[English] 日本語
Yorodumi
- PDB-7kgt: Crystal Structure of HLA-A*0201 in complex with SARS-CoV-2 N226-234 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7kgt
TitleCrystal Structure of HLA-A*0201 in complex with SARS-CoV-2 N226-234
Components
  • Beta-2-microglobulin
  • MHC class I antigen
  • Nucleoprotein
KeywordsIMMUNE SYSTEM / HLA-A*0201 / T cell / SARS-CoV-2 / COVID-19 / viral peptide / TCR
Function / homology
Function and homology information


response to host immune response / viral RNA genome packaging / negative regulation of interferon-beta production / poly(U) RNA binding / Maturation of nucleoprotein / 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 ...response to host immune response / viral RNA genome packaging / negative regulation of interferon-beta production / poly(U) RNA binding / Maturation of nucleoprotein / 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 / : / : / 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 / VEGFR2 mediated vascular permeability / cellular response to iron ion / lumenal side of endoplasmic reticulum membrane / 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 / molecular condensate scaffold activity / 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 / TAK1-dependent IKK and NF-kappa-B activation / NOD1/2 Signaling Pathway / T cell mediated cytotoxicity / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / DDX58/IFIH1-mediated induction of interferon-alpha/beta / 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 / RNA stem-loop binding / Interleukin-1 signaling / 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 / Interferon alpha/beta 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 / viral capsid / tertiary granule lumen / DAP12 signaling / PIP3 activates AKT signaling / negative regulation of neuron projection development / iron ion transport / T cell differentiation in thymus / ER-Phagosome pathway / Transcription of SARS-CoV-2 sgRNAs / protein refolding / host cell endoplasmic reticulum-Golgi intermediate compartment / viral nucleocapsid / early endosome membrane / host cell Golgi apparatus / protein homotetramerization / Translation of Structural Proteins / Virion Assembly and Release / amyloid fibril formation / host extracellular space / Induction of Cell-Cell Fusion / intracellular iron ion homeostasis / Attachment and Entry / learning or memory / host cell perinuclear region of cytoplasm / immune response / Amyloid fiber formation / endoplasmic reticulum lumen / ribonucleoprotein complex / Golgi membrane / external side of plasma membrane / lysosomal membrane / focal adhesion
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
ACETATE ION / : / Nucleoprotein / Beta-2-microglobulin / MHC class I antigen
Similarity search - Component
Biological speciesHomo sapiens (human)
Severe acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å
AuthorsSzeto, C. / Chatzileontiadou, D.S.M. / Riboldi-Tunnicliffe, A. / Gras, S.
Funding support Australia, 2items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)1110429 Australia
National Health and Medical Research Council (NHMRC, Australia)1159272 Australia
CitationJournal: Iscience / Year: 2021
Title: The presentation of SARS-CoV-2 peptides by the common HLA-A*02:01 molecule.
Authors: Szeto, C. / Chatzileontiadou, D.S.M. / Nguyen, A.T. / Sloane, H. / Lobos, C.A. / Jayasinghe, D. / Halim, H. / Smith, C. / Riboldi-Tunnicliffe, A. / Grant, E.J. / Gras, S.
History
DepositionOct 18, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 20, 2021Provider: repository / Type: Initial release
Revision 1.1Aug 11, 2021Group: Database references / Category: citation / database_2
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 / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 18, 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: MHC class I antigen
B: Beta-2-microglobulin
C: Nucleoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,3297
Polymers45,0223
Non-polymers3074
Water7,440413
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3790 Å2
ΔGint-30 kcal/mol
Surface area19340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.287, 79.684, 111.117
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein , 2 types, 2 molecules AB

#1: Protein MHC class I antigen


Mass: 32153.523 Da / Num. of mol.: 1 / Mutation: A245V
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) / Strain (production host): BL21(DE3) / References: UniProt: Q861F7
#2: Protein Beta-2-microglobulin


Mass: 11748.160 Da / Num. of mol.: 1
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) / Strain (production host): BL21(DE3) / References: UniProt: P61769

-
Protein/peptide , 1 types, 1 molecules C

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


Mass: 1120.323 Da / Num. of mol.: 1 / Fragment: residues 226-234 / Source method: obtained synthetically / Details: synthesized
Source: (synth.) Severe acute respiratory syndrome coronavirus 2
References: UniProt: P0DTC9

-
Non-polymers , 4 types, 417 molecules

#4: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cd
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-ACT / ACETATE ION


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


Mass: 18.015 Da / Num. of mol.: 413 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.96 Å3/Da / Density % sol: 58.5 % / Mosaicity: 0.15 °
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 20% PEG3350 w/v, 0.2M KFormate, 1mM CdCl2

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95369 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 15, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95369 Å / Relative weight: 1
ReflectionResolution: 1.9→48.08 Å / Num. obs: 42802 / % possible obs: 99.7 % / Redundancy: 6.8 % / CC1/2: 0.995 / Rmerge(I) obs: 0.136 / Net I/σ(I): 10.1 / Num. measured all: 289860 / Scaling rejects: 624
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Net I/σ(I) obs% possible all
1.9-1.946.61.3171777127040.7582.399
9.11-48.085.50.05625174600.99421.199.3

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
PHENIX1.18.2_3874refinement
XDSdata reduction
Aimless0.5.1data scaling
PHASERphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3GSO

3gso


Resolution: 1.9→45.57 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 18.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2053 2146 5.02 %
Rwork0.1692 40589 -
obs0.1709 42735 99.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 88.97 Å2 / Biso mean: 25.5147 Å2 / Biso min: 8.35 Å2
Refinement stepCycle: final / Resolution: 1.9→45.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3124 0 7 413 3544
Biso mean--39.45 34.42 -
Num. residues----380
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9-1.940.30451460.24762652279899
1.94-1.990.28961390.213426712810100
1.99-2.050.22271290.19962659278899
2.05-2.110.261530.19262636278999
2.11-2.170.20761410.1842674281599
2.18-2.250.22361440.18232641278599
2.25-2.340.22431480.17622678282699
2.34-2.450.22881680.177126472815100
2.45-2.580.2741220.180627452867100
2.58-2.740.22861380.17927042842100
2.74-2.950.20851300.183127232853100
2.95-3.250.19181490.172927152864100
3.25-3.720.20081520.160327532905100
3.72-4.680.13351340.129327872921100
4.68-45.570.18371530.15429043057100

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more