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- PDB-7s8r: Crystal Structure of HLA A*1101 in complex with SALEWIKNK, an 9-m... -

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Basic information

Entry
Database: PDB / ID: 7s8r
TitleCrystal Structure of HLA A*1101 in complex with SALEWIKNK, an 9-mer epitope from Influenza B
Components
  • Beta-2-microglobulin
  • HLA class I histocompatibility antigen, A alpha chain
  • Matrix protein 1 peptide SALEWIKNK
KeywordsIMMUNE SYSTEM / HLA A*1101 / influenza B / TCR / T cell
Function / homology
Function and homology information


viral budding from plasma membrane / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / 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 / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent ...viral budding from plasma membrane / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / 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 / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / negative regulation of forebrain neuron differentiation / regulation of erythrocyte differentiation / peptide antigen assembly with MHC class I protein complex / ER to Golgi transport vesicle membrane / regulation of iron ion transport / response to molecule of bacterial origin / MHC class I peptide loading complex / 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 / MHC class I protein complex / negative regulation of neurogenesis / positive regulation of receptor-mediated endocytosis / peptide antigen assembly with MHC class II protein complex / multicellular organismal-level iron ion homeostasis / MHC class II protein complex / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / specific granule lumen / recycling endosome membrane / phagocytic vesicle membrane / positive regulation of cellular senescence / peptide antigen binding / antigen processing and presentation of exogenous peptide antigen via MHC class II / negative regulation of epithelial cell proliferation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / positive regulation of immune response / Interferon gamma signaling / positive regulation of T cell activation / Modulation by Mtb of host immune system / sensory perception of smell / negative regulation of neuron projection development / tertiary granule lumen / DAP12 signaling / positive regulation of protein binding / MHC class II protein complex binding / late endosome membrane / iron ion transport / ER-Phagosome pathway / early endosome membrane / T cell differentiation in thymus / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / structural constituent of virion / learning or memory / immune response / Amyloid fiber formation / endoplasmic reticulum lumen / Golgi membrane / external side of plasma membrane / lysosomal membrane / signaling receptor binding / focal adhesion / Neutrophil degranulation / host cell nucleus / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / virion membrane / Golgi apparatus / endoplasmic reticulum / protein homodimerization activity / RNA binding / extracellular space / extracellular exosome / extracellular region / identical protein binding / membrane / plasma membrane / cytosol
Similarity search - Function
Matrix protein 1 / Influenza matrix M1, N-terminal / Influenza matrix M1, C-terminal / Influenza matrix M1, N-terminal subdomain 1 / Influenza matrix M1, N-terminal subdomain 2 / Influenza virus matrix protein M1 / Influenza Matrix protein (M1) / Influenza Matrix protein (M1) C-terminal domain / Influenza Matrix protein (M1) C-terminal domain / MHC class I alpha chain, alpha1 alpha2 domains ...Matrix protein 1 / Influenza matrix M1, N-terminal / Influenza matrix M1, C-terminal / Influenza matrix M1, N-terminal subdomain 1 / Influenza matrix M1, N-terminal subdomain 2 / Influenza virus matrix protein M1 / Influenza Matrix protein (M1) / Influenza Matrix protein (M1) C-terminal domain / Influenza Matrix protein (M1) C-terminal domain / 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
Matrix 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: 2.95 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 1.3Nov 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: HLA class I histocompatibility antigen, A alpha chain
B: Beta-2-microglobulin
C: Matrix protein 1 peptide SALEWIKNK
D: HLA class I histocompatibility antigen, A alpha chain
E: Beta-2-microglobulin
F: Matrix protein 1 peptide SALEWIKNK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,48911
Polymers90,2246
Non-polymers2655
Water45025
1
A: HLA class I histocompatibility antigen, A alpha chain
B: Beta-2-microglobulin
C: Matrix protein 1 peptide SALEWIKNK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,2325
Polymers45,1123
Non-polymers1202
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4700 Å2
ΔGint-33 kcal/mol
Surface area19250 Å2
MethodPISA
2
D: HLA class I histocompatibility antigen, A alpha chain
E: Beta-2-microglobulin
F: Matrix protein 1 peptide SALEWIKNK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,2576
Polymers45,1123
Non-polymers1453
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4830 Å2
ΔGint-33 kcal/mol
Surface area19730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.330, 120.410, 122.330
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121

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Components

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Protein , 2 types, 4 molecules ADBE

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


Mass: 32142.363 Da / Num. of mol.: 2
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.: 2 / 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

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Protein/peptide , 1 types, 2 molecules CF

#3: Protein/peptide Matrix protein 1 peptide SALEWIKNK / M1


Mass: 1090.272 Da / Num. of mol.: 2 / Fragment: UNP residues 41-49 / Source method: obtained synthetically / Source: (synth.) Influenza B virus / References: UniProt: P13879

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Non-polymers , 3 types, 30 molecules

#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 25 / 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: 2.91 Å3/Da / Density % sol: 57.75 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 2M Ammonium Sulfate, 0.1 Tris pH 8, 0.2 Lithium Sulfate, 2% PEG 400

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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: 2.95→46.43 Å / Num. obs: 21329 / % possible obs: 93.8 % / Redundancy: 3.6 % / Biso Wilson estimate: 53.06 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.114 / Net I/σ(I): 10.1 / Num. measured all: 76936
Reflection shellResolution: 2.95→3.13 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.583 / Num. unique obs: 3472 / CC1/2: 0.791 / % possible all: 96.1

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
PDB_EXTRACT3.27data extraction
PHASERphasing
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4MJ5

4mj5


Resolution: 2.95→46.43 Å / Cor.coef. Fo:Fc: 0.864 / Cor.coef. Fo:Fc free: 0.783 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.515
RfactorNum. reflection% reflectionSelection details
Rfree0.278 881 4.87 %RANDOM
Rwork0.226 ---
obs0.228 18085 79.2 %-
Displacement parametersBiso max: 96.98 Å2 / Biso mean: 28.53 Å2 / Biso min: 3 Å2
Baniso -1Baniso -2Baniso -3
1-0.4028 Å20 Å20 Å2
2--0.2153 Å20 Å2
3----0.618 Å2
Refine analyzeLuzzati coordinate error obs: 0.46 Å
Refinement stepCycle: final / Resolution: 2.95→46.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6316 0 13 31 6360
Biso mean--51.23 5.58 -
Num. residues----768
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d2252SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes1124HARMONIC5
X-RAY DIFFRACTIONt_it6500HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion800SEMIHARMONIC5
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_contact6586SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d6500HARMONIC20.007
X-RAY DIFFRACTIONt_angle_deg8818HARMONIC20.95
X-RAY DIFFRACTIONt_omega_torsion2.19
X-RAY DIFFRACTIONt_other_torsion19.24
LS refinement shellResolution: 2.95→3.03 Å / Rfactor Rfree error: 0 / Total num. of bins used: 44
RfactorNum. reflection% reflection
Rfree0.4668 22 5.34 %
Rwork0.3074 390 -
all0.3153 412 -
obs--25 %

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