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- PDB-9f13: Crystal structure of HLA-C*12:02 in complex with KAYNVTQAF (KF9),... -

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Basic information

Entry
Database: PDB / ID: 9f13
TitleCrystal structure of HLA-C*12:02 in complex with KAYNVTQAF (KF9), a 9-mer epitope from SARS-CoV-2 Nucleocapsid (N266-274)
Components
  • Beta-2-microglobulin
  • HLA class I histocompatibility antigen C alpha chain
  • Nucleoprotein
KeywordsIMMUNE SYSTEM / human leukocyte antigen / major histocompatibility complex / HLA-C12 / HLA-C*12:02 / SARS-CoV-2 / Nucleocapsid
Function / homology
Function and homology information


: / response to host immune response / viral RNA genome packaging / negative regulation of interferon-beta production / Maturation of nucleoprotein / poly(U) RNA binding / intracellular membraneless organelle / positive regulation of NLRP3 inflammasome complex assembly / antigen processing and presentation of peptide antigen via MHC class I / MHC class I protein binding ...: / response to host immune response / viral RNA genome packaging / negative regulation of interferon-beta production / Maturation of nucleoprotein / poly(U) RNA binding / intracellular membraneless organelle / positive regulation of NLRP3 inflammasome complex assembly / antigen processing and presentation of peptide antigen via MHC class I / MHC class I protein binding / CD28 dependent PI3K/Akt signaling / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / protein sequestering activity / negative regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / transferrin transport / VEGFR2 mediated vascular permeability / cellular response to iron ion / Endosomal/Vacuolar pathway / lumenal side of endoplasmic reticulum membrane / 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 / molecular condensate scaffold activity / 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 / NOD1/2 Signaling Pathway / TAK1-dependent IKK and NF-kappa-B activation / T cell mediated cytotoxicity / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / DDX58/IFIH1-mediated induction of interferon-alpha/beta / 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 / RNA stem-loop binding / specific granule lumen / Interleukin-1 signaling / 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 / Interferon alpha/beta signaling / Modulation by Mtb of host immune system / late endosome membrane / sensory perception of smell / viral capsid / positive regulation of cellular senescence / tertiary granule lumen / DAP12 signaling / T cell differentiation in thymus / PIP3 activates AKT signaling / negative regulation of neuron projection development / ER-Phagosome pathway / protein refolding / viral nucleocapsid / Transcription of SARS-CoV-2 sgRNAs / host cell endoplasmic reticulum-Golgi intermediate compartment / early endosome membrane / protein homotetramerization / Translation of Structural Proteins / Virion Assembly and Release / host extracellular space / host cell Golgi apparatus / amyloid fibril formation / Induction of Cell-Cell Fusion / intracellular iron ion homeostasis / Attachment and Entry / learning or memory / host cell perinuclear region of cytoplasm / immune response / endoplasmic reticulum lumen / ribonucleoprotein complex / Amyloid fiber formation / Golgi membrane / lysosomal membrane / external side of plasma membrane / focal adhesion / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity
Similarity search - Function
Nucleocapsid protein, betacoronavirus / Nucleocapsid protein, coronavirus / Nucleocapsid protein, C-terminal / Nucleocapsid protein, N-terminal / Nucleocapsid (N) protein, C-terminal domain, coronavirus / Nucleocapsid (N) protein, N-terminal domain, coronavirus / Coronavirus nucleocapsid / Coronavirus nucleocapsid (CoV N) protein N-terminal (NTD) domain profile. / Coronavirus nucleocapsid (CoV N) protein C-terminal (CTD) domain profile. / MHC class I, alpha chain, C-terminal ...Nucleocapsid protein, betacoronavirus / Nucleocapsid protein, coronavirus / Nucleocapsid protein, C-terminal / Nucleocapsid protein, N-terminal / Nucleocapsid (N) protein, C-terminal domain, coronavirus / Nucleocapsid (N) protein, N-terminal domain, coronavirus / Coronavirus nucleocapsid / Coronavirus nucleocapsid (CoV N) protein N-terminal (NTD) domain profile. / Coronavirus nucleocapsid (CoV N) protein C-terminal (CTD) domain profile. / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / 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
Nucleoprotein / Beta-2-microglobulin / HLA class I histocompatibility antigen C alpha chain
Similarity search - Component
Biological speciesHomo sapiens (human)
Severe acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.61 Å
AuthorsAhn, Y.M. / Maddumage, J.C. / Chatzileontiadou, D.S.M. / Gras, S.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia) Australia
Citation
Journal: Nat Commun / Year: 2025
Title: Molecular basis of potent antiviral HLA-C-restricted CD8 + T cell response to an immunodominant SARS-CoV-2 nucleocapsid epitope.
Authors: Goto, Y. / Ahn, Y.M. / Toyoda, M. / Hamana, H. / Jin, Y. / Aritsu, Y. / Nakama, T. / Tajima, Y. / Maddumage, J.C. / Li, H. / Kitamatsu, M. / Kishi, H. / Yonekawa, A. / Jayasinghe, D. / ...Authors: Goto, Y. / Ahn, Y.M. / Toyoda, M. / Hamana, H. / Jin, Y. / Aritsu, Y. / Nakama, T. / Tajima, Y. / Maddumage, J.C. / Li, H. / Kitamatsu, M. / Kishi, H. / Yonekawa, A. / Jayasinghe, D. / Shimono, N. / Nagasaki, Y. / Minami, R. / Toya, T. / Sekiya, N. / Tomita, Y. / Chatzileontiadou, D.S.M. / Nakata, H. / Nakagawa, S. / Sakagami, T. / Ueno, T. / Gras, S. / Motozono, C.
#1: Journal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams /
Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.
History
DepositionApr 18, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 6, 2025Provider: repository / Type: Initial release
Revision 1.1Sep 10, 2025Group: 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

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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 C alpha chain
B: Beta-2-microglobulin
C: Nucleoprotein


Theoretical massNumber of molelcules
Total (without water)53,8573
Polymers53,8573
Non-polymers00
Water3,747208
1
A: HLA class I histocompatibility antigen C alpha chain
B: Beta-2-microglobulin
C: Nucleoprotein

A: HLA class I histocompatibility antigen C alpha chain
B: Beta-2-microglobulin
C: Nucleoprotein


Theoretical massNumber of molelcules
Total (without water)107,7146
Polymers107,7146
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area12780 Å2
ΔGint-36 kcal/mol
Surface area34230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.102, 77.123, 83.110
Angle α, β, γ (deg.)90.000, 100.201, 90.000
Int Tables number5
Space group name H-MI121
Space group name HallC2y(x,y,-x+z)
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z+1/2
#4: -x+1/2,y+1/2,-z+1/2

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Components

#1: Protein HLA class I histocompatibility antigen C alpha chain / HLA-C protein / MHC class I antigen / MHC class I protein


Mass: 40935.680 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-C, HLA-Cw
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q546I6
#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
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P61769
#3: Protein/peptide Nucleoprotein / N / Nucleocapsid protein / NC / Protein N


Mass: 1042.164 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Severe acute respiratory syndrome coronavirus 2
References: UniProt: P0DTC9
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 208 / 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

Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 2% PEG400, 20% PEG3350

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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: Feb 27, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953732 Å / Relative weight: 1
ReflectionResolution: 1.61→47.9 Å / Num. obs: 49905 / % possible obs: 100 % / Redundancy: 6.7 % / Biso Wilson estimate: 21.04 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.076 / Rpim(I) all: 0.032 / Rrim(I) all: 0.082 / Net I/σ(I): 14.8
Reflection shellResolution: 1.61→1.64 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.489 / Mean I/σ(I) obs: 3.7 / Num. unique obs: 2442 / CC1/2: 0.922 / Rpim(I) all: 0.202 / Rrim(I) all: 0.53 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.21rc1_5127refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.61→45.27 Å / SU ML: 0.1865 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 23.9193
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.231 2588 5.19 %
Rwork0.2038 47303 -
obs0.2052 49891 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.21 Å2
Refinement stepCycle: LAST / Resolution: 1.61→45.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3167 0 0 208 3375
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00353315
X-RAY DIFFRACTIONf_angle_d0.65264513
X-RAY DIFFRACTIONf_chiral_restr0.047456
X-RAY DIFFRACTIONf_plane_restr0.0056599
X-RAY DIFFRACTIONf_dihedral_angle_d14.30781247
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.61-1.640.26661390.24042632X-RAY DIFFRACTION99.96
1.64-1.670.30281420.22092590X-RAY DIFFRACTION99.85
1.67-1.710.24251320.22822626X-RAY DIFFRACTION99.96
1.71-1.750.24221500.21892621X-RAY DIFFRACTION99.93
1.75-1.790.26131420.21732641X-RAY DIFFRACTION99.96
1.79-1.840.2841350.23072614X-RAY DIFFRACTION100
1.84-1.90.27011400.23572632X-RAY DIFFRACTION99.96
1.9-1.960.26671550.22092589X-RAY DIFFRACTION99.96
1.96-2.030.27691390.22312634X-RAY DIFFRACTION100
2.03-2.110.27291480.22332618X-RAY DIFFRACTION100
2.11-2.210.23651420.21282617X-RAY DIFFRACTION99.96
2.21-2.320.26391420.21882626X-RAY DIFFRACTION99.89
2.32-2.470.21271480.22462621X-RAY DIFFRACTION100
2.47-2.660.24061600.21752625X-RAY DIFFRACTION100
2.66-2.930.21941410.22472646X-RAY DIFFRACTION100
2.93-3.350.25511390.20872631X-RAY DIFFRACTION99.93
3.35-4.220.20111500.18542641X-RAY DIFFRACTION99.79
4.22-45.270.18691440.15762699X-RAY DIFFRACTION99.51

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