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- PDB-7luz: GQTVTK segment from the Nucleoprotein of SARS-CoV-2, residues 243-248 -

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Basic information

Entry
Database: PDB / ID: 7luz
TitleGQTVTK segment from the Nucleoprotein of SARS-CoV-2, residues 243-248
ComponentsNucleoprotein GQTVTK
KeywordsPROTEIN FIBRIL / amyloid fibril
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 / positive regulation of NLRP3 inflammasome complex assembly / intracellular non-membrane-bounded organelle / 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 / positive regulation of NLRP3 inflammasome complex assembly / intracellular non-membrane-bounded organelle / 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
Biological speciesSevere acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 1.101 Å
Model detailsAmyloid Fibril
AuthorsBalbirnie, M. / Sawaya, M.R. / Eisenberg, D.S. / Cascio, D.
Funding support United States, 3items
OrganizationGrant numberCountry
Department of Energy (DOE, United States)DE-FC02-02ER63421 United States
National Science Foundation (NSF, United States)MCB 1616265 United States
National Institutes of Health/National Institute on Aging (NIH/NIA)R01 AG048120 United States
CitationJournal: Biorxiv / Year: 2021
Title: Inhibition of amyloid formation of the Nucleoprotein of SARS-CoV-2.
Authors: Tayeb-Fligelman, E. / Cheng, X. / Tai, C. / Bowler, J.T. / Griner, S. / Sawaya, M.R. / Seidler, P.M. / Jiang, Y.X. / Lu, J. / Rosenberg, G.M. / Salwinski, L. / Abskharon, R. / Zee, C.T. / ...Authors: Tayeb-Fligelman, E. / Cheng, X. / Tai, C. / Bowler, J.T. / Griner, S. / Sawaya, M.R. / Seidler, P.M. / Jiang, Y.X. / Lu, J. / Rosenberg, G.M. / Salwinski, L. / Abskharon, R. / Zee, C.T. / Hou, K. / Li, Y. / Boyer, D.R. / Murray, K.A. / Falcon, G. / Anderson, D.H. / Cascio, D. / Saelices, L. / Damoiseaux, R. / Guo, F. / Eisenberg, D.S.
History
DepositionFeb 23, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 17, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2021Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Mar 6, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2
Item: _citation.journal_id_ISSN / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nucleoprotein GQTVTK


Theoretical massNumber of molelcules
Total (without water)6341
Polymers6341
Non-polymers00
Water19811
1
A: Nucleoprotein GQTVTK

A: Nucleoprotein GQTVTK

A: Nucleoprotein GQTVTK

A: Nucleoprotein GQTVTK

A: Nucleoprotein GQTVTK

A: Nucleoprotein GQTVTK

A: Nucleoprotein GQTVTK

A: Nucleoprotein GQTVTK

A: Nucleoprotein GQTVTK

A: Nucleoprotein GQTVTK

A: Nucleoprotein GQTVTK

A: Nucleoprotein GQTVTK

A: Nucleoprotein GQTVTK

A: Nucleoprotein GQTVTK

A: Nucleoprotein GQTVTK

A: Nucleoprotein GQTVTK

A: Nucleoprotein GQTVTK

A: Nucleoprotein GQTVTK


Theoretical massNumber of molelcules
Total (without water)11,40718
Polymers11,40718
Non-polymers00
Water32418
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_545x,y-1,z1
crystal symmetry operation1_565x,y+1,z1
crystal symmetry operation1_535x,y-2,z1
crystal symmetry operation1_575x,y+2,z1
crystal symmetry operation1_525x,y-3,z1
crystal symmetry operation1_585x,y+3,z1
crystal symmetry operation1_515x,y-4,z1
crystal symmetry operation1_595x,y+4,z1
crystal symmetry operation2_656-x+1,y+1/2,-z+11
crystal symmetry operation2_646-x+1,y-1/2,-z+11
crystal symmetry operation2_666-x+1,y+3/2,-z+11
crystal symmetry operation2_636-x+1,y-3/2,-z+11
crystal symmetry operation2_676-x+1,y+5/2,-z+11
crystal symmetry operation2_626-x+1,y-5/2,-z+11
crystal symmetry operation2_686-x+1,y+7/2,-z+11
crystal symmetry operation2_616-x+1,y-7/2,-z+11
crystal symmetry operation2_606-x+1,y-9/2,-z+11
Unit cell
Length a, b, c (Å)19.570, 4.780, 22.930
Angle α, β, γ (deg.)90.000, 93.997, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 633.714 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Severe acute respiratory syndrome coronavirus 2
References: UniProt: P0DTC9
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 11 / 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: 1.69 Å3/Da / Density % sol: 27.14 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 2M Ammonium Sulfate, HEPES, pH 7.5, PEG 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 20, 2020
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.1→22.874 Å / Num. obs: 1726 / % possible obs: 87.1 % / Redundancy: 2.71 % / Biso Wilson estimate: 11.978 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.085 / Rrim(I) all: 0.105 / Χ2: 0.884 / Net I/σ(I): 6.02
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.1-1.172.0240.4461.371700.8430.60750.9
1.17-1.262.6360.4531.952610.8220.57285.3
1.26-1.372.8790.2952.942650.9240.36496.4
1.37-1.512.8060.2483.582520.9150.31295.1
1.51-1.723.0390.1496.242330.9830.1896.3
1.72-2.032.7010.0897.971970.9890.1197
2.03-2.622.8570.05813.291820.9970.072100
2.62-22.8742.50.04815.211660.9930.05995.4

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Processing

Software
NameVersionClassification
XDSJan 31, 2020data reduction
XSCALEJan 31, 2020data scaling
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
SHELXD2013/2phasing
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 1.101→22.874 Å / Cor.coef. Fo:Fc: 0.987 / Cor.coef. Fo:Fc free: 0.984 / SU B: 1.392 / SU ML: 0.026 / Cross valid method: THROUGHOUT / ESU R: 0.034 / ESU R Free: 0.034
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1497 173 10.023 %
Rwork0.1237 1553 -
all0.126 --
obs-1726 87.481 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 10.078 Å2
Baniso -1Baniso -2Baniso -3
1-0.474 Å20 Å2-0.704 Å2
2---0.517 Å2-0 Å2
3---0.14 Å2
Refinement stepCycle: LAST / Resolution: 1.101→22.874 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms44 0 0 11 55
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01343
X-RAY DIFFRACTIONr_bond_other_d0.0010.01847
X-RAY DIFFRACTIONr_angle_refined_deg1.71.78357
X-RAY DIFFRACTIONr_angle_other_deg1.2291.67108
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.25455
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.734301
X-RAY DIFFRACTIONr_dihedral_angle_3_deg8.683159
X-RAY DIFFRACTIONr_chiral_restr0.0570.27
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0249
X-RAY DIFFRACTIONr_gen_planes_other00.027
X-RAY DIFFRACTIONr_nbd_refined0.0660.23
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1580.222
X-RAY DIFFRACTIONr_nbtor_refined0.1160.218
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0780.233
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.060.24
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.0480.21
X-RAY DIFFRACTIONr_nbd_other0.20.214
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1040.25
X-RAY DIFFRACTIONr_mcbond_it0.7190.76923
X-RAY DIFFRACTIONr_mcbond_other0.6760.75522
X-RAY DIFFRACTIONr_mcangle_it0.8361.13927
X-RAY DIFFRACTIONr_mcangle_other0.831.14828
X-RAY DIFFRACTIONr_scbond_it0.920.87320
X-RAY DIFFRACTIONr_scbond_other0.9110.88320
X-RAY DIFFRACTIONr_scangle_it0.7281.27130
X-RAY DIFFRACTIONr_scangle_other0.7241.27730
X-RAY DIFFRACTIONr_lrange_it4.08512.25538
X-RAY DIFFRACTIONr_lrange_other1.0188.88836
X-RAY DIFFRACTIONr_rigid_bond_restr1.02390
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
1.101-1.130.39760.276530.2861420.6460.73141.54930.267
1.13-1.1610.33990.274790.281470.7980.8259.86390.26
1.161-1.1940.27590.255850.2571420.7810.85366.19720.247
1.194-1.2310.225110.221010.221220.8160.87591.80330.204
1.231-1.2710.088110.186980.1711100.9630.91599.09090.158
1.271-1.3160.229110.21000.2031150.9370.92796.52170.173
1.316-1.3650.196120.1631000.1661180.9240.94494.91530.147
1.365-1.4210.199100.191950.1921160.9650.92790.51720.16
1.421-1.4840.19110.144990.1481120.9220.96398.21430.129
1.484-1.5560.218120.1291050.1361190.9370.97198.31930.118
1.556-1.640.177100.126890.1321030.970.97696.11650.108
1.64-1.7390.17270.125690.128800.9430.975950.109
1.739-1.8580.17590.097780.102880.960.98398.86360.086
1.858-2.0060.09780.096770.096890.9910.98995.50560.088
2.006-2.1950.1690.081790.086880.9750.9921000.079
2.195-2.4520.13490.074740.079830.9880.9931000.075
2.452-2.8260.16750.073490.082550.9890.99698.18180.08
2.826-3.4470.05250.073500.071580.9970.99794.82760.09
3.447-4.8210.09760.07480.073570.9950.99694.73680.079
4.821-22.8740.12130.276250.263290.9950.96196.55170.339

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