[English] 日本語
Yorodumi
- PDB-7uw3: Structure of SARS-CoV-2 Nucleocapsid Protein N-Terminal Domain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7uw3
TitleStructure of SARS-CoV-2 Nucleocapsid Protein N-Terminal Domain
ComponentsNucleoprotein
KeywordsVIRAL PROTEIN / COVID-19 / Nucleoprotein / N-terminal domain
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 / MHC class I protein binding / CD28 dependent PI3K/Akt signaling / SARS-CoV-2 targets host intracellular signalling and regulatory pathways ...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 / MHC class I protein binding / CD28 dependent PI3K/Akt signaling / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / protein sequestering activity / VEGFR2 mediated vascular permeability / molecular condensate scaffold activity / TAK1-dependent IKK and NF-kappa-B activation / NOD1/2 Signaling Pathway / DDX58/IFIH1-mediated induction of interferon-alpha/beta / MHC class I protein complex / RNA stem-loop binding / Interleukin-1 signaling / Interferon alpha/beta signaling / viral capsid / PIP3 activates AKT signaling / Transcription of SARS-CoV-2 sgRNAs / host cell endoplasmic reticulum-Golgi intermediate compartment / viral nucleocapsid / host cell Golgi apparatus / 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 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.
Similarity search - Domain/homology
Biological speciesSevere acute respiratory syndrome coronavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsCalero, G.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM082251-11 United States
CitationJournal: J.Am.Chem.Soc. / Year: 2022
Title: Atomic-Resolution Structure of SARS-CoV-2 Nucleocapsid Protein N-Terminal Domain.
Authors: Sarkar, S. / Runge, B. / Russell, R.W. / Movellan, K.T. / Calero, D. / Zeinalilathori, S. / Quinn, C.M. / Lu, M. / Calero, G. / Gronenborn, A.M. / Polenova, T.
History
DepositionMay 2, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 10, 2023Provider: repository / Type: Initial release
Revision 1.1May 17, 2023Group: 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 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Nucleoprotein
B: Nucleoprotein
C: Nucleoprotein
D: Nucleoprotein


Theoretical massNumber of molelcules
Total (without water)59,9794
Polymers59,9794
Non-polymers00
Water3,873215
1
A: Nucleoprotein


Theoretical massNumber of molelcules
Total (without water)14,9951
Polymers14,9951
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Nucleoprotein


Theoretical massNumber of molelcules
Total (without water)14,9951
Polymers14,9951
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Nucleoprotein


Theoretical massNumber of molelcules
Total (without water)14,9951
Polymers14,9951
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Nucleoprotein


Theoretical massNumber of molelcules
Total (without water)14,9951
Polymers14,9951
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.943, 93.066, 96.820
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

-
Components

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


Mass: 14994.733 Da / Num. of mol.: 4 / Fragment: N-terminal domain (UNP residues 40-174)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus
Production host: Escherichia coli (E. coli) / References: UniProt: P0DTC9
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 215 / 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: 2.21 Å3/Da / Density % sol: 44.44 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 30% PEG4000, 100 mM MES, pH 6.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-1 / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER2 S 16M / Detector: PIXEL / Date: Jul 30, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.7→37.41 Å / Num. obs: 57729 / % possible obs: 99.9 % / Redundancy: 13.5 % / Biso Wilson estimate: 32.95 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.097 / Rpim(I) all: 0.039 / Rrim(I) all: 0.1 / Χ2: 0.81 / Net I/σ(I): 12.8
Reflection shellResolution: 1.7→1.73 Å / Num. unique obs: 3009 / CC1/2: 0.21

-
Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PHENIX1.19.2_4158refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 6M3M

6m3m


Resolution: 1.7→37.41 Å / SU ML: 0.3598 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 41.5447
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2993 2259 3.91 %
Rwork0.2827 55461 -
obs0.2834 57720 97.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 54.71 Å2
Refinement stepCycle: LAST / Resolution: 1.7→37.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3727 0 0 215 3942
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033834
X-RAY DIFFRACTIONf_angle_d0.69165227
X-RAY DIFFRACTIONf_chiral_restr0.0471545
X-RAY DIFFRACTIONf_plane_restr0.0058689
X-RAY DIFFRACTIONf_dihedral_angle_d12.54311366
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.740.4708960.42052340X-RAY DIFFRACTION66.61
1.74-1.780.42551260.41453297X-RAY DIFFRACTION94.12
1.78-1.820.39061300.40573499X-RAY DIFFRACTION98.99
1.82-1.870.42031370.40423521X-RAY DIFFRACTION99.67
1.87-1.930.49121460.39453503X-RAY DIFFRACTION99.89
1.93-1.990.45831280.38023545X-RAY DIFFRACTION99.86
1.99-2.060.40261450.36383533X-RAY DIFFRACTION99.89
2.06-2.140.39861480.36393503X-RAY DIFFRACTION99.75
2.14-2.240.34231680.34973504X-RAY DIFFRACTION99.81
2.24-2.360.38481210.34383593X-RAY DIFFRACTION100
2.36-2.50.41311500.3523536X-RAY DIFFRACTION100
2.51-2.70.41341340.3343581X-RAY DIFFRACTION99.95
2.7-2.970.36311440.3283563X-RAY DIFFRACTION99.87
2.97-3.40.31571420.28893569X-RAY DIFFRACTION99.22
3.4-4.280.27011670.23043627X-RAY DIFFRACTION99.95
4.28-37.410.18781770.20173747X-RAY DIFFRACTION99.24

+
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