[English] 日本語
Yorodumi
- PDB-7lv2: GSQASS segment from the Nucleoprotein of SARS-CoV-2, residues 179-184 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7lv2
TitleGSQASS segment from the Nucleoprotein of SARS-CoV-2, residues 179-184
ComponentsNucleoprotein GSQASS
KeywordsPROTEIN FIBRIL / amyloid fibril
Function / homology
Function and homology information


cytoplasmic capsid assembly / viral RNA genome packaging / response to host immune response / negative regulation of interferon-beta production / RNA stem-loop binding / Maturation of nucleoprotein / positive regulation of NLRP3 inflammasome complex assembly / intracellular non-membrane-bounded organelle / CD28 dependent PI3K/Akt signaling / MHC class I protein binding ...cytoplasmic capsid assembly / viral RNA genome packaging / response to host immune response / negative regulation of interferon-beta production / RNA stem-loop binding / Maturation of nucleoprotein / positive regulation of NLRP3 inflammasome complex assembly / intracellular non-membrane-bounded organelle / CD28 dependent PI3K/Akt signaling / MHC class I protein binding / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / molecular condensate scaffold activity / protein sequestering activity / VEGFR2 mediated vascular permeability / TAK1-dependent IKK and NF-kappa-B activation / DDX58/IFIH1-mediated induction of interferon-alpha/beta / NOD1/2 Signaling Pathway / MHC class I protein complex / Interleukin-1 signaling / viral capsid / Interferon alpha/beta signaling / PIP3 activates AKT signaling / Transcription of SARS-CoV-2 sgRNAs / host cell endoplasmic reticulum-Golgi intermediate compartment / host cell Golgi apparatus / viral nucleocapsid / Translation of Structural Proteins / Virion Assembly and Release / host extracellular space / Induction of Cell-Cell Fusion / Attachment and Entry / host cell perinuclear region of cytoplasm / ribonucleoprotein complex / SARS-CoV-2 activates/modulates innate and adaptive immune responses / protein homodimerization activity / RNA binding / extracellular region / identical protein binding / cytoplasm
Similarity search - Function
Nucleocapsid protein, betacoronavirus / Nucleocapsid (N) protein, C-terminal domain, coronavirus / Nucleocapsid (N) protein, N-terminal domain, coronavirus / Coronavirus nucleocapsid (CoV N) protein N-terminal (NTD) domain profile. / Coronavirus nucleocapsid (CoV N) protein C-terminal (CTD) domain profile. / Nucleocapsid protein, coronavirus / Nucleocapsid protein, N-terminal / Coronavirus nucleocapsid / Nucleocapsid protein, C-terminal
Similarity search - Domain/homology
Biological speciesSevere acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.301 Å
Model detailsAmyloid Fibril
AuthorsHou, K. / Sawaya, M.R. / Eisenberg, D.S. / Cascio, D.
Funding support United States, 3items
OrganizationGrant numberCountry
Department of Energy (DOE, United States)DE-FC02-02ER63421 United States
National Science Foundation (NSF, United States)MCB 1616265 United States
National Institutes of Health/National Institute on Aging (NIH/NIA)R01 AG048120 United States
CitationJournal: Biorxiv / Year: 2021
Title: Inhibition of amyloid formation of the Nucleoprotein of SARS-CoV-2.
Authors: Tayeb-Fligelman, E. / Cheng, X. / Tai, C. / Bowler, J.T. / Griner, S. / Sawaya, M.R. / Seidler, P.M. / Jiang, Y.X. / Lu, J. / Rosenberg, G.M. / Salwinski, L. / Abskharon, R. / Zee, C.T. / ...Authors: Tayeb-Fligelman, E. / Cheng, X. / Tai, C. / Bowler, J.T. / Griner, S. / Sawaya, M.R. / Seidler, P.M. / Jiang, Y.X. / Lu, J. / Rosenberg, G.M. / Salwinski, L. / Abskharon, R. / Zee, C.T. / Hou, K. / Li, Y. / Boyer, D.R. / Murray, K.A. / Falcon, G. / Anderson, D.H. / Cascio, D. / Saelices, L. / Damoiseaux, R. / Guo, F. / Eisenberg, D.S.
History
DepositionFeb 23, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 17, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2021Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Mar 6, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2
Item: _citation.journal_id_ISSN / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Nucleoprotein GSQASS


Theoretical massNumber of molelcules
Total (without water)5361
Polymers5361
Non-polymers00
Water543
1
A: Nucleoprotein GSQASS

A: Nucleoprotein GSQASS

A: Nucleoprotein GSQASS

A: Nucleoprotein GSQASS

A: Nucleoprotein GSQASS

A: Nucleoprotein GSQASS

A: Nucleoprotein GSQASS

A: Nucleoprotein GSQASS

A: Nucleoprotein GSQASS

A: Nucleoprotein GSQASS

A: Nucleoprotein GSQASS

A: Nucleoprotein GSQASS

A: Nucleoprotein GSQASS

A: Nucleoprotein GSQASS

A: Nucleoprotein GSQASS

A: Nucleoprotein GSQASS


Theoretical massNumber of molelcules
Total (without water)8,56816
Polymers8,56816
Non-polymers00
Water28816
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
crystal symmetry operation1_655x+1,y,z1
crystal symmetry operation1_355x-2,y,z1
crystal symmetry operation1_755x+2,y,z1
crystal symmetry operation1_255x-3,y,z1
crystal symmetry operation1_855x+3,y,z1
crystal symmetry operation1_155x-4,y,z1
crystal symmetry operation4_556x+1/2,-y+1/2,-z+11
crystal symmetry operation4_456x-1/2,-y+1/2,-z+11
crystal symmetry operation4_656x+3/2,-y+1/2,-z+11
crystal symmetry operation4_356x-3/2,-y+1/2,-z+11
crystal symmetry operation4_756x+5/2,-y+1/2,-z+11
crystal symmetry operation4_256x-5/2,-y+1/2,-z+11
crystal symmetry operation4_156x-7/2,-y+1/2,-z+11
crystal symmetry operation4_856x+7/2,-y+1/2,-z+11
Unit cell
Length a, b, c (Å)4.770, 13.600, 42.440
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein/peptide Nucleoprotein GSQASS / N / Nucleocapsid protein / NC / Protein N


Mass: 535.507 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Severe acute respiratory syndrome coronavirus 2
References: UniProt: P0DTC9
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.29 Å3/Da / Density % sol: 4.3 % / Description: Needle
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: sodium potassium tartrate, lithium sulfate, TRIS, pH 7.0

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 20, 2020
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.3→12.951 Å / Num. obs: 809 / % possible obs: 93.2 % / Redundancy: 2.266 % / Biso Wilson estimate: 15.771 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.126 / Rrim(I) all: 0.161 / Χ2: 0.874 / Net I/σ(I): 3.47
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.3-1.392.4321.0450.691390.5671.30695.9
1.39-1.52.2950.7341.021390.6360.92897.9
1.5-1.642.2990.342.531270.9120.43194.8
1.64-1.842.3030.3462.27990.9110.44196.1
1.84-2.122.2820.125.041030.9870.15289.6
2.12-2.62.1760.1226.13910.9820.15397.8
2.6-3.682.0150.0577.78660.9950.07585.7
3.68-12.95120.0519.62450.9980.06676.3

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
XDSJan 31, 2020data reduction
XSCALEJan 31, 2020data scaling
PHASER2.8.3phasing
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: ideal beta strand AAAAAA

Resolution: 1.301→12.951 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.98 / Cross valid method: THROUGHOUT / ESU R: 0.102 / ESU R Free: 0.085
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.242 79 9.9 %
Rwork0.2488 719 -
all0.248 --
obs-798 94.438 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 10.668 Å2
Baniso -1Baniso -2Baniso -3
1--1.126 Å2-0 Å20 Å2
2--1.716 Å2-0 Å2
3----0.59 Å2
Refinement stepCycle: LAST / Resolution: 1.301→12.951 Å /
ProteinNucleic acidLigandSolventTotal
Num. atoms37 0 0 3 40
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.01445
X-RAY DIFFRACTIONr_bond_other_d0.0350.01939
X-RAY DIFFRACTIONr_angle_refined_deg1.7511.6362
X-RAY DIFFRACTIONr_angle_other_deg6.8041.72696
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.30159
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.435301
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.137157
X-RAY DIFFRACTIONr_chiral_restr0.1290.27
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0263
X-RAY DIFFRACTIONr_gen_planes_other0.0040.029
X-RAY DIFFRACTIONr_nbd_refined0.0580.21
X-RAY DIFFRACTIONr_symmetry_nbd_other0.220.218
X-RAY DIFFRACTIONr_nbtor_refined0.1330.221
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.1760.232
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0370.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1110.27
X-RAY DIFFRACTIONr_nbd_other0.2360.214
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2010.25
X-RAY DIFFRACTIONr_mcbond_it1.6621.06328
X-RAY DIFFRACTIONr_mcbond_other1.4111.0227
X-RAY DIFFRACTIONr_mcangle_it2.3881.5133
X-RAY DIFFRACTIONr_mcangle_other2.481.54734
X-RAY DIFFRACTIONr_scbond_it2.3711.23917
X-RAY DIFFRACTIONr_scbond_other1.6761.16416
X-RAY DIFFRACTIONr_scangle_it3.7621.83126
X-RAY DIFFRACTIONr_scangle_other3.3611.81226
X-RAY DIFFRACTIONr_lrange_it3.37811.77939
X-RAY DIFFRACTIONr_lrange_other3.63110.96938
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.301-1.3340.72850.441500.46560.5270.6898.21430.429
1.334-1.3710.47760.438510.442580.2870.59998.27590.441
1.371-1.410.20350.402440.385550.4860.68989.09090.398
1.41-1.4530.47450.443490.446550.4380.65198.18180.455
1.453-1.50.55460.373520.386580.2360.7371000.355
1.5-1.5520.27760.301530.299590.6360.8151000.287
1.552-1.6090.23750.302390.296500.7890.915880.293
1.609-1.6740.2140.232370.231420.4190.91897.6190.213
1.674-1.7470.49440.3350.33410.7360.88995.12190.266
1.747-1.8310.32440.401380.391430.9160.83197.67440.367
1.831-1.9270.15520.275300.258410.90.92578.04880.249
1.927-2.0420.48340.202370.218420.8420.95797.6190.188
2.042-2.1790.08240.218360.209400.9620.9571000.196
2.179-2.3480.31350.225420.234470.8630.9191000.209
2.348-2.5630.320.171270.175310.7740.96793.54840.16
2.563-2.8520.41730.192250.207300.9650.98293.33330.191
2.852-3.2670.53430.111200.125260.6110.9988.46150.132
3.267-3.9390.07320.165230.143300.9930.9883.33330.163
3.939-5.3290.08530.171210.153260.9970.98192.30770.181
5.329-12.9510.4710.35590.358130.96176.92310.29

+
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