[English] 日本語
Yorodumi
- PDB-6iex: Crystal structure of HLA-B*4001 in complex with SARS-CoV derived ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6iex
TitleCrystal structure of HLA-B*4001 in complex with SARS-CoV derived peptide N216-225 GETALALLLL
Components
  • Beta-2-microglobulin
  • GLY-GLU-THR-ALA-LEU-ALA-LEU-LEU-LEU-LEU
  • MHC class I antigen
KeywordsIMMUNE SYSTEM / HLA-B*4001 / SARS-CoV / N216-225
Function / homology
Function and homology information


SARS-CoV-1-host interactions / Translation of Structural Proteins / Virion Assembly and Release / viral RNA genome packaging / Transcription of SARS-CoV-1 sgRNAs / negative regulation of interferon-beta production / Maturation of nucleoprotein / antigen processing and presentation / SARS-CoV-1 modulates host translation machinery / SARS-CoV-1 targets host intracellular signalling and regulatory pathways ...SARS-CoV-1-host interactions / Translation of Structural Proteins / Virion Assembly and Release / viral RNA genome packaging / Transcription of SARS-CoV-1 sgRNAs / negative regulation of interferon-beta production / Maturation of nucleoprotein / antigen processing and presentation / SARS-CoV-1 modulates host translation machinery / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / Attachment and Entry / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / negative regulation of iron ion transport / lumenal side of endoplasmic reticulum membrane / T cell mediated cytotoxicity / cellular response to iron(III) ion / 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 / transferrin transport / regulation of iron ion transport / regulation of erythrocyte differentiation / negative regulation of receptor-mediated endocytosis / HFE-transferrin receptor complex / response to molecule of bacterial origin / MHC class I peptide loading complex / cellular response to iron ion / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / MHC class I protein complex / peptide antigen assembly with MHC class II protein complex / negative regulation of neurogenesis / positive regulation of receptor-mediated endocytosis / cellular response to nicotine / MHC class II protein complex / positive regulation of T cell mediated cytotoxicity / multicellular organismal-level iron ion homeostasis / specific granule lumen / peptide antigen binding / antigen processing and presentation of exogenous peptide antigen via MHC class II / phagocytic vesicle membrane / positive regulation of immune response / recycling endosome membrane / positive regulation of T cell activation / Interferon gamma signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / negative regulation of epithelial cell proliferation / SARS-CoV-1 activates/modulates innate immune responses / viral capsid / Modulation by Mtb of host immune system / sensory perception of smell / positive regulation of cellular senescence / tertiary granule lumen / DAP12 signaling / MHC class II protein complex binding / T cell differentiation in thymus / late endosome membrane / negative regulation of neuron projection development / ER-Phagosome pathway / protein refolding / viral nucleocapsid / early endosome membrane / host cell endoplasmic reticulum-Golgi intermediate compartment / amyloid fibril formation / protein homotetramerization / molecular adaptor activity / host cell Golgi apparatus / intracellular iron ion homeostasis / learning or memory / immune response / host cell perinuclear region of cytoplasm / endoplasmic reticulum lumen / Amyloid fiber formation / ribonucleoprotein complex / 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 / cell surface / endoplasmic reticulum / Golgi apparatus / protein homodimerization activity / extracellular space / DNA binding / RNA binding / extracellular exosome / extracellular region / identical protein binding / membrane / plasma membrane / cytosol
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-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
MHC class I antigen / MHC class I antigen / Nucleoprotein / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
SARS coronavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.314 Å
AuthorsJi, W. / Niu, L. / Peng, W. / Zhang, Y. / Shi, Y. / Qi, J. / Gao, G.F. / Liu, W.J.
CitationJournal: Mol.Immunol. / Year: 2019
Title: Salt bridge-forming residues positioned over viral peptides presented by MHC class I impacts T-cell recognition in a binding-dependent manner.
Authors: Ji, W. / Niu, L. / Peng, W. / Zhang, Y. / Cheng, H. / Gao, F. / Shi, Y. / Qi, J. / Gao, G.F. / Liu, W.J.
History
DepositionSep 17, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 18, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 31, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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
Revision 1.2Oct 16, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: MHC class I antigen
B: Beta-2-microglobulin
C: GLY-GLU-THR-ALA-LEU-ALA-LEU-LEU-LEU-LEU


Theoretical massNumber of molelcules
Total (without water)44,6873
Polymers44,6873
Non-polymers00
Water2,036113
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4210 Å2
ΔGint-20 kcal/mol
Surface area18810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.482, 69.274, 120.936
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein MHC class I antigen


Mass: 31794.154 Da / Num. of mol.: 1 / Fragment: UNP residues 25-298
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-B / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): K-12 / References: UniProt: F4NBU6, UniProt: A0A499S0B6*PLUS
#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 / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): K-12 / References: UniProt: P61769
#3: Protein/peptide GLY-GLU-THR-ALA-LEU-ALA-LEU-LEU-LEU-LEU


Mass: 1013.229 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SARS coronavirus / References: UniProt: P59595*PLUS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 113 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.46 Å3/Da / Density % sol: 50 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.1M sodium citrate tribasic dehydrate, pH 6.5 and 18% w-v polyethylene glycol 3350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97907 Å
DetectorType: SDMS / Detector: FILM / Date: Oct 12, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97907 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 19343 / % possible obs: 99.9 % / Redundancy: 7.1 % / Net I/σ(I): 20.3
Reflection shellResolution: 2.3→2.38 Å

-
Processing

Software
NameVersionClassification
PHENIX1.7_650refinement
XDSdata reduction
XDSdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.314→41.832 Å / SU ML: 0.29 / Cross valid method: NONE / σ(F): 0 / Phase error: 28.09
RfactorNum. reflection% reflection
Rfree0.2606 985 5.09 %
Rwork0.2108 --
obs0.2133 19343 97.21 %
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Bsol: 30.166 Å2 / ksol: 0.326 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--15.5873 Å20 Å2-0 Å2
2--16.2802 Å20 Å2
3----0.6929 Å2
Refinement stepCycle: LAST / Resolution: 2.314→41.832 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3142 0 0 113 3255
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063227
X-RAY DIFFRACTIONf_angle_d0.9174375
X-RAY DIFFRACTIONf_dihedral_angle_d17.8541203
X-RAY DIFFRACTIONf_chiral_restr0.067452
X-RAY DIFFRACTIONf_plane_restr0.003577
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.314-2.4360.36491340.26242387X-RAY DIFFRACTION91
2.436-2.58860.30741280.2442544X-RAY DIFFRACTION96
2.5886-2.78840.3021310.24012589X-RAY DIFFRACTION97
2.7884-3.06890.35421580.23422626X-RAY DIFFRACTION99
3.0689-3.51280.24661440.21562655X-RAY DIFFRACTION99
3.5128-4.4250.23111340.1832721X-RAY DIFFRACTION100
4.425-41.83930.21421560.1982836X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.68940.0469-0.36670.555-0.08120.4234-0.0150.0526-0.0764-0.02660.0538-0.09560.01560.182800.21760.0043-0.00910.22380.00180.197115.064610.33528.8548
20.53980.4305-0.1230.3539-0.17360.4530.17350.17620.1196-0.0555-0.00090.0413-0.1117-0.233800.28190.03440.02950.30380.08860.367-11.56391.976329.8119
30.1657-0.01590.03730.11280.19090.3491-0.05430.0118-0.0646-0.17970.05250.03790.0832-0.187-00.25080.02650.0050.27860.07730.24225.24962.806433.8358
40.16150.0598-0.01540.0880.02030.0815-0.08810.0207-0.0023-0.1725-0.0299-0.47560.07120.19430.00080.30780.0213-0.00380.38720.10580.449915.49216.814135.8255
50.13750.10570.04630.1058-0.00370.0621-0.00390.1796-0.1911-0.2116-0.03240.02450.1271-0.0020.00180.25240.02270.00780.2790.09190.346510.06446.166725.873
60.0165-0.0382-0.04440.08550.10.1165-0.0021-0.18210.02380.2499-0.00230.1145-0.05490.075600.4383-0.0256-0.04350.3760.06180.33529.96528.275142.1471
70.015-0.0132-0.02130.01160.01860.02930.0762-0.17120.00730.05360.02260.1727-0.1902-0.13200.32630.0168-0.01870.55080.00960.47232.16974.810642.1458
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 1:174)
2X-RAY DIFFRACTION2chain 'A' and (resseq 175:274)
3X-RAY DIFFRACTION3chain 'B' and (resseq 1:28)
4X-RAY DIFFRACTION4chain 'B' and (resseq 29:51)
5X-RAY DIFFRACTION5chain 'B' and (resseq 52:71)
6X-RAY DIFFRACTION6chain 'B' and (resseq 72:90)
7X-RAY DIFFRACTION7chain 'B' and (resseq 91:99)

+
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