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- PDB-9f5l: SARS-CoV-2 Nucleocapsid N-terminal domain (NTD) mutant A119S -

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Basic information

Entry
Database: PDB / ID: 9f5l
TitleSARS-CoV-2 Nucleocapsid N-terminal domain (NTD) mutant A119S
ComponentsNucleoprotein
KeywordsVIRAL PROTEIN / SARS-CoV-2 / Nucelocapsid / N-terminal domain / Zeta P. 2
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: 2.363 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
DepositionApr 29, 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
B: Nucleoprotein
C: Nucleoprotein
D: Nucleoprotein


Theoretical massNumber of molelcules
Total (without water)59,6424
Polymers59,6424
Non-polymers00
Water2,702150
1
A: Nucleoprotein


Theoretical massNumber of molelcules
Total (without water)14,9111
Polymers14,9111
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Nucleoprotein


Theoretical massNumber of molelcules
Total (without water)14,9111
Polymers14,9111
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Nucleoprotein


Theoretical massNumber of molelcules
Total (without water)14,9111
Polymers14,9111
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Nucleoprotein


Theoretical massNumber of molelcules
Total (without water)14,9111
Polymers14,9111
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.871, 92.203, 99.166
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 14910.591 Da / Num. of mol.: 4 / Mutation: A119S
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 150 / Source method: isolated from a natural source / Formula: H2O
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: 2.26 Å3/Da / Density % sol: 45.65 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 200mM Sodium acetate trihydrate 100mM Tris-HCl pH 8.5 30% PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.97598 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 23, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97598 Å / Relative weight: 1
ReflectionResolution: 2.363→99.11 Å / Num. obs: 22537 / % possible obs: 99.2 % / Redundancy: 6.8 % / CC1/2: 0.963 / Χ2: 0.94 / Net I/σ(I): 3.1
Reflection shellResolution: 2.363→2.49 Å / Redundancy: 12.1 % / Mean I/σ(I) obs: 1.3 / Num. unique obs: 2266 / CC1/2: 0.386 / Χ2: 0.98 / % possible all: 97.8

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Processing

Software
NameVersionClassification
BUSTER2.10.4refinement
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: 2.363→50.62 Å / Cor.coef. Fo:Fc: 0.827 / Cor.coef. Fo:Fc free: 0.825 / SU R Cruickshank DPI: 0.584 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.609 / SU Rfree Blow DPI: 0.322 / SU Rfree Cruickshank DPI: 0.323
RfactorNum. reflection% reflectionSelection details
Rfree0.3229 1179 -RANDOM
Rwork0.3135 ---
obs0.314 22492 98.9 %-
Displacement parametersBiso mean: 40.43 Å2
Baniso -1Baniso -2Baniso -3
1-9.4547 Å20 Å20 Å2
2---8.7878 Å20 Å2
3----0.6669 Å2
Refine analyzeLuzzati coordinate error obs: 0.49 Å
Refinement stepCycle: LAST / Resolution: 2.363→50.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3852 0 0 150 4002
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0053960HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.775385HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1313SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes678HARMONIC5
X-RAY DIFFRACTIONt_it3960HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion503SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact2519SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion2.58
X-RAY DIFFRACTIONt_other_torsion15.6
LS refinement shellResolution: 2.363→2.38 Å
RfactorNum. reflection% reflection
Rfree0.3544 27 -
Rwork0.4067 --
obs--100 %
Refinement TLS params.

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)
12.1847-1.45480.71537.14490.34031.36080.16860.41610.31650.41610.1299-0.06910.3165-0.0691-0.29850.1784-0.0065-0.06080.1308-0.01170.125510.9835-16.818-21.2052
22.9842-0.74580.73752.75-0.61763.9585-0.08370.1225-0.20990.12250.0637-0.116-0.2099-0.1160.01990.14390.02560.04290.048-0.00750.135836.3221-32.775-32.3025
35.52340.0797-1.18053.4625-0.38522.41630.0625-0.1284-0.1226-0.1284-0.0865-0.2282-0.1226-0.22820.0240.10390.0342-0.03730.2142-0.13720.196510.2301-41.1795-36.6071
41.8781-0.60140.9333.1603-1.22713.7674-0.1111.1053-0.37861.10530.14020.0011-0.37860.0011-0.02920.70850.05710.25940.04990.01190.1443-5.907-44.2743-8.1162
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|48 - A|171 }A48 - 171
2X-RAY DIFFRACTION2{ B|48 - B|171 }B48 - 171
3X-RAY DIFFRACTION3{ C|48 - C|171 }C48 - 171
4X-RAY DIFFRACTION4{ D|49 - D|171 }D49 - 171

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