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- PDB-6wzo: Structure of SARS-CoV-2 Nucleocapsid dimerization domain, P1 form -

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Basic information

Entry
Database: PDB / ID: 6wzo
TitleStructure of SARS-CoV-2 Nucleocapsid dimerization domain, P1 form
ComponentsNucleoprotein
KeywordsVIRAL PROTEIN / SARS-CoV-2 / COVID-19 / nucleocapsid / RNA binding
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 / MOLECULAR REPLACEMENT / Resolution: 1.42 Å
AuthorsYe, Q. / Corbett, K.D.
Citation
Journal: Protein Sci. / Year: 2020
Title: Architecture and self-assembly of the SARS-CoV-2 nucleocapsid protein.
Authors: Ye, Q. / West, A.M.V. / Silletti, S. / Corbett, K.D.
#1: Journal: Biorxiv / Year: 2020
Title: Architecture and self-assembly of the SARS-CoV-2 nucleocapsid protein.
Authors: Ye, Q. / West, A.M.V. / Silletti, S. / Corbett, K.D.
#2: Journal: Protein Sci. / Year: 2020
Title: Architecture and self-assembly of the SARS-CoV-2 ucleocapsid protein
Authors: Ye, Q. / West, A.M.V. / Silletti, S. / Corbett, K.D.
History
DepositionMay 14, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 27, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 17, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Jun 24, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.3Sep 9, 2020Group: Database references / Category: citation / citation_author
Revision 1.4Apr 7, 2021Group: Database references / Category: citation / citation_author
Revision 1.5Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model
Item: _citation.journal_id_ISSN / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)54,1294
Polymers54,1294
Non-polymers00
Water11,133618
1
A: Nucleoprotein
B: Nucleoprotein


Theoretical massNumber of molelcules
Total (without water)27,0642
Polymers27,0642
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5210 Å2
ΔGint-28 kcal/mol
Surface area11460 Å2
MethodPISA
2
C: Nucleoprotein
D: Nucleoprotein


Theoretical massNumber of molelcules
Total (without water)27,0642
Polymers27,0642
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5230 Å2
ΔGint-28 kcal/mol
Surface area11430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.718, 50.061, 69.337
Angle α, β, γ (deg.)106.499, 90.094, 97.145
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

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


Mass: 13532.190 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Production host: Escherichia coli (E. coli) / References: UniProt: P0DTC9
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 618 / 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: 2.67 Å3/Da / Density % sol: 53.85 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 100 mM Sodium acetate pH 4.5, 50 mM Sodium/potassium tartrate, and 34% polyethylene glycol PEG 3350

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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: May 12, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.42→66.43 Å / Num. obs: 96446 / % possible obs: 91.1 % / Redundancy: 3.7 % / Biso Wilson estimate: 18 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.046 / Net I/σ(I): 16.8
Reflection shellResolution: 1.42→1.44 Å / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 3 / Num. unique obs: 3939 / CC1/2: 0.957 / Rrim(I) all: 0.363

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2GIB

2gib


Resolution: 1.42→66.43 Å / SU ML: 0.1297 / Cross valid method: FREE R-VALUE / σ(F): 1.16 / Phase error: 20.042
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1732 4733 4.91 %
Rwork0.1573 91660 -
obs0.1581 96393 91.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.83 Å2
Refinement stepCycle: LAST / Resolution: 1.42→66.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3491 0 0 618 4109
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00733591
X-RAY DIFFRACTIONf_angle_d0.88824858
X-RAY DIFFRACTIONf_chiral_restr0.0783499
X-RAY DIFFRACTIONf_plane_restr0.0073643
X-RAY DIFFRACTIONf_dihedral_angle_d25.71871338
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.42-1.430.2432970.25332579X-RAY DIFFRACTION75.59
1.43-1.450.24921290.23142428X-RAY DIFFRACTION73.2
1.45-1.470.27761500.22482906X-RAY DIFFRACTION85.22
1.47-1.490.23651750.21012952X-RAY DIFFRACTION89.45
1.49-1.510.21721470.20082990X-RAY DIFFRACTION88.52
1.51-1.530.22281560.19023077X-RAY DIFFRACTION91.92
1.53-1.550.23831410.18843081X-RAY DIFFRACTION91.46
1.55-1.570.18461680.18053072X-RAY DIFFRACTION91.84
1.57-1.60.20321600.17013091X-RAY DIFFRACTION92.33
1.6-1.620.17051660.16823071X-RAY DIFFRACTION91.73
1.62-1.650.19011800.16033099X-RAY DIFFRACTION93.98
1.65-1.680.16451390.15853163X-RAY DIFFRACTION91.8
1.68-1.710.20891460.16363110X-RAY DIFFRACTION93.43
1.71-1.750.20291650.16963115X-RAY DIFFRACTION91.98
1.75-1.790.19411450.17483125X-RAY DIFFRACTION92.82
1.79-1.830.19791680.16933096X-RAY DIFFRACTION92.07
1.83-1.870.19751540.16412999X-RAY DIFFRACTION90.55
1.87-1.930.17111880.15463001X-RAY DIFFRACTION89.96
1.93-1.980.18161550.16112706X-RAY DIFFRACTION81.09
1.98-2.050.1831700.1633212X-RAY DIFFRACTION95.86
2.05-2.120.19511710.15073199X-RAY DIFFRACTION96.2
2.12-2.20.16891670.1563222X-RAY DIFFRACTION95.2
2.2-2.30.15441630.1473199X-RAY DIFFRACTION95.35
2.3-2.430.17551510.14923237X-RAY DIFFRACTION95.52
2.43-2.580.16421680.15023208X-RAY DIFFRACTION95.88
2.58-2.780.16051680.1573172X-RAY DIFFRACTION94.86
2.78-3.060.16961660.15283138X-RAY DIFFRACTION93.92
3.06-3.50.17911670.16333086X-RAY DIFFRACTION92.28
3.5-4.410.1451630.14093081X-RAY DIFFRACTION91.77
4.41-66.430.15831500.14733245X-RAY DIFFRACTION96.2
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)
12.077184307430.3802795678770.1317058069430.577528185095-0.2243753764181.28079098511-0.0113465753639-0.1301231600740.09196529553710.0401137417039-0.0180654015505-0.015636193225-0.0524757719948-0.008269363845050.03154163340220.1623792847660.01108344620020.002492902505310.100346578766-0.01867279030780.147273027645-3.0960871896615.7686016847-0.78477096852
21.96012013440.03054977367930.03447974343230.369778765485-0.09308608692081.33798411177-0.0978368196790.1982328826680.121017047423-0.03098648229470.04940146195350.0533517273225-0.0356839951797-0.1225603564340.05017862929910.168728321117-0.00800682158886-0.0024861521850.1546281042760.006287778833470.172808333923-14.629156722515.4241687481-13.6150394079
31.83518867208-0.02527956522830.02239123740190.531414237224-0.06145615041671.72230739344-0.0859132328228-0.171147860472-0.09416817769550.02559942874990.04907726730540.07317591489650.0234709874386-0.1574895834310.04043143057380.1449628746920.0017063792631-0.0001608505787380.1367976903210.006531139803280.1436530207610.64627978163838.961169122528.6343092606
41.85760505045-0.181803496156-0.2124826076030.614864204037-0.1865129719791.57649171942-0.01840474489820.0989003156414-0.107504448546-0.0308587437585-0.0175086393631-0.05078316449360.05332435133520.03814659083980.04455664943080.15533681165-0.00835281569169-0.003302252944410.111763142526-0.01656139266680.15169909423112.189795097438.656648713715.6900012927
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B
3X-RAY DIFFRACTION3chain C
4X-RAY DIFFRACTION4chain D

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