[English] 日本語
Yorodumi
- PDB-9f7a: SARS-CoV-2 Nucleocapsid N-terminal domain (NTD) mutant P80R -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9f7a
TitleSARS-CoV-2 Nucleocapsid N-terminal domain (NTD) mutant P80R
ComponentsNucleoprotein
KeywordsVIRAL PROTEIN / SARS-CoV-2 / Nucelocapsid / N-terminal domain / Gamma variant
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 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsDhamotharan, K. / Schlundt, A.
Funding support Germany, 4items
OrganizationGrant numberCountry
German Research Foundation (DFG)SCHL2062/2-1 and 2-2 Germany
German Research Foundation (DFG)161793742 Germany
Other governmentGoethe-Corona-Funds
Other governmentJohanna Quandt Young Academy at Goethe (stipend number 2019/AS01)
CitationJournal: Nat Commun / Year: 2024
Title: A core network in the SARS-CoV-2 nucleocapsid NTD mediates structural integrity and selective RNA-binding.
Authors: Dhamotharan, K. / Korn, S.M. / Wacker, A. / Becker, M.A. / Gunther, S. / Schwalbe, H. / Schlundt, A.
History
DepositionMay 3, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 20, 2024Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2024Group: 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Nucleoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,0202
Polymers14,9551
Non-polymers651
Water90150
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area80 Å2
ΔGint-25 kcal/mol
Surface area7270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.753, 66.753, 121.214
Angle α, β, γ (deg.)90, 90, 120
Int Tables number179
Space group name H-MP6522

-
Components

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


Mass: 14954.669 Da / Num. of mol.: 1 / Mutation: P80R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0DTC9
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 50 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.61 Å3/Da / Density % sol: 52.96 %
Crystal growTemperature: 285 K / Method: vapor diffusion, sitting drop / pH: 9 / Details: 22% PEG 3350 200mM Zinc Acetate dihydrate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.97626 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 30, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97626 Å / Relative weight: 1
ReflectionResolution: 1.9→121.21 Å / Num. obs: 13269 / % possible obs: 99.9 % / Redundancy: 36.4 % / CC1/2: 1 / Χ2: 1 / Net I/σ(I): 20.2
Reflection shellResolution: 1.9→1.94 Å / Mean I/σ(I) obs: 0.3 / Num. unique obs: 815 / CC1/2: 0.38 / Χ2: 0.97 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
REFMAC5.8.0430 (refmacat 0.4.88)refinement
REFMAC5.8.0430 (refmacat 0.4.88)refinement
Coot0.9.8.8model building
BUCCANEER3.5.2model building
Aimless0.7.13data scaling
pointless1.12.15data scaling
STARANISO2.3.74data scaling
autoPROC1.1.7data reduction
XDSBUILT 20230630data reduction
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→57.81 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.919 / SU B: 10.779 / SU ML: 0.277 / Cross valid method: FREE R-VALUE / ESU R: 0.18 / ESU R Free: 0.187
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.3477 692 5.239 %RANDOM
Rwork0.277 12517 --
all0.281 ---
obs-13209 99.909 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 77.817 Å2
Baniso -1Baniso -2Baniso -3
1-1.782 Å20.891 Å20 Å2
2--1.782 Å2-0 Å2
3----5.782 Å2
Refinement stepCycle: LAST / Resolution: 1.9→57.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms921 0 1 50 972
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.012949
X-RAY DIFFRACTIONr_bond_other_d0.0030.016870
X-RAY DIFFRACTIONr_angle_refined_deg1.7821.8131292
X-RAY DIFFRACTIONr_angle_other_deg0.7211.7671994
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.5295115
X-RAY DIFFRACTIONr_dihedral_angle_2_deg14.17658
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.53910139
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.1921046
X-RAY DIFFRACTIONr_chiral_restr0.0780.2133
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021164
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02242
X-RAY DIFFRACTIONr_nbd_refined0.1860.2158
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1560.2729
X-RAY DIFFRACTIONr_nbtor_refined0.1670.2444
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0770.2496
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.150.241
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3210.212
X-RAY DIFFRACTIONr_nbd_other0.1260.220
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1710.23
X-RAY DIFFRACTIONr_mcbond_it7.3277.468466
X-RAY DIFFRACTIONr_mcbond_other7.3257.469466
X-RAY DIFFRACTIONr_mcangle_it10.16813.399579
X-RAY DIFFRACTIONr_mcangle_other10.16213.406580
X-RAY DIFFRACTIONr_scbond_it7.3617.976483
X-RAY DIFFRACTIONr_scbond_other7.2767.956481
X-RAY DIFFRACTIONr_scangle_it10.10814.39713
X-RAY DIFFRACTIONr_scangle_other10.10114.396714
X-RAY DIFFRACTIONr_lrange_it13.17268.2921020
X-RAY DIFFRACTIONr_lrange_other13.27368.311015
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
1.9-1.9490.548550.5218850.5229410.7690.77599.89370.509
1.949-2.0030.482560.4938610.4929190.7330.77399.78240.473
2.003-2.0610.478610.4538350.4558980.7920.899.77730.42
2.061-2.1240.573450.48430.4078880.7870.841000.362
2.124-2.1940.425420.417990.4118420.8650.85899.88120.379
2.194-2.270.316470.3767810.3728290.910.87899.87940.337
2.27-2.3560.462430.3837560.3877990.8040.8831000.351
2.356-2.4520.356360.3417280.3427660.8880.91599.73890.299
2.452-2.5610.51340.3297180.3387520.860.9311000.287
2.561-2.6860.395300.3376820.347120.9030.9231000.299
2.686-2.8310.384270.3526550.3536820.8860.9131000.315
2.831-3.0020.348330.3176160.3196500.9330.92699.84620.277
3.002-3.2080.468340.315790.3186130.8460.9331000.291
3.208-3.4650.377230.2945510.2975740.9040.9451000.285
3.465-3.7940.298290.2725000.2745290.9340.9551000.272
3.794-4.2390.238150.2354750.2354900.9720.9651000.241
4.239-4.8910.339240.2054180.2124420.9430.9711000.213
4.891-5.9790.347260.2013590.2113850.9440.9751000.218
5.979-8.4110.273210.2182900.2223110.9690.9631000.235
8.411-57.810.312110.2861860.2881990.9260.93298.9950.33

+
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