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- PDB-7uxx: Crystal structure of SARS-CoV-2 nucleocapsid protein C-terminal domain -

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Basic information

Entry
Database: PDB / ID: 7uxx
TitleCrystal structure of SARS-CoV-2 nucleocapsid protein C-terminal domain
ComponentsNucleoprotein
KeywordsRNA BINDING PROTEIN / Viral protein / SARS-CoV-2 / CTD / nucleocapsid
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
ACETATE ION / Nucleoprotein
Similarity search - Component
Biological speciesSevere acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsBezerra, E.H.S. / Tonoli, C.C.C. / Soprano, A.S. / Franchini, K.G. / Trivella, D.B.B. / Benedetti, C.E.
Funding support Brazil, 3items
OrganizationGrant numberCountry
Other government01.20.0003.00 Brazil
Other government Brazil
Other government Brazil
CitationJournal: Sci Rep / Year: 2022
Title: Discovery and structural characterization of chicoric acid as a SARS-CoV-2 nucleocapsid protein ligand and RNA binding disruptor.
Authors: Mercaldi, G.F. / Bezerra, E.H.S. / Batista, F.A.H. / Tonoli, C.C.C. / Soprano, A.S. / Shimizu, J.F. / Nagai, A. / da Silva, J.C. / Filho, H.V.R. / do Nascimento Faria, J. / da Cunha, M.G. / ...Authors: Mercaldi, G.F. / Bezerra, E.H.S. / Batista, F.A.H. / Tonoli, C.C.C. / Soprano, A.S. / Shimizu, J.F. / Nagai, A. / da Silva, J.C. / Filho, H.V.R. / do Nascimento Faria, J. / da Cunha, M.G. / Zeri, A.C.M. / Nascimento, A.F.Z. / Proenca-Modena, J.L. / Bajgelman, M.C. / Rocco, S.A. / Lopes-de-Oliveira, P.S. / Cordeiro, A.T. / Bruder, M. / Marques, R.E. / Sforca, M.L. / Franchini, K.G. / Benedetti, C.E. / Figueira, A.C.M. / Trivella, D.B.B.
History
DepositionMay 6, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 22, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 16, 2022Group: 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
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: Nucleoprotein
BBB: Nucleoprotein
CCC: Nucleoprotein
DDD: Nucleoprotein
EEE: Nucleoprotein
FFF: Nucleoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,21610
Polymers76,8806
Non-polymers3354
Water17,276959
1
AAA: Nucleoprotein
CCC: Nucleoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,7193
Polymers25,6272
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5610 Å2
ΔGint-30 kcal/mol
Surface area11210 Å2
MethodPISA
2
BBB: Nucleoprotein
DDD: Nucleoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,7784
Polymers25,6272
Non-polymers1512
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5800 Å2
ΔGint-30 kcal/mol
Surface area11220 Å2
MethodPISA
3
EEE: Nucleoprotein
FFF: Nucleoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,7193
Polymers25,6272
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5440 Å2
ΔGint-30 kcal/mol
Surface area11320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.615, 119.750, 128.568
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 12813.391 Da / Num. of mol.: 6
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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 959 / 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: 2.2 Å3/Da / Density % sol: 44.2 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.3
Details: 100 mM Tris-HCl (pH 8.3), 30% PEG 4000, 0.2 M sodium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: LNLS SIRUS / Beamline: MANACA / Wavelength: 1.3236 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Dec 10, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.3236 Å / Relative weight: 1
ReflectionResolution: 1.85→43.81 Å / Num. obs: 58500 / % possible obs: 99.95 % / Redundancy: 2 % / CC1/2: 0.997 / Net I/σ(I): 9.33
Reflection shellResolution: 1.85→1.916 Å / Redundancy: 2 % / Num. unique obs: 5760 / CC1/2: 0.887 / % possible all: 99.98

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Processing

Software
NameVersionClassification
MxCuBEdata collection
XDSdata reduction
SCALAdata scaling
MOLREPphasing
REFMAC5.8.0258refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7C22

7c22


Resolution: 1.85→43.81 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.94 / SU B: 3.143 / SU ML: 0.093 / Cross valid method: FREE R-VALUE / ESU R: 0.14 / ESU R Free: 0.131
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.207 2915 4.984 %
Rwork0.1628 55576 -
all0.165 --
obs-58491 99.976 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 19.406 Å2
Baniso -1Baniso -2Baniso -3
1--1.387 Å2-0 Å2-0 Å2
2--0.627 Å2-0 Å2
3---0.76 Å2
Refinement stepCycle: LAST / Resolution: 1.85→43.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5256 0 22 959 6237
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0135483
X-RAY DIFFRACTIONr_bond_other_d0.0020.0174987
X-RAY DIFFRACTIONr_angle_refined_deg1.5981.6697408
X-RAY DIFFRACTIONr_angle_other_deg1.4711.58811623
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.135663
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.63822.092306
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.93515937
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.9331538
X-RAY DIFFRACTIONr_chiral_restr0.0830.2705
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.026201
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021213
X-RAY DIFFRACTIONr_nbd_refined0.2140.21120
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1970.24785
X-RAY DIFFRACTIONr_nbtor_refined0.1760.22653
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0870.22182
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1960.2675
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1840.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1530.237
X-RAY DIFFRACTIONr_nbd_other0.2120.2159
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1390.237
X-RAY DIFFRACTIONr_mcbond_it1.6471.6932650
X-RAY DIFFRACTIONr_mcbond_other1.6471.6932649
X-RAY DIFFRACTIONr_mcangle_it2.5992.5193313
X-RAY DIFFRACTIONr_mcangle_other2.5982.5193314
X-RAY DIFFRACTIONr_scbond_it2.4762.0462833
X-RAY DIFFRACTIONr_scbond_other2.4762.0472834
X-RAY DIFFRACTIONr_scangle_it3.892.9314095
X-RAY DIFFRACTIONr_scangle_other3.8892.9324096
X-RAY DIFFRACTIONr_lrange_it6.32621.9766652
X-RAY DIFFRACTIONr_lrange_other6.32521.9746652
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.8980.2252600.2114015X-RAY DIFFRACTION100
1.898-1.950.2462200.1953912X-RAY DIFFRACTION99.9516
1.95-2.0070.2392120.2013834X-RAY DIFFRACTION100
2.007-2.0680.2332020.1893751X-RAY DIFFRACTION99.9747
2.068-2.1360.2341920.1763589X-RAY DIFFRACTION99.9736
2.136-2.2110.2331520.1613557X-RAY DIFFRACTION100
2.211-2.2940.21860.1553410X-RAY DIFFRACTION100
2.294-2.3880.2141600.1633251X-RAY DIFFRACTION100
2.388-2.4940.2511600.1653138X-RAY DIFFRACTION99.9697
2.494-2.6160.2111680.1583001X-RAY DIFFRACTION100
2.616-2.7570.2151540.1532861X-RAY DIFFRACTION99.9668
2.757-2.9240.2011380.142746X-RAY DIFFRACTION100
2.924-3.1260.1931430.1352560X-RAY DIFFRACTION99.963
3.126-3.3760.1841050.1472413X-RAY DIFFRACTION99.9603
3.376-3.6980.183980.1532224X-RAY DIFFRACTION100
3.698-4.1330.1641010.1362016X-RAY DIFFRACTION100
4.133-4.7710.1691120.1411787X-RAY DIFFRACTION100
4.771-5.8390.171670.1841542X-RAY DIFFRACTION100
5.839-8.2390.236460.2181241X-RAY DIFFRACTION99.9224
8.239-43.810.294390.199728X-RAY DIFFRACTION99.3523

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