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- PDB-7o05: Crystal structure of SARS-CoV-2 N-CTD -

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Basic information

Entry
Database: PDB / ID: 7o05
TitleCrystal structure of SARS-CoV-2 N-CTD
ComponentsNucleoprotein
KeywordsVIRAL PROTEIN / Nucleocapsid
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 ...: / 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 / NOD1/2 Signaling Pathway / TAK1-dependent IKK and NF-kappa-B activation / 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 / viral nucleocapsid / Transcription of SARS-CoV-2 sgRNAs / host cell endoplasmic reticulum-Golgi intermediate compartment / Translation of Structural Proteins / Virion Assembly and Release / host extracellular space / host cell Golgi apparatus / 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: 1.94 Å
AuthorsCiges-Tomas, J.R. / Vilar, M.
Funding support Spain, 1items
OrganizationGrant numberCountry
Spanish Ministry of Science, Innovation, and UniversitiesCOV20/01265 Spain
CitationJournal: Commun Biol / Year: 2022
Title: Identification of a guanine-specific pocket in the protein N of SARS-CoV-2.
Authors: Rafael Ciges-Tomas, J. / Franco, M.L. / Vilar, M.
History
DepositionMar 25, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 13, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 26, 2022Group: 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
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)61,5614
Polymers61,5614
Non-polymers00
Water6,233346
1
A: Nucleoprotein
C: Nucleoprotein


Theoretical massNumber of molelcules
Total (without water)30,7802
Polymers30,7802
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5200 Å2
ΔGint-26 kcal/mol
Surface area11420 Å2
MethodPISA
2
B: Nucleoprotein
D: Nucleoprotein


Theoretical massNumber of molelcules
Total (without water)30,7802
Polymers30,7802
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5140 Å2
ΔGint-29 kcal/mol
Surface area11600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.843, 44.818, 59.123
Angle α, β, γ (deg.)92.040, 96.200, 90.000
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 15390.200 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: MGSSHHHHHHSSGENLYFQS- correspond to the purification tag
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.: 346 / Source method: isolated from a natural source / Formula: H2O

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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: 2.32 Å3/Da / Density % sol: 47.09 %
Crystal growTemperature: 294 K / Method: vapor diffusion
Details: 0.1 M tri-Sodium citrate pH 4.5; 0.1 M bisTris pH 5.5; 25% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97926 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 11, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 1.94→58.74 Å / Num. obs: 32080 / % possible obs: 96.2 % / Redundancy: 3.4 % / CC1/2: 0.984 / Rmerge(I) obs: 0.167 / Rpim(I) all: 0.109 / Rrim(I) all: 0.2 / Net I/σ(I): 6.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.94-2.043.50.8441683647530.7040.5270.997296.6
6.12-44.793.30.063331710110.9920.040.07513.595.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
Aimless0.7.4data scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6WZO

6wzo


Resolution: 1.94→44.79 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.936 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.183 / ESU R Free: 0.167 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.233 1635 5.1 %RANDOM
Rwork0.1772 ---
obs0.18 30433 96.08 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 83.99 Å2 / Biso mean: 28.385 Å2 / Biso min: 12.32 Å2
Baniso -1Baniso -2Baniso -3
1--2.74 Å2-0.12 Å2-0.38 Å2
2--0.66 Å2-0.79 Å2
3---2.17 Å2
Refinement stepCycle: final / Resolution: 1.94→44.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3504 0 0 346 3850
Biso mean---37.75 -
Num. residues----440
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0193693
X-RAY DIFFRACTIONr_bond_other_d00.023477
X-RAY DIFFRACTIONr_angle_refined_deg1.8281.9385003
X-RAY DIFFRACTIONr_angle_other_deg3.66938000
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6845454
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.18823.556180
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.1115625
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3021528
X-RAY DIFFRACTIONr_chiral_restr0.1180.2512
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0214284
X-RAY DIFFRACTIONr_gen_planes_other0.0170.02928
LS refinement shellResolution: 1.94→1.985 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.31 124 -
Rwork0.269 2272 -
obs--96.46 %

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