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- PDB-8iv3: Crystal structure of SARS-CoV2 N-NTD complexed with 5-Benzyloxygramine -

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Basic information

Entry
Database: PDB / ID: 8iv3
TitleCrystal structure of SARS-CoV2 N-NTD complexed with 5-Benzyloxygramine
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
Chem-DJU / Nucleoprotein
Similarity search - Component
Biological speciesSevere acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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 25, 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)68,4925
Polymers68,2124
Non-polymers2801
Water4,071226
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)58.586, 92.014, 96.584
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-DJU / N,N-dimethyl-1-(5-phenylmethoxy-1H-indol-3-yl)methanamine / 5-Benzyloxygramine


Mass: 280.364 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H20N2O / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 226 / 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: 1.91 Å3/Da / Density % sol: 35.54 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7
Details: spermine tetrahydrochlorid, 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 05A / Wavelength: 0.99984 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Jul 1, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99984 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. obs: 41952 / % possible obs: 99.7 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.032 / Net I/σ(I): 37.713
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.458 / Num. unique obs: 4115 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
HKL-2000data scaling
PDB_EXTRACTdata extraction
PHENIXphasing
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→27.17 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 33.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.286 1994 4.76 %
Rwork0.2371 --
obs0.2394 41888 99.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9→27.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3971 0 21 226 4218
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006
X-RAY DIFFRACTIONf_angle_d0.895
X-RAY DIFFRACTIONf_dihedral_angle_d7.177565
X-RAY DIFFRACTIONf_chiral_restr0.055568
X-RAY DIFFRACTIONf_plane_restr0.009738
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.940.4141360.34652753X-RAY DIFFRACTION98
1.94-20.34191370.33392814X-RAY DIFFRACTION100
2-2.060.39791400.31282825X-RAY DIFFRACTION100
2.06-2.120.35761410.31882803X-RAY DIFFRACTION100
2.12-2.20.35661470.3012824X-RAY DIFFRACTION100
2.2-2.290.38271390.2942830X-RAY DIFFRACTION100
2.29-2.390.34041490.29652839X-RAY DIFFRACTION100
2.39-2.520.38741320.29832859X-RAY DIFFRACTION100
2.52-2.670.33521440.28092855X-RAY DIFFRACTION100
2.67-2.880.28981430.28352855X-RAY DIFFRACTION100
2.88-3.170.30041450.24962875X-RAY DIFFRACTION100
3.17-3.630.26461460.23172887X-RAY DIFFRACTION100
3.63-4.560.24881450.18852910X-RAY DIFFRACTION100
4.56-27.170.23121500.18042965X-RAY DIFFRACTION97
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)
14.9146-0.72320.40653.7861-1.21393.48190.08070.1139-0.5580.16160.1885-0.1530.36650.1861-0.30250.22980.0303-0.050.47610.02420.381613.7423-4.4274-20.7282
22.3567-0.2751.02241.61540.14211.9562-0.2613-0.7573-0.40851.01630.1604-0.11710.3576-0.3657-0.09470.54530.1745-0.11160.76370.04250.346110.4917-4.4558-3.7098
32.1219-0.38240.06281.5517-0.41811.4192-0.2859-0.53110.4057-0.090.1366-0.35810.0743-0.12530.11620.25550.0351-0.03240.51760.00360.26958.05762.2791-15.402
40.9464-0.0639-0.52953.48380.86771.7050.0487-0.6845-0.59260.3210.2991-0.04440.8947-0.345-0.22590.5936-0.0542-0.21430.55820.23120.855418.8063-24.4447-9.279
53.6486-0.37320.35091.5059-0.40282.371-0.1996-0.776-0.21040.20130.15890.1348-0.044-0.23740.03750.23710.08660.01760.53650.06930.24852.8116-2.6256-13.9654
62.6586-0.37260.27461.2534-0.80970.5186-0.37790.13620.2815-0.01970.3185-0.4437-0.32890.3210.07440.26480.0447-0.01250.5259-0.06570.289515.02051.0399-19.7743
72.6248-0.53821.65922.5994-1.03421.24260.161-0.23-0.23190.36320.0398-0.0630.24650.0272-0.05990.86770.421-0.31931.009-0.1410.429617.1752-3.3265-2.4765
82.4142-0.1496-1.32543.7937-0.13723.1050.09790.1439-0.07220.24920.0998-0.8045-0.4879-0.58560.02760.37780.0274-0.02920.34290.04390.31338.8529-30.2449-24.3307
92.2619-1.3766-0.65041.1063-0.20383.08260.00840.5965-0.277-0.4629-0.1264-1.9635-0.370.4309-0.10840.4974-0.09260.12250.4837-0.00791.302222.6539-27.1403-29.9437
100.8859-0.295-0.03962.84620.07392.15930.17230.08940.05450.0001-0.0019-0.0519-0.446-0.5948-0.15350.45060.05060.07030.40140.0370.28823.9092-28.2545-27.3931
113.4107-1.84620.02332.1985-2.10413.6549-0.31880.20020.13270.0185-0.5079-0.528-0.08870.2533-0.02080.8501-0.20980.4630.4956-0.04660.996620.537-23.1115-37.7647
121.67540.72320.17272.2651.69721.82980.19730.0059-0.46510.31150.2084-1.7425-0.10.29070.11030.4311-0.0493-0.10880.2590.05010.717615.8331-33.5791-24.7103
131.6549-1.9485-0.26363.825-0.52070.4985-0.1347-0.0849-0.09360.9157-0.2406-0.1805-0.2963-0.08710.21370.495-0.1038-0.09860.4054-0.0370.977431.9917-2.928-15.0834
140.7276-1.23720.75362.2409-1.35510.8165-0.1527-0.2872-0.73620.1299-0.22070.24630.6937-0.01780.16560.743-0.06250.17150.62860.2131.741633.7777-23.8264-10.7599
150.0876-0.2782-0.0040.86170.0130.0032-0.14840.1356-0.3973-0.4214-0.0559-0.13370.02880.0354-0.1830.6849-0.16790.1190.3067-0.27881.683838.9889-20.6273-23.2625
161.2063-0.0829-0.1692.53310.8220.9069-0.26450.3162-0.5837-0.741-0.18610.4889-0.0345-0.41130.32740.4334-0.0729-0.15390.4958-0.11091.24137.1511-10.0363-23.9218
171.717-0.47080.72832.29890.52670.6005-0.1537-0.5508-0.4760.4903-0.6624-0.1050.1429-0.37830.44840.8263-0.131-0.02410.7297-0.00321.095928.893-16.64272.4051
182.12520.0564-0.19371.1823-0.14841.0088-0.2350.0785-1.3305-0.2766-0.07720.31630.178-0.06130.19270.2516-0.02330.02820.3455-0.04040.988440.7777-8.384-19.6938
190.48810.3509-0.31060.7465-0.66460.5912-0.22380.2935-0.4362-0.38830.2313-0.21680.2991-0.13750.22840.3857-0.1743-0.02220.455-0.16191.332328.3604-14.1311-24.7009
202.49060.7049-1.22880.288-0.93894.48770.16-0.1832-0.2588-0.49830.0104-0.23050.3413-0.0068-0.08890.7724-0.20630.18160.51560.11031.143529.9213-23.1047-16.9077
213.0968-2.03070.63352.86480.60213.394-0.10590.32540.075-0.7298-0.38391.1759-0.4219-0.44880.10190.71820.1603-0.25780.374-0.05990.3734-7.37970.8144-39.2696
222.16580.63850.17121.3038-0.19291.21050.21640.4386-0.0171-1.7049-0.44620.10220.28670.37810.0051.16720.27430.05610.4638-0.00180.28392.0505-3.3097-43.6673
232.85280.8863-0.42222.0875-0.85652.67370.51430.26060.0318-0.01560.05630.67410.3192-0.5674-0.21750.62660.0016-0.26860.5801-0.09451.163-23.52894.763-32.4489
241.7151-0.4194-0.47981.5713-0.56910.98670.2611-0.0608-0.765-2.078-0.5250.39810.40930.1821-0.21331.3990.2545-0.17330.2247-0.28950.039-2.4391-3.9771-41.6202
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 49 through 56 )
2X-RAY DIFFRACTION2chain 'A' and (resid 57 through 74 )
3X-RAY DIFFRACTION3chain 'A' and (resid 75 through 91 )
4X-RAY DIFFRACTION4chain 'A' and (resid 92 through 107 )
5X-RAY DIFFRACTION5chain 'A' and (resid 108 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 67 )
9X-RAY DIFFRACTION9chain 'B' and (resid 68 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 175 )
13X-RAY DIFFRACTION13chain 'C' and (resid 47 through 56 )
14X-RAY DIFFRACTION14chain 'C' and (resid 57 through 64 )
15X-RAY DIFFRACTION15chain 'C' and (resid 65 through 74 )
16X-RAY DIFFRACTION16chain 'C' and (resid 75 through 91 )
17X-RAY DIFFRACTION17chain 'C' and (resid 92 through 107 )
18X-RAY DIFFRACTION18chain 'C' and (resid 108 through 155 )
19X-RAY DIFFRACTION19chain 'C' and (resid 156 through 165 )
20X-RAY DIFFRACTION20chain 'C' and (resid 166 through 175 )
21X-RAY DIFFRACTION21chain 'D' and (resid 48 through 67 )
22X-RAY DIFFRACTION22chain 'D' and (resid 68 through 91 )
23X-RAY DIFFRACTION23chain 'D' and (resid 92 through 107 )
24X-RAY DIFFRACTION24chain 'D' and (resid 108 through 175 )

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