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- PDB-9f7a: SARS-CoV-2 Nucleocapsid N-terminal domain (NTD) mutant P80R -

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Basic information

Entry
Database: PDB / ID: 9f7a
TitleSARS-CoV-2 Nucleocapsid N-terminal domain (NTD) mutant P80R
ComponentsNucleoprotein
KeywordsVIRAL PROTEIN / SARS-CoV-2 / Nucelocapsid / N-terminal domain / Gamma variant
Function / homology
Function and homology information


: / response to host immune response / viral RNA genome packaging / negative regulation of interferon-beta production / Maturation of nucleoprotein / poly(U) RNA binding / 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 / Maturation of nucleoprotein / poly(U) RNA binding / 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: 1.9 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
DepositionMay 3, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,0202
Polymers14,9551
Non-polymers651
Water90150
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area80 Å2
ΔGint-25 kcal/mol
Surface area7270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.753, 66.753, 121.214
Angle α, β, γ (deg.)90, 90, 120
Int Tables number179
Space group name H-MP6522

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Components

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


Mass: 14954.669 Da / Num. of mol.: 1 / Mutation: P80R
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-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 50 / 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: 2.61 Å3/Da / Density % sol: 52.96 %
Crystal growTemperature: 285 K / Method: vapor diffusion, sitting drop / pH: 9 / Details: 22% PEG 3350 200mM Zinc Acetate dihydrate

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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: 0.97626 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 30, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97626 Å / Relative weight: 1
ReflectionResolution: 1.9→121.21 Å / Num. obs: 13269 / % possible obs: 99.9 % / Redundancy: 36.4 % / CC1/2: 1 / Χ2: 1 / Net I/σ(I): 20.2
Reflection shellResolution: 1.9→1.94 Å / Mean I/σ(I) obs: 0.3 / Num. unique obs: 815 / CC1/2: 0.38 / Χ2: 0.97 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0430 (refmacat 0.4.88)refinement
REFMAC5.8.0430 (refmacat 0.4.88)refinement
Coot0.9.8.8model building
BUCCANEER3.5.2model building
Aimless0.7.13data scaling
pointless1.12.15data scaling
STARANISO2.3.74data scaling
autoPROC1.1.7data reduction
XDSBUILT 20230630data reduction
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→57.81 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.919 / SU B: 10.779 / SU ML: 0.277 / Cross valid method: FREE R-VALUE / ESU R: 0.18 / ESU R Free: 0.187
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.3477 692 5.239 %RANDOM
Rwork0.277 12517 --
all0.281 ---
obs-13209 99.909 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 77.817 Å2
Baniso -1Baniso -2Baniso -3
1-1.782 Å20.891 Å20 Å2
2--1.782 Å2-0 Å2
3----5.782 Å2
Refinement stepCycle: LAST / Resolution: 1.9→57.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms921 0 1 50 972
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.012949
X-RAY DIFFRACTIONr_bond_other_d0.0030.016870
X-RAY DIFFRACTIONr_angle_refined_deg1.7821.8131292
X-RAY DIFFRACTIONr_angle_other_deg0.7211.7671994
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.5295115
X-RAY DIFFRACTIONr_dihedral_angle_2_deg14.17658
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.53910139
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.1921046
X-RAY DIFFRACTIONr_chiral_restr0.0780.2133
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021164
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02242
X-RAY DIFFRACTIONr_nbd_refined0.1860.2158
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1560.2729
X-RAY DIFFRACTIONr_nbtor_refined0.1670.2444
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0770.2496
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.150.241
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3210.212
X-RAY DIFFRACTIONr_nbd_other0.1260.220
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1710.23
X-RAY DIFFRACTIONr_mcbond_it7.3277.468466
X-RAY DIFFRACTIONr_mcbond_other7.3257.469466
X-RAY DIFFRACTIONr_mcangle_it10.16813.399579
X-RAY DIFFRACTIONr_mcangle_other10.16213.406580
X-RAY DIFFRACTIONr_scbond_it7.3617.976483
X-RAY DIFFRACTIONr_scbond_other7.2767.956481
X-RAY DIFFRACTIONr_scangle_it10.10814.39713
X-RAY DIFFRACTIONr_scangle_other10.10114.396714
X-RAY DIFFRACTIONr_lrange_it13.17268.2921020
X-RAY DIFFRACTIONr_lrange_other13.27368.311015
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
1.9-1.9490.548550.5218850.5229410.7690.77599.89370.509
1.949-2.0030.482560.4938610.4929190.7330.77399.78240.473
2.003-2.0610.478610.4538350.4558980.7920.899.77730.42
2.061-2.1240.573450.48430.4078880.7870.841000.362
2.124-2.1940.425420.417990.4118420.8650.85899.88120.379
2.194-2.270.316470.3767810.3728290.910.87899.87940.337
2.27-2.3560.462430.3837560.3877990.8040.8831000.351
2.356-2.4520.356360.3417280.3427660.8880.91599.73890.299
2.452-2.5610.51340.3297180.3387520.860.9311000.287
2.561-2.6860.395300.3376820.347120.9030.9231000.299
2.686-2.8310.384270.3526550.3536820.8860.9131000.315
2.831-3.0020.348330.3176160.3196500.9330.92699.84620.277
3.002-3.2080.468340.315790.3186130.8460.9331000.291
3.208-3.4650.377230.2945510.2975740.9040.9451000.285
3.465-3.7940.298290.2725000.2745290.9340.9551000.272
3.794-4.2390.238150.2354750.2354900.9720.9651000.241
4.239-4.8910.339240.2054180.2124420.9430.9711000.213
4.891-5.9790.347260.2013590.2113850.9440.9751000.218
5.979-8.4110.273210.2182900.2223110.9690.9631000.235
8.411-57.810.312110.2861860.2881990.9260.93298.9950.33

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