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- PDB-8iqj: Crystal structure of SARS-CoV2 N-NTD -

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Basic information

Entry
Database: PDB / ID: 8iqj
TitleCrystal structure of SARS-CoV2 N-NTD
ComponentsNucleoprotein
KeywordsVIRAL PROTEIN / nucleocapsid protein
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: 2.3 Å
AuthorsHong, J.Y. / Hou, M.H.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, Taiwan)109-2327-B-005-005 Taiwan
CitationJournal: Biophys.J. / Year: 2024
Title: Targeting protein-protein interaction interfaces with antiviral N protein inhibitor in SARS-CoV-2.
Authors: Hong, J.Y. / Lin, S.C. / Kehn-Hall, K. / Zhang, K.M. / Luo, S.Y. / Wu, H.Y. / Chang, S.Y. / Hou, M.H.
History
DepositionMar 16, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 7, 2024Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title

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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)68,2124
Polymers68,2124
Non-polymers00
Water2,450136
1
A: Nucleoprotein


Theoretical massNumber of molelcules
Total (without water)17,0531
Polymers17,0531
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Nucleoprotein


Theoretical massNumber of molelcules
Total (without water)17,0531
Polymers17,0531
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Nucleoprotein


Theoretical massNumber of molelcules
Total (without water)17,0531
Polymers17,0531
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Nucleoprotein


Theoretical massNumber of molelcules
Total (without water)17,0531
Polymers17,0531
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.801, 93.125, 97.608
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 17053.031 Da / Num. of mol.: 4 / Fragment: N-terminal domain
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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 136 / 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: 1.96 Å3/Da / Density % sol: 37.21 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.005 M Spermine tetrahydrochloride, 0.05 M Potassium Chloride, 0.05 M Bis-Tris HCl pH 7.0, 31 % PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 07A / Wavelength: 0.97625 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Apr 14, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. obs: 23778 / % possible obs: 96.6 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 20.772
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.435 / Mean I/σ(I) obs: 3.77 / Num. unique obs: 2411 / CC1/2: 0.915 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487)refinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→30 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 31.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2888 1985 8.37 %
Rwork0.2319 --
obs0.2365 23727 96.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3969 0 0 136 4105
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003
X-RAY DIFFRACTIONf_angle_d0.625
X-RAY DIFFRACTIONf_dihedral_angle_d16.7271493
X-RAY DIFFRACTIONf_chiral_restr0.042568
X-RAY DIFFRACTIONf_plane_restr0.006735
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.350.42041400.33991508X-RAY DIFFRACTION95
2.35-2.420.40931400.321577X-RAY DIFFRACTION100
2.42-2.490.3461430.32481602X-RAY DIFFRACTION100
2.49-2.570.39851600.32721570X-RAY DIFFRACTION100
2.57-2.660.32431340.31361591X-RAY DIFFRACTION100
2.66-2.760.32931510.29541590X-RAY DIFFRACTION100
2.76-2.890.33591440.28541595X-RAY DIFFRACTION100
2.89-3.040.3291480.27921597X-RAY DIFFRACTION100
3.04-3.230.30951410.2571589X-RAY DIFFRACTION100
3.23-3.480.33811560.24551618X-RAY DIFFRACTION100
3.48-3.830.2987970.21841113X-RAY DIFFRACTION69
3.83-4.380.24531250.18621404X-RAY DIFFRACTION86
4.38-5.520.22521460.17681655X-RAY DIFFRACTION100
5.52-300.2211600.17931733X-RAY DIFFRACTION100
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)
14.00131.0715-1.26685.8712-3.48027.4838-0.3907-0.213-0.36460.44710.2979-0.75940.7719-0.18080.34290.37950.094-0.11580.4929-0.02280.552713.8702-8.1153-11.5832
22.2373-0.5558-1.94939.3419-0.47032.5918-0.2103-0.51390.60240.45210.0712-0.4642-0.13950.08740.09920.23660.0525-0.13790.5959-0.06230.50957.92251.7006-11.7513
34.42231.4027-2.84165.05854.50298.1969-0.7056-0.3473-0.79520.1340.9731.32831.2961-0.5176-0.11610.6871-0.1338-0.220.52940.23311.026818.79-24.7522-9.5431
47.58310.230.29376.65370.26114.059-0.1408-1.0736-0.31120.32780.0410.10350.16010.01030.08040.2490.07330.00890.57480.03710.27023.7107-5.8599-13.5086
52.0962-0.1025-0.36478.7424-1.30232.7292-0.14980.27920.93620.1052-0.00060.8571-0.6706-0.1370.08350.30670.1134-0.02130.5903-0.0560.4092-0.13616.3682-16.2542
66.7095-1.0131.65785.4426-1.61190.8207-0.31830.27850.2304-0.30960.3341-1.0932-0.78860.0138-0.03170.2556-0.01080.01940.506-0.04880.416614.97010.9599-19.8683
76.74080.76064.60438.9288-3.33445.0426-0.107-0.41210.24240.8373-0.5050.0496-0.41750.28890.40291.04570.3347-0.39140.8445-0.22510.611217.0201-3.4308-2.571
86.4667-1.2105-3.44082.7171-0.97634.0854-0.1120.9125-0.3257-0.62060.2836-0.3431-0.1594-0.70660.03680.3366-0.067-0.04320.40490.07060.355310.2553-37.3831-31.9914
98.35310.2806-1.45847.5174-0.88717.32270.2449-0.01590.27580.5620.1408-2.0246-0.82340.1766-0.16640.5911-0.066-0.06260.34990.04120.747516.4678-26.4594-25.4538
103.4676-0.127-0.02766.15170.57133.95720.26740.17110.31330.11420.09080.1997-0.5212-0.519-0.35510.31740.06330.05660.29220.05620.25393.8179-28.8793-27.7897
112.5614-2.96250.5323.4552-0.91393.824-1.10370.5577-1.5451-1.0864-0.0835-1.2329-0.01950.67150.12340.7954-0.25340.46940.7168-0.07330.854919.9572-23.9528-38.7877
125.5453.7399-0.56066.33741.57592.53480.08280.0439-0.4483-0.13320.2033-2.5302-0.23790.0361-0.12840.33230.0261-0.00150.29280.00010.83916.7138-37.737-30.3281
133.26484.09723.42526.93921.75487.1715-0.0998-0.7619-1.39621.91290.2481-1.31020.2421-0.4102-0.23650.8683-0.0468-0.0440.41280.11170.656514.0595-27.281-15.3764
143.7069-2.8962-1.62435.6291-2.82935.63060.07570.0992-1.07510.5169-0.0659-0.6366-0.0980.26780.27180.0953-0.1511-0.07130.37410.03611.042532.0272-2.9988-15.2048
150.26381.2749-0.68719.9096-5.28822.90920.2349-0.9973-0.1172-0.6692-0.6137-0.07032.31760.7820.44530.89920.08010.04040.73740.12940.874733.6959-23.9663-10.6247
161.94192.346-0.39714.5897-1.50931.4582-0.24690.464-0.5604-1.24790.27860.49990.4999-0.1848-0.73590.7964-0.122-0.22250.209-0.2631.618839.1022-20.9342-23.6136
176.15071.1362-1.14531.37312.27295.6859-0.77560.7514-0.4995-0.388-0.32750.6571-0.1019-0.44370.89450.3766-0.0225-0.14010.4788-0.12070.984137.255-10.0952-24.1452
189.3607-1.22861.91817.65673.9733.6015-0.9786-1.12970.12262.2815-0.6268-0.7515-0.27590.00571.76871.0590.1726-0.0070.60710.03810.748828.7856-16.77182.4599
197.71781.5915-0.86643.7487-0.38662.8815-0.32810.1406-1.19-0.13030.00990.90870.4291-0.19480.44140.3165-0.01470.01250.3737-0.06080.849143.1721-10.8733-19.9727
207.42220.2544-0.95144.2379-2.35961.9856-0.06060.3116-0.0822-0.762-0.2577-0.28030.0609-0.6315-0.04480.2952-0.0435-0.1080.4792-0.15670.988530.1382-6.194-21.9228
217.8735-0.90780.41958.2176-4.80568.63031.2972-1.7364-0.3539-0.0956-0.93670.74980.993-0.8976-0.48450.7649-0.3173-0.05370.6040.06851.159829.901-23.1385-17.2022
226.0727-2.68630.4987.2247-1.06825.594-0.07860.5551-0.782-0.6331-0.70171.07550.3799-0.15630.57770.58990.09580.05340.4693-0.1010.3241-4.2407-7.5848-32.8034
231.9268-0.41-0.20952.9311-0.4552.97110.32310.81540.01-2.4817-0.76830.3105-0.3194-0.01180.31621.44170.4623-0.18990.4522-0.0730.3961-1.990.0099-44.1969
243.44871.5166-0.11963.2034-2.735.07280.57380.57531.3765-0.11490.2621.78420.3978-1.2681-0.30350.69250.1172-0.40650.7054-0.04541.4613-25.2054.6196-30.8903
250.99191.0051-0.00722.8031-0.35861.79530.37420.04930.045-2.0557-0.20080.22070.3745-0.33650.15771.27470.284-0.18170.3773-0.07930.435-5.296-6.9763-41.797
261.3217-1.22372.32213.3806-1.52864.19320.08890.18040.1079-1.6502-0.19010.2789-0.7973-0.03340.47851.10350.19370.02170.49-0.00960.1952-0.81677.2617-40.1581
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 49 through 64 )
2X-RAY DIFFRACTION2chain 'A' and (resid 65 through 91 )
3X-RAY DIFFRACTION3chain 'A' and (resid 92 through 107 )
4X-RAY DIFFRACTION4chain 'A' and (resid 108 through 135 )
5X-RAY DIFFRACTION5chain 'A' and (resid 136 through 145 )
6X-RAY DIFFRACTION6chain 'A' and (resid 146 through 165 )
7X-RAY DIFFRACTION7chain 'A' and (resid 166 through 175 )
8X-RAY DIFFRACTION8chain 'B' and (resid 48 through 57 )
9X-RAY DIFFRACTION9chain 'B' and (resid 58 through 84 )
10X-RAY DIFFRACTION10chain 'B' and (resid 85 through 135 )
11X-RAY DIFFRACTION11chain 'B' and (resid 136 through 145 )
12X-RAY DIFFRACTION12chain 'B' and (resid 146 through 165 )
13X-RAY DIFFRACTION13chain 'B' and (resid 166 through 175 )
14X-RAY DIFFRACTION14chain 'C' and (resid 47 through 56 )
15X-RAY DIFFRACTION15chain 'C' and (resid 57 through 64 )
16X-RAY DIFFRACTION16chain 'C' and (resid 65 through 74 )
17X-RAY DIFFRACTION17chain 'C' and (resid 75 through 91 )
18X-RAY DIFFRACTION18chain 'C' and (resid 92 through 107 )
19X-RAY DIFFRACTION19chain 'C' and (resid 108 through 145 )
20X-RAY DIFFRACTION20chain 'C' and (resid 146 through 165 )
21X-RAY DIFFRACTION21chain 'C' and (resid 166 through 175 )
22X-RAY DIFFRACTION22chain 'D' and (resid 48 through 56 )
23X-RAY DIFFRACTION23chain 'D' and (resid 57 through 91 )
24X-RAY DIFFRACTION24chain 'D' and (resid 92 through 101 )
25X-RAY DIFFRACTION25chain 'D' and (resid 102 through 155 )
26X-RAY DIFFRACTION26chain 'D' and (resid 156 through 175 )

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