protein serine/threonine kinase inhibitor 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 ...symbiont-mediated suppression of host PKR/eIFalpha signaling / protein serine/threonine kinase inhibitor 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 / symbiont-mediated suppression of host ISG15-protein conjugation / protein homotetramerization / amyloid fibril formation / intracellular iron ion homeostasis / host cell cytoplasm / learning or memory / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / Amyloid fiber formation / endoplasmic reticulum lumen / Golgi membrane / external side of plasma membrane / lysosomal membrane / focal adhesion / 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 B non-structural protein (NS1) / Influenza non-structural protein (NS1) / 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 ...Influenza B non-structural protein (NS1) / Influenza non-structural protein (NS1) / 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 / S15/NS1, RNA-binding / 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
Non-structural protein 1 / Beta-2-microglobulin / MHC class I antigen
Similarity search - Component
Biological speciesHomo sapiens (human)
Influenza B virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.87 Å
AuthorsNguyen, A.T. / Szeto, C. / Gras, S.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)1159272 Australia
CitationJournal: Plos Pathog. / Year: 2022
Title: HLA-A*11:01-restricted CD8+ T cell immunity against influenza A and influenza B viruses in Indigenous and non-Indigenous people.
Authors: Habel, J.R. / Nguyen, A.T. / Rowntree, L.C. / Szeto, C. / Mifsud, N.A. / Clemens, E.B. / Loh, L. / Chen, W. / Rockman, S. / Nelson, J. / Davies, J. / Miller, A. / Tong, S.Y.C. / Rossjohn, J. ...Authors: Habel, J.R. / Nguyen, A.T. / Rowntree, L.C. / Szeto, C. / Mifsud, N.A. / Clemens, E.B. / Loh, L. / Chen, W. / Rockman, S. / Nelson, J. / Davies, J. / Miller, A. / Tong, S.Y.C. / Rossjohn, J. / Gras, S. / Purcell, A.W. / Hensen, L. / Kedzierska, K. / Illing, P.T.
History
DepositionSep 19, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 23, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 30, 2022Group: 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.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Oct 18, 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: HLA class I histocompatibility antigen, A alpha chain
B: Beta-2-microglobulin
C: Non-structural protein 1 peptide RVLVNGTFLK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,2664
Polymers45,1703
Non-polymers961
Water4,143230
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4730 Å2
ΔGint-33 kcal/mol
Surface area19180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.875, 82.262, 57.027
Angle α, β, γ (deg.)90.000, 113.040, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein HLA class I histocompatibility antigen, A alpha chain


Mass: 32142.363 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-A / Plasmid: pET / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: U5YJK1
#2: 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 / Plasmid: pET / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P61769
#3: Protein/peptide Non-structural protein 1 peptide RVLVNGTFLK / NS1 / NS1A


Mass: 1148.398 Da / Num. of mol.: 1 / Fragment: UNP residues 186-195 / Source method: obtained synthetically / Details: peptide from Influenza B / Source: (synth.) Influenza B virus / References: UniProt: P12601
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 230 / 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: 2.43 Å3/Da / Density % sol: 49.41 % / Mosaicity: 0.18 °
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 26% PEG 3350, 0.1M BisTris pH 6.3, 0.2M Lithium Sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 12M / Detector: PIXEL / Date: Oct 17, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.82→46.82 Å / Num. obs: 38748 / % possible obs: 99.9 % / Redundancy: 6.8 % / Biso Wilson estimate: 26.21 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.125 / Rpim(I) all: 0.052 / Rrim(I) all: 0.135 / Net I/σ(I): 9.9 / Num. measured all: 265223 / Scaling rejects: 113
Reflection shellResolution: 1.82→1.86 Å / Redundancy: 7 % / Rmerge(I) obs: 1.183 / Num. unique obs: 2267 / CC1/2: 0.682 / Rpim(I) all: 0.481 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
Aimless0.7.4data scaling
XDSdata processing
PDB_EXTRACT3.27data extraction
Cootmodel building
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4MJ5

4mj5


Resolution: 1.87→25.39 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.912 / SU R Cruickshank DPI: 0.142 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.143 / SU Rfree Blow DPI: 0.13 / SU Rfree Cruickshank DPI: 0.13
RfactorNum. reflection% reflectionSelection details
Rfree0.225 1904 5.33 %RANDOM
Rwork0.194 ---
obs0.196 35694 99.8 %-
Displacement parametersBiso max: 98.71 Å2 / Biso mean: 29.98 Å2 / Biso min: 12.28 Å2
Baniso -1Baniso -2Baniso -3
1--2.0143 Å20 Å26.9701 Å2
2--8.1121 Å20 Å2
3----6.0978 Å2
Refine analyzeLuzzati coordinate error obs: 0.25 Å
Refinement stepCycle: final / Resolution: 1.87→25.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3153 0 5 230 3388
Biso mean--44.61 35.5 -
Num. residues----384
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1133SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes568HARMONIC5
X-RAY DIFFRACTIONt_it3261HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion403SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3843SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d3261HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg4429HARMONIC21.04
X-RAY DIFFRACTIONt_omega_torsion3.6
X-RAY DIFFRACTIONt_other_torsion17.16
LS refinement shellResolution: 1.87→1.88 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.3021 40 5.6 %
Rwork0.1995 674 -
all0.2055 714 -
obs--99.71 %

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