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- PDB-7o35: Crystal Structure of SARS-CoV-2 N-CTD in complex with GTP (I) -

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Basic information

Entry
Database: PDB / ID: 7o35
TitleCrystal Structure of SARS-CoV-2 N-CTD in complex with GTP (I)
ComponentsNucleoprotein
KeywordsVIRAL PROTEIN / Nucleocapsid
Function / homology
Function and homology information


cytoplasmic capsid assembly / viral RNA genome packaging / response to host immune response / negative regulation of interferon-beta production / RNA stem-loop binding / Maturation of nucleoprotein / intracellular non-membrane-bounded organelle / positive regulation of NLRP3 inflammasome complex assembly / CD28 dependent PI3K/Akt signaling / MHC class I protein binding ...cytoplasmic capsid assembly / viral RNA genome packaging / response to host immune response / negative regulation of interferon-beta production / RNA stem-loop binding / Maturation of nucleoprotein / intracellular non-membrane-bounded organelle / positive regulation of NLRP3 inflammasome complex assembly / CD28 dependent PI3K/Akt signaling / MHC class I protein binding / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / molecular condensate scaffold activity / protein sequestering activity / VEGFR2 mediated vascular permeability / TAK1-dependent IKK and NF-kappa-B activation / DDX58/IFIH1-mediated induction of interferon-alpha/beta / NOD1/2 Signaling Pathway / MHC class I protein complex / Interleukin-1 signaling / viral capsid / Interferon alpha/beta signaling / PIP3 activates AKT signaling / Transcription of SARS-CoV-2 sgRNAs / host cell endoplasmic reticulum-Golgi intermediate compartment / host cell Golgi apparatus / viral nucleocapsid / 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 (N) protein, C-terminal domain, coronavirus / Nucleocapsid (N) protein, N-terminal domain, coronavirus / Coronavirus nucleocapsid (CoV N) protein N-terminal (NTD) domain profile. / Coronavirus nucleocapsid (CoV N) protein C-terminal (CTD) domain profile. / Nucleocapsid protein, coronavirus / Nucleocapsid protein, N-terminal / Coronavirus nucleocapsid / Nucleocapsid protein, C-terminal
Similarity search - Domain/homology
GUANOSINE-5'-TRIPHOSPHATE / Nucleoprotein
Similarity search - Component
Biological speciesSevere acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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
DepositionApr 1, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,0845
Polymers61,5614
Non-polymers5231
Water7,963442
1
A: Nucleoprotein
B: Nucleoprotein


Theoretical massNumber of molelcules
Total (without water)30,7802
Polymers30,7802
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5210 Å2
ΔGint-31 kcal/mol
Surface area12610 Å2
MethodPISA
2
C: Nucleoprotein
D: Nucleoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,3043
Polymers30,7802
Non-polymers5231
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5820 Å2
ΔGint-28 kcal/mol
Surface area11720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.773, 92.719, 68.728
Angle α, β, γ (deg.)90.000, 90.010, 90.000
Int Tables number4
Space group name H-MP1211

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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: The initial residues MGSSHHHHHHGENLYFQS- correspond to the purification tag.
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P0DTC9
#2: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE / Guanosine triphosphate


Mass: 523.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: GTP, energy-carrying molecule*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 442 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.27 Å3/Da / Density % sol: 45.71 %
Crystal growTemperature: 294 K / Method: vapor diffusion / pH: 4.6 / Details: 30% PEG 3350 0.1 M sodium acetate pH 4.6 / PH range: 4.6-7.5

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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: Nov 19, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 1.8→92.72 Å / Num. obs: 50472 / % possible obs: 99.4 % / Redundancy: 6.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.066 / Rpim(I) all: 0.027 / Rrim(I) all: 0.071 / Net I/σ(I): 17.8 / Num. measured all: 341444
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
1.8-1.846.40.3951860129260.9610.1690.434.997.8
9-92.726.10.03726164300.9980.0160.04137.999.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
Aimless0.5.1data scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6WZO

6wzo


Resolution: 1.8→68.73 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.943 / WRfactor Rfree: 0.2045 / WRfactor Rwork: 0.158 / FOM work R set: 0.8723 / SU B: 2.626 / SU ML: 0.08 / SU R Cruickshank DPI: 0.104 / SU Rfree: 0.1097 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.104 / ESU R Free: 0.11 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2033 2511 5 %RANDOM
Rwork0.1558 ---
obs0.1581 47930 99.18 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 124.72 Å2 / Biso mean: 29.782 Å2 / Biso min: 14.16 Å2
Baniso -1Baniso -2Baniso -3
1--2.15 Å20 Å20.18 Å2
2--4.25 Å20 Å2
3----2.1 Å2
Refinement stepCycle: final / Resolution: 1.8→68.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3629 0 32 442 4103
Biso mean--73.52 38.25 -
Num. residues----454
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.023805
X-RAY DIFFRACTIONr_bond_other_d0.0020.023557
X-RAY DIFFRACTIONr_angle_refined_deg1.9371.955155
X-RAY DIFFRACTIONr_angle_other_deg1.0638196
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.495460
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.24823.736182
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.08915643
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5181526
X-RAY DIFFRACTIONr_chiral_restr0.1250.2528
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0214357
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02941
LS refinement shellResolution: 1.8→1.847 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.256 182 -
Rwork0.211 3480 -
all-3662 -
obs--97.47 %

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