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- PDB-7s8q: Crystal Structure of HLA A*1101 in complex with KTNGNAFIGK, an 10... -

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Basic information

Entry
Database: PDB / ID: 7s8q
TitleCrystal Structure of HLA A*1101 in complex with KTNGNAFIGK, an 10-mer epitope from Influenza B
Components
  • Beta-2-microglobulin
  • HLA class I histocompatibility antigen, A alpha chain
  • Nucleoprotein peptide KTNGNAFIGK
KeywordsIMMUNE SYSTEM / HLA A*1101 / influenza B / TCR / T cell
Function / homology
Function and homology information


helical viral capsid / 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 ...helical viral capsid / 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 / viral penetration into host nucleus / 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 / host cell / negative regulation of neuron projection development / ER-Phagosome pathway / protein refolding / viral nucleocapsid / early endosome membrane / protein homotetramerization / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / endoplasmic reticulum lumen / ribonucleoprotein complex / Amyloid fiber formation / Golgi membrane / lysosomal membrane / external side of plasma membrane / focal adhesion / Neutrophil degranulation / symbiont entry into host cell / 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 virus nucleoprotein (NP) / Influenza virus nucleoprotein / 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 virus nucleoprotein (NP) / Influenza virus nucleoprotein / 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
Nucleoprotein / Beta-2-microglobulin / MHC class I antigen
Similarity search - Component
Biological speciesHomo sapiens (human)
Influenza B virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.08 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

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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: Nucleoprotein peptide KTNGNAFIGK
D: HLA class I histocompatibility antigen, A alpha chain
E: Beta-2-microglobulin
F: Nucleoprotein peptide KTNGNAFIGK


Theoretical massNumber of molelcules
Total (without water)90,1466
Polymers90,1466
Non-polymers00
Water9,476526
1
A: HLA class I histocompatibility antigen, A alpha chain
B: Beta-2-microglobulin
C: Nucleoprotein peptide KTNGNAFIGK


Theoretical massNumber of molelcules
Total (without water)45,0733
Polymers45,0733
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4460 Å2
ΔGint-14 kcal/mol
Surface area18620 Å2
MethodPISA
2
D: HLA class I histocompatibility antigen, A alpha chain
E: Beta-2-microglobulin
F: Nucleoprotein peptide KTNGNAFIGK


Theoretical massNumber of molelcules
Total (without water)45,0733
Polymers45,0733
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4480 Å2
ΔGint-13 kcal/mol
Surface area18810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.481, 119.481, 63.460
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number78
Space group name H-MP43

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Components

#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
#3: Protein/peptide Nucleoprotein peptide KTNGNAFIGK / Nucleocapsid protein / Protein N


Mass: 1051.197 Da / Num. of mol.: 2 / Fragment: UNP residues 511-520 / Source method: obtained synthetically / Details: peptide from Influenza B / Source: (synth.) Influenza B virus / References: UniProt: P04666
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 526 / Source method: isolated from a natural source / Formula: H2O
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: 2.51 Å3/Da / Density % sol: 51.04 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 20% PEG 3350, 0.1M BisTris pH 6.5

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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: 2.08→43.5 Å / Num. obs: 53875 / % possible obs: 99.5 % / Redundancy: 13.8 % / Biso Wilson estimate: 32.64 Å2 / CC1/2: 0.997 / Net I/σ(I): 11.1
Reflection shellResolution: 2.08→2.14 Å / Redundancy: 12.3 % / Mean I/σ(I) obs: 2 / Num. unique obs: 3912 / CC1/2: 0.589 / % possible all: 93.5

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimlessdata scaling
BUSTERrefinement
PDB_EXTRACT3.27data extraction
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4MJ5

4mj5


Resolution: 2.08→29.87 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.941 / SU R Cruickshank DPI: 0.183 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.19 / SU Rfree Blow DPI: 0.162 / SU Rfree Cruickshank DPI: 0.161
RfactorNum. reflection% reflectionSelection details
Rfree0.217 2615 4.86 %RANDOM
Rwork0.173 ---
obs0.175 53839 99.6 %-
Displacement parametersBiso max: 116.48 Å2 / Biso mean: 35.06 Å2 / Biso min: 12.9 Å2
Baniso -1Baniso -2Baniso -3
1-0.1619 Å20 Å20 Å2
2--0.1619 Å20 Å2
3----0.3237 Å2
Refine analyzeLuzzati coordinate error obs: 0.23 Å
Refinement stepCycle: final / Resolution: 2.08→29.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6303 0 0 526 6829
Biso mean---42.15 -
Num. residues----769
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d2252SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes1131HARMONIC5
X-RAY DIFFRACTIONt_it6487HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion801SEMIHARMONIC5
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_contact7386SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d6487HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg8800HARMONIC21.05
X-RAY DIFFRACTIONt_omega_torsion3.63
X-RAY DIFFRACTIONt_other_torsion17.45
LS refinement shellResolution: 2.08→2.1 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.201 50 4.64 %
Rwork0.2329 1027 -
all0.2313 1077 -
obs--83.23 %

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