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- PDB-9f7c: SARS-CoV-2 Nucleocapsid N-terminal domain (NTD) mutant S105I -

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Basic information

Entry
Database: PDB / ID: 9f7c
TitleSARS-CoV-2 Nucleocapsid N-terminal domain (NTD) mutant S105I
ComponentsNucleoprotein
KeywordsVIRAL PROTEIN / SARS-CoV-2 / Nucelocapsid / 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 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nucleoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,0513
Polymers14,9211
Non-polymers1312
Water93752
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.616, 58.616, 111.588
Angle α, β, γ (deg.)90, 90, 90
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-201-

ZN

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Components

#1: Protein Nucleoprotein


Mass: 14920.671 Da / Num. of mol.: 1 / Mutation: S105I
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.: 2 / Source method: isolated from a natural source / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 52 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 3.22 Å3/Da / Density % sol: 61.82 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 22% PEG 3350 200mM Zinc Acetate dihydrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 5, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→41.45 Å / Num. obs: 13840 / % possible obs: 99.3 % / Redundancy: 12.4 % / CC1/2: 0.999 / Χ2: 0.95 / Net I/σ(I): 15.8
Reflection shellResolution: 2→2.05 Å / Mean I/σ(I) obs: 1.2 / Num. unique obs: 921 / CC1/2: 0.938 / Χ2: 0.89

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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
CRANK22.0.339phasing
RefinementMethod to determine structure: SAD / Resolution: 2→41.45 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.943 / WRfactor Rfree: 0.288 / WRfactor Rwork: 0.253 / SU B: 10.743 / SU ML: 0.15 / Average fsc free: 0.9104 / Average fsc overall: 0.9401 / Average fsc work: 0.9416 / Cross valid method: FREE R-VALUE / ESU R: 0.175 / ESU R Free: 0.161
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.2733 685 4.978 %RANDOM
Rwork0.2411 13075 --
all0.243 ---
obs-13760 99.761 %-
Solvent computationIon probe radii: 0.9 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 81.96 Å2
Baniso -1Baniso -2Baniso -3
1-2.817 Å2-0 Å20 Å2
2--2.817 Å20 Å2
3----5.633 Å2
Refinement stepCycle: LAST / Resolution: 2→41.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1046 0 2 52 1100
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0121079
X-RAY DIFFRACTIONr_bond_other_d0.0030.0161000
X-RAY DIFFRACTIONr_ext_dist_refined_b00.013669
X-RAY DIFFRACTIONr_angle_refined_deg2.5611.8171469
X-RAY DIFFRACTIONr_angle_other_deg0.881.7722299
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7165133
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.17359
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.33710163
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.1371051
X-RAY DIFFRACTIONr_chiral_restr0.1030.2149
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021324
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02266
X-RAY DIFFRACTIONr_nbd_refined0.1990.2132
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1690.2834
X-RAY DIFFRACTIONr_nbtor_refined0.1740.2487
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0780.2575
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1260.239
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3370.222
X-RAY DIFFRACTIONr_nbd_other0.1780.240
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1050.24
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.0750.23
X-RAY DIFFRACTIONr_mcbond_it4.785.673535
X-RAY DIFFRACTIONr_mcbond_other4.7795.672535
X-RAY DIFFRACTIONr_mcangle_it6.42710.212667
X-RAY DIFFRACTIONr_mcangle_other6.42310.207668
X-RAY DIFFRACTIONr_scbond_it6.0495.962544
X-RAY DIFFRACTIONr_scbond_other6.0475.969542
X-RAY DIFFRACTIONr_scangle_it7.98310.803802
X-RAY DIFFRACTIONr_scangle_other7.97810.798803
X-RAY DIFFRACTIONr_lrange_it10.05468.2484131
X-RAY DIFFRACTIONr_lrange_other10.05468.1834109
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
2-2.0520.382410.3659140.3659780.8720.86297.64830.344
2.052-2.1080.434520.3239320.3289840.8430.8881000.29
2.108-2.1690.39500.3248890.3289400.8880.90899.89360.303
2.169-2.2350.293400.2788720.2789120.9460.9341000.25
2.235-2.3080.27470.3018310.2998810.9560.92899.65950.266
2.308-2.3890.281480.2678200.2688690.9420.95299.88490.236
2.389-2.4790.351360.2827960.2858340.9230.94999.76020.256
2.479-2.580.236450.2477530.2467980.960.9621000.228
2.58-2.6940.376440.2487370.2547810.9360.9641000.228
2.694-2.8250.269310.2417130.2427440.9610.9641000.221
2.825-2.9770.262230.2516850.2517080.9520.9611000.242
2.977-3.1570.322350.2426390.2476750.9450.96399.85190.243
3.157-3.3730.281390.2666030.2676420.9580.9571000.268
3.373-3.6420.231380.2495590.2485970.9640.9651000.252
3.642-3.9860.332270.2335320.2385590.9350.9691000.242
3.986-4.4510.19260.1954820.1945080.980.9761000.221
4.451-5.130.271200.1864300.1894500.9580.9761000.214
5.13-6.2590.248180.2253800.2263980.9680.9681000.28
6.259-8.7530.239120.2573100.2573220.9470.9531000.302
8.753-41.450.28130.2811960.2812100.94699.52380.351
Refinement TLS params.Method: refined / Origin x: 32.4779 Å / Origin y: 10.936 Å / Origin z: 17.8841 Å
111213212223313233
T0.0732 Å2-0.0085 Å20.0393 Å2-0.0447 Å20.0253 Å2--0.0426 Å2
L3.7488 °20.1273 °2-0.8268 °2-5.8488 °21.8284 °2--5.363 °2
S0.0026 Å °-0.2411 Å °-0.2079 Å °-0.1629 Å °-0.0345 Å °-0.0818 Å °0.2794 Å °-0.2881 Å °0.0319 Å °
Refinement TLS groupSelection: ALL

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