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- PDB-9f5j: SARS-CoV-2 Nucleocapsid N-terminal domain (NTD) mutant Q58I -

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Basic information

Entry
Database: PDB / ID: 9f5j
TitleSARS-CoV-2 Nucleocapsid N-terminal domain (NTD) mutant Q58I
ComponentsNucleoprotein
KeywordsVIRAL PROTEIN / SARS-CoV-2 / Nucelocapsid / 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 / SAD / Resolution: 2.2 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,2756
Polymers29,8252
Non-polymers4504
Water2,486138
1
A: Nucleoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,1373
Polymers14,9131
Non-polymers2252
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Nucleoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,1373
Polymers14,9131
Non-polymers2252
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.78, 49.715, 114.248
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: 14912.609 Da / Num. of mol.: 2
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: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cd / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 138 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.28 Å3/Da / Density % sol: 46.09 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 200mM Ammonium sulfate 10mM Cadmium chloride 25% PEG Smear Medium 100mM HEPES pH 7.5 30mM Manganese 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: 1.8929 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 29, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.8929 Å / Relative weight: 1
ReflectionResolution: 2.2→114.25 Å / Num. obs: 14476 / % possible obs: 100 % / Redundancy: 43.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.104 / Rpim(I) all: 0.022 / Rrim(I) all: 0.106 / Χ2: 1.06 / Net I/av σ(I): 25 / Net I/σ(I): 25
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2
9.07-114.2534.20.0648.92630.9990.0120.0610.79
2.2-2.2733.70.6116.412570.9870.1480.6291.28

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Processing

Software
NameVersionClassification
REFMAC5.8.0430 (refmacat 0.4.88)refinement
BUSTER2.10.4refinement
PDB-REDO8.12refinement
Coot0.9.8.8model building
BUCCANEER3.5.2model building
CRANK22.0.339phasing
Aimless0.7.13data scaling
pointless1.12.15data scaling
STARANISO2.3.74data scaling
autoPROC1.1.7data reduction
XDSBUILT 20230630data reduction
RefinementMethod to determine structure: SAD / Resolution: 2.2→57.124 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.935 / SU B: 9.209 / SU ML: 0.138 / Cross valid method: FREE R-VALUE / ESU R: 0.275 / ESU R Free: 0.209
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2423 718 4.982 %
Rwork0.2024 13693 -
all0.204 --
obs-14411 99.868 %
Solvent computationIon probe radii: 1 Å / Shrinkage radii: 1 Å / VDW probe radii: 1.3 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 49.466 Å2
Baniso -1Baniso -2Baniso -3
1-2.053 Å20 Å20 Å2
2--2.428 Å2-0 Å2
3----4.48 Å2
Refinement stepCycle: LAST / Resolution: 2.2→57.124 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1896 0 4 138 2038
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0121958
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161791
X-RAY DIFFRACTIONr_ext_dist_refined_b0.0010.013267
X-RAY DIFFRACTIONr_angle_refined_deg1.9091.8042659
X-RAY DIFFRACTIONr_angle_other_deg0.6861.7634119
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.535241
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.758514
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.56710286
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.2571090
X-RAY DIFFRACTIONr_chiral_restr0.1030.2274
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022381
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02479
X-RAY DIFFRACTIONr_nbd_refined0.2030.2270
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1940.21482
X-RAY DIFFRACTIONr_nbtor_refined0.1790.2933
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0850.21057
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1360.294
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0220.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2660.212
X-RAY DIFFRACTIONr_nbd_other0.2170.252
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1580.210
X-RAY DIFFRACTIONr_mcbond_it2.5963.569973
X-RAY DIFFRACTIONr_mcbond_other2.5963.57973
X-RAY DIFFRACTIONr_mcangle_it3.8126.3961211
X-RAY DIFFRACTIONr_mcangle_other3.8146.41212
X-RAY DIFFRACTIONr_scbond_it4.3923.97985
X-RAY DIFFRACTIONr_scbond_other4.3833.962983
X-RAY DIFFRACTIONr_scangle_it5.1617.0961448
X-RAY DIFFRACTIONr_scangle_other5.1597.11449
X-RAY DIFFRACTIONr_lrange_it7.03644.3257606
X-RAY DIFFRACTIONr_lrange_other7.01544.0587540
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
2.2-2.2570.221540.2299970.22910550.9580.96699.62090.214
2.257-2.3190.315440.2159550.21910050.9530.97299.4030.197
2.319-2.3860.268430.2179700.21910150.9510.97199.8030.203
2.386-2.4590.292570.2038890.2089480.9490.97499.7890.188
2.459-2.540.252490.2178860.2199360.9620.97199.89320.202
2.54-2.6290.274440.2088570.2119010.9540.9771000.197
2.629-2.7280.215460.1858100.1878590.970.97999.65080.18
2.728-2.8390.224390.2078240.2088630.9670.9731000.198
2.839-2.9650.223330.2057780.2058110.9630.9741000.198
2.965-3.1090.19340.2087570.2077910.9720.9731000.203
3.109-3.2770.275400.2126890.2157300.9460.97299.8630.209
3.277-3.4750.294470.2196590.2247060.9630.9721000.22
3.475-3.7140.258340.2156330.2176670.9670.9731000.216
3.714-4.010.314250.1936010.1976260.9480.9781000.198
4.01-4.390.235260.1695460.1725720.9740.981000.176
4.39-4.9050.213260.1735090.1755350.9770.981000.185
4.905-5.6570.206330.184360.1824690.9710.981000.189
5.657-6.9110.182200.2063940.2044140.9820.9751000.213
6.911-9.7030.316140.1983110.2023250.9450.9711000.208
9.703-57.1240.173100.291920.2832020.9780.931000.297
Refinement TLS params.

Method: refined / 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)
12.65460.2303-0.62342.7456-0.20062.21010.0344-0.20450.17150.1974-0.08250.01040.0181-0.11150.04820.0163-0.01040.00430.0302-0.02020.015337.17067.678392.2073
21.82570.4133-0.26562.64990.09724.0236-0.03880.12730.0299-0.15730.07470.2302-0.1581-0.1071-0.03590.06560.0006-0.01170.0427-0.00950.042932.08042.793465.0852
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLA48 - 177
2X-RAY DIFFRACTION2ALLB48 - 174

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