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- PDB-9exb: SARS-CoV-2 Nucleocapsid N-terminal domain NTD -

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Basic information

Entry
Database: PDB / ID: 9exb
TitleSARS-CoV-2 Nucleocapsid N-terminal domain NTD
ComponentsNucleoprotein
KeywordsVIRAL PROTEIN / SARS-CoV-2 / Nucleocapsid / 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 / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsDhamotharan, K. / Schlundt, A. / Guenther, S.
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 6, 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)59,5784
Polymers59,5784
Non-polymers00
Water3,981221
1
A: Nucleoprotein


Theoretical massNumber of molelcules
Total (without water)14,8951
Polymers14,8951
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Nucleoprotein


Theoretical massNumber of molelcules
Total (without water)14,8951
Polymers14,8951
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Nucleoprotein


Theoretical massNumber of molelcules
Total (without water)14,8951
Polymers14,8951
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Nucleoprotein


Theoretical massNumber of molelcules
Total (without water)14,8951
Polymers14,8951
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.916, 93.073, 96.936
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: 14894.591 Da / Num. of mol.: 4
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.: 221 / 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: 2.24 Å3/Da / Density % sol: 45.02 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 20% PEG 6000 100mM MES pH 6.0 10mM Zinc Chloride

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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: 0.9762 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 6, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.3→96.98 Å / Num. obs: 24362 / % possible obs: 99.7 % / Redundancy: 21 % / Biso Wilson estimate: 1.02 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.203 / Rpim(I) all: 0.062 / Rrim(I) all: 0.212 / Net I/σ(I): 11.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
8.91-96.9818.30.06339.25010.9980.020.0661.1799.9
2.3-2.38224.0690.923590.5991.2244.2521.03100

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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
autoPROC1.1.17data reduction
XDSBUILT 20230630data reduction
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→67.14 Å / Cor.coef. Fo:Fc: 0.9 / Cor.coef. Fo:Fc free: 0.871 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.485 / SU Rfree Blow DPI: 0.306
RfactorNum. reflection% reflectionSelection details
Rfree0.32 1154 -RANDOM
Rwork0.2686 ---
obs0.271 24288 99.7 %-
Displacement parametersBiso mean: 63.61 Å2
Baniso -1Baniso -2Baniso -3
1-19.9827 Å20 Å20 Å2
2---5.2236 Å20 Å2
3----14.7591 Å2
Refine analyzeLuzzati coordinate error obs: 0.41 Å
Refinement stepCycle: LAST / Resolution: 2.3→67.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3913 0 0 221 4134
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0077838HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.914114HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2250SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes1263HARMONIC5
X-RAY DIFFRACTIONt_it4024HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion512SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact5685SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion2.76
X-RAY DIFFRACTIONt_other_torsion14.12
LS refinement shellResolution: 2.3→2.31 Å
RfactorNum. reflection% reflection
Rfree0.4006 32 -
Rwork0.3991 --
obs0.3992 486 100 %
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)
11.67470.22120.70630.6283-0.02910.0287-0.0794-0.0759-0.0482-0.07590.09930.1295-0.04820.1295-0.0199-0.0007-0.0402-0.01990.05840.0062-0.0776-10.2399-4.494912.3706
20.1953-0.59650.03252.5174-0.00730.21620.09230.0319-0.13340.0319-0.02340.1618-0.13340.1618-0.06890.034-0.01250.0246-0.0692-0.0135-0.0336-10.8123-29.564227.2736
30.0959-0.0506-0.71240.7751-0.40961.16240.04280.30190.03670.3019-0.1287-0.10.0367-0.10.08590.112-0.0669-0.0538-0.06640.0283-0.06485.077-1.702640.9066
40.5994-0.6385-0.376300.30131.2252-0.11280.0650.18790.065-0.06180.04130.18790.04130.1746-0.01520.0389-0.0035-0.08560.03090.202422.3257-13.006218.0096
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A48 - 172
2X-RAY DIFFRACTION2{ B|* }B47 - 174
3X-RAY DIFFRACTION3{ C|* }C48 - 173
4X-RAY DIFFRACTION4{ D|* }D47 - 174

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