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- PDB-8j6x: Crystal structure of SARS-CoV2 N-NTD complexed with 5-Benzyloxygr... -

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Basic information

Entry
Database: PDB / ID: 8j6x
TitleCrystal structure of SARS-CoV2 N-NTD complexed with 5-Benzyloxygramine derivative (P3-8)
ComponentsNucleoprotein
KeywordsVIRAL PROTEIN / Severe acute respiratory syndrome coronavirus 2 nucleocapsid protein 5-Benzyloxygramine
Function / homology
Function and homology information


cytoplasmic capsid assembly / viral RNA genome packaging / response to host immune response / negative regulation of interferon-beta production / Maturation of nucleoprotein / intracellular non-membrane-bounded 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 ...cytoplasmic capsid assembly / viral RNA genome packaging / response to host immune response / negative regulation of interferon-beta production / Maturation of nucleoprotein / intracellular non-membrane-bounded 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 / Interleukin-1 signaling / RNA stem-loop binding / Interferon alpha/beta signaling / viral capsid / 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, C-terminal / Nucleocapsid protein, N-terminal / Coronavirus nucleocapsid
Similarity search - Domain/homology
Biological speciesSevere acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 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
DepositionApr 26, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,5215
Polymers68,2124
Non-polymers3081
Water50428
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.722, 92.859, 97.508
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: Chemical ChemComp-U2H / ~{N}-methyl-~{N}-[(5-phenylmethoxy-1~{H}-indol-3-yl)methyl]propan-1-amine


Mass: 308.417 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H24N2O / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 28 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 1.95 Å3/Da / Density % sol: 36.88 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7
Details: spermine tetrahydrochloride, potassium chloride, Bis-Tris HCl (pH 7.0), 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: 0.97626 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Sep 28, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97626 Å / Relative weight: 1
ReflectionResolution: 2.7→30 Å / Num. obs: 15467 / % possible obs: 99.8 % / Redundancy: 5.9 % / Rmerge(I) obs: 0.075 / Net I/σ(I): 21.18
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 6 % / Rmerge(I) obs: 0.428 / Mean I/σ(I) obs: 4.743 / Num. unique obs: 1500

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→26.91 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 30.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2793 1538 9.98 %
Rwork0.231 --
obs0.2359 15405 99.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.7→26.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3958 0 23 28 4009
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003
X-RAY DIFFRACTIONf_angle_d0.592
X-RAY DIFFRACTIONf_dihedral_angle_d6.366566
X-RAY DIFFRACTIONf_chiral_restr0.04567
X-RAY DIFFRACTIONf_plane_restr0.005735
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.770.34391220.33621168X-RAY DIFFRACTION93
2.77-2.860.39961370.32321231X-RAY DIFFRACTION100
2.86-2.980.37261480.32581243X-RAY DIFFRACTION100
2.98-3.110.36451390.29141256X-RAY DIFFRACTION100
3.11-3.280.3781410.29251249X-RAY DIFFRACTION100
3.28-3.480.35381400.29181255X-RAY DIFFRACTION100
3.48-3.750.31231450.25191255X-RAY DIFFRACTION99
3.75-4.130.25341360.20721258X-RAY DIFFRACTION100
4.13-4.720.23141380.19171280X-RAY DIFFRACTION100
4.72-5.940.23521420.19021302X-RAY DIFFRACTION100
5.94-26.910.20491500.1791370X-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)
13.2966-0.3294-0.37033.9932-0.82842.9968-0.2185-0.41120.01440.60520.097-0.69180.25210.5660.09910.3840.1216-0.130.6105-0.03770.487211.6222-4.5407-9.0259
23.4086-0.31750.43242.99490.51841.6418-0.0716-0.35970.5156-0.1942-0.055-0.0594-0.09120.12150.0650.2690.0086-0.02190.54470.04360.40168.13552.312-15.5439
33.31332.4155-0.86314.1921.78044.61710.2761-0.0828-0.92330.5180.10640.16171.3605-0.421-0.34270.736-0.1792-0.32380.63520.18260.94418.7887-24.5281-9.3757
44.11550.11880.23993.2452-0.38721.8924-0.1737-0.3805-0.24470.14030.1707-0.0223-0.1858-0.2276-0.00290.30470.0776-0.01360.58570.02830.28674.8962-2.4428-16.7672
51.33211.3515-1.01041.3601-1.13585.0857-0.564-0.2890.08870.57040.2074-0.91430.3746-0.15940.3080.63530.147-0.1780.718-0.17430.44917.44340.134-7.081
64.2576-1.0552-2.92655.77930.79553.37460.31910.09110.17310.0897-0.0255-0.2745-0.766-0.4482-0.21250.41450.0181-0.02670.43160.10910.32748.6525-30.6257-24.7616
71.03380.05161.23014.92190.5632.50520.1159-0.1735-0.25930.0131-0.0624-0.6463-0.4507-0.19150.05530.43530.0580.11280.4020.00560.56879.8426-30.0628-26.6483
83.19541.2305-0.42074.84160.28783.21650.03990.11340.0414-0.3464-0.1087-0.638-0.8237-0.00770.03290.53910.1190.07320.44410.09830.35219.2154-26.2149-31.6974
94.13540.7215-1.0965.15820.16312.51230.0652-0.1389-0.4349-0.13770.1959-1.6425-0.43210.439-0.23550.3095-0.04480.05580.34890.02710.808616.6221-37.5253-30.246
101.23981.93680.57343.6189-0.91895.77740.517-1.113-0.4536-0.3351-0.0181-1.3148-0.3413-0.043-0.38160.61770.0710.0370.33930.08620.685613.9091-27.0765-15.2425
113.3781-2.0771-1.3868.3074-0.07911.58420.0505-0.1054-0.82381.3141-0.854-0.96310.2928-0.39530.69080.5551-0.02-0.15170.4434-0.12440.93932.1493-2.9339-15.254
120.15330.5186-0.12689.1043-8.24578.42030.1197-0.12020.33910.2367-1.08490.97551.74030.26790.92360.9114-0.080.19280.72390.05281.063233.7068-23.8303-10.5908
132.8130.176-1.1732.1850.28986.1609-0.14010.4142-0.9265-0.3842-0.14260.88451.0003-0.24540.37350.485-0.0491-0.05720.4802-0.19651.091337.9969-13.886-24.1218
148.31241.235-1.40545.6955-1.38044.07470.4535-1.02870.01420.7761-0.5282-0.9764-0.77090.04470.14760.7262-0.068-0.10190.6910.13020.985729.0134-17.12651.8307
155.43381.6697-0.71391.47490.50843.172-0.31920.285-1.81510.0651-0.14470.52910.7667-0.13970.33350.3907-0.01120.07560.3741-0.08210.912542.788-11.5814-16.9511
164.21630.43390.32251.3838-1.20451.9935-0.12260.35860.0776-0.3851-0.04090.2144-0.3854-0.24070.26730.3745-0.0351-0.18110.5017-0.1980.866538.177-3.6906-24.3774
171.6185-1.20180.65195.6991-2.94822.5156-0.3634-0.2895-0.1855-0.50560.3409-0.03641.0063-0.31810.01210.6146-0.05710.06310.5127-0.07261.162229.1597-18.9705-20.8161
184.5794-0.7186-0.4731.40171.92182.71650.09940.74820.2355-1.5534-0.69260.42680.1764-0.26970.40541.03730.1946-0.16220.4327-0.01190.4261-4.93981.0827-42.0055
193.52510.65520.32282.72621.25790.5789-0.25240.8952-0.7534-0.29350.1279-0.34380.55070.38450.21731.03140.4570.51311.00460.01710.64989.2614-6.0053-41.2102
201.19040.4398-1.48770.54930.35575.20.02340.33230.0095-0.376-0.09760.23680.3128-0.3218-0.51351.10190.3167-0.56660.5477-0.17090.5065-7.5959-4.0364-43.1222
215.04760.2085-0.29791.1137-1.76712.8052-0.20290.84140.7938-0.50180.08691.27930.048-1.1453-0.10170.56930.1451-0.31130.7244-0.21181.0925-24.9044.6243-31.0707
224.20872.4763-0.06012.3826-0.90340.81310.49050.99171.1748-1.2869-0.50020.87030.4331-0.38270.06840.73430.215-0.29370.5896-0.0490.6877-12.13940.5167-37.4606
230.26440.54130.34611.1150.8361.6994-0.19270.1283-0.1812-0.53940.3117-0.01890.41040.0369-0.09251.64840.1268-0.32390.4951-0.14410.4735-7.2719-8.6164-47.6908
242.3932-0.113-1.29831.1568-0.26150.78660.01230.05420.6036-1.10510.0212-0.44030.48460.44430.07090.84120.16580.13270.440.00490.49012.5027-10.9899-39.1829
253.14920.0864-0.25780.4342-0.15153.0110.4658-0.28280.332-0.9953-0.1675-0.3359-0.48430.4444-0.01950.72010.1430.16840.5114-0.02290.24073.96984.0306-37.5728
260.7302-0.7432-1.22381.1841.22782.05470.24960.13040.1635-0.6173-0.42050.4415-0.2581-0.16190.06651.180.31810.01280.6611-0.42910.4532-5.052510.3711-42.8014
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 49 through 74 )
2X-RAY DIFFRACTION2chain 'A' and (resid 75 through 91 )
3X-RAY DIFFRACTION3chain 'A' and (resid 92 through 107 )
4X-RAY DIFFRACTION4chain 'A' and (resid 108 through 155 )
5X-RAY DIFFRACTION5chain 'A' and (resid 156 through 175 )
6X-RAY DIFFRACTION6chain 'B' and (resid 48 through 67 )
7X-RAY DIFFRACTION7chain 'B' and (resid 68 through 101 )
8X-RAY DIFFRACTION8chain 'B' and (resid 102 through 145 )
9X-RAY DIFFRACTION9chain 'B' and (resid 146 through 165 )
10X-RAY DIFFRACTION10chain 'B' and (resid 166 through 175 )
11X-RAY DIFFRACTION11chain 'C' and (resid 47 through 56 )
12X-RAY DIFFRACTION12chain 'C' and (resid 57 through 64 )
13X-RAY DIFFRACTION13chain 'C' and (resid 65 through 91 )
14X-RAY DIFFRACTION14chain 'C' and (resid 92 through 107 )
15X-RAY DIFFRACTION15chain 'C' and (resid 108 through 135 )
16X-RAY DIFFRACTION16chain 'C' and (resid 136 through 155 )
17X-RAY DIFFRACTION17chain 'C' and (resid 156 through 175 )
18X-RAY DIFFRACTION18chain 'D' and (resid 48 through 74 )
19X-RAY DIFFRACTION19chain 'D' and (resid 75 through 84 )
20X-RAY DIFFRACTION20chain 'D' and (resid 85 through 91 )
21X-RAY DIFFRACTION21chain 'D' and (resid 92 through 101 )
22X-RAY DIFFRACTION22chain 'D' and (resid 102 through 113 )
23X-RAY DIFFRACTION23chain 'D' and (resid 114 through 135 )
24X-RAY DIFFRACTION24chain 'D' and (resid 136 through 155 )
25X-RAY DIFFRACTION25chain 'D' and (resid 156 through 165 )
26X-RAY DIFFRACTION26chain 'D' and (resid 166 through 175 )

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