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- PDB-7uxz: Crystal structure of SARS-CoV-2 nucleocapsid protein C-terminal d... -

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Basic information

Entry
Database: PDB / ID: 7uxz
TitleCrystal structure of SARS-CoV-2 nucleocapsid protein C-terminal domain complexed with Chicoric acid
ComponentsNucleoprotein
KeywordsRNA BINDING PROTEIN/Viral Protein / SARS-CoV-2 / CTD / nucleocapsid / Chicoric acid / N protein / RNA BINDING PROTEIN / RNA BINDING PROTEIN-Viral Protein complex
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 / positive regulation of NLRP3 inflammasome complex assembly / intracellular non-membrane-bounded organelle / 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 / positive regulation of NLRP3 inflammasome complex assembly / intracellular non-membrane-bounded organelle / MHC class I protein binding / CD28 dependent PI3K/Akt signaling / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / RNA stem-loop binding / 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 / 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, C-terminal / Nucleocapsid protein, N-terminal / Coronavirus nucleocapsid
Similarity search - Domain/homology
Chem-GKP / DI(HYDROXYETHYL)ETHER / Nucleoprotein
Similarity search - Component
Biological speciesSevere acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.733 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)77,90214
Polymers76,8806
Non-polymers1,0218
Water13,944774
1
AAA: Nucleoprotein
BBB: Nucleoprotein
hetero molecules


  • defined by author&software
  • Evidence: gel filtration
  • 26.3 kDa, 2 polymers
Theoretical massNumber of molelcules
Total (without water)26,3226
Polymers25,6272
Non-polymers6964
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5980 Å2
ΔGint-31 kcal/mol
Surface area11450 Å2
MethodPISA
2
CCC: Nucleoprotein
DDD: Nucleoprotein
hetero molecules


  • defined by author&software
  • 25.7 kDa, 2 polymers
Theoretical massNumber of molelcules
Total (without water)25,7193
Polymers25,6272
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5510 Å2
ΔGint-31 kcal/mol
Surface area11240 Å2
MethodPISA
3
EEE: Nucleoprotein
FFF: Nucleoprotein
hetero molecules


  • defined by author&software
  • 25.9 kDa, 2 polymers
Theoretical massNumber of molelcules
Total (without water)25,8605
Polymers25,6272
Non-polymers2343
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5860 Å2
ΔGint-40 kcal/mol
Surface area11370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.669, 120.655, 128.503
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 6 molecules AAABBBCCCDDDEEEFFF

#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

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Non-polymers , 6 types, 782 molecules

#2: Chemical ChemComp-GKP / (2R,3R)-2,3-bis{[(2E)-3-(3,4-dihydroxyphenyl)prop-2-enoyl]oxy}butanedioic acid / Chicoric acid


Mass: 474.371 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H18O12 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 774 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 0.9772 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Aug 4, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9772 Å / Relative weight: 1
ReflectionResolution: 1.73→43.98 Å / Num. obs: 71415 / % possible obs: 99.86 % / Redundancy: 10.6 % / CC1/2: 0.995 / Net I/σ(I): 9.46
Reflection shellResolution: 1.73→1.79 Å / Num. unique obs: 6959 / CC1/2: 0.509

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Processing

Software
NameVersionClassification
MxCuBEdata collection
autoPROCdata reduction
PHASERphasing
REFMAC5.8.0258refinement
autoPROCdata processing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7C22

7c22


Resolution: 1.733→43.98 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.944 / SU B: 3.019 / SU ML: 0.092 / Cross valid method: FREE R-VALUE / ESU R: 0.117 / ESU R Free: 0.115
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2149 3571 5 %
Rwork0.174 67843 -
all0.176 --
obs-71414 99.87 %
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: 20.275 Å2
Baniso -1Baniso -2Baniso -3
1--0.833 Å2-0 Å20 Å2
2--0.805 Å2-0 Å2
3---0.028 Å2
Refinement stepCycle: LAST / Resolution: 1.733→43.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5250 0 68 774 6092
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0135582
X-RAY DIFFRACTIONr_bond_other_d0.0020.0175066
X-RAY DIFFRACTIONr_angle_refined_deg1.6281.6787546
X-RAY DIFFRACTIONr_angle_other_deg1.4841.58911815
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0275677
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.78722.066305
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.74915955
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.5661538
X-RAY DIFFRACTIONr_chiral_restr0.080.2715
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.026319
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021225
X-RAY DIFFRACTIONr_nbd_refined0.2180.21135
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1940.24706
X-RAY DIFFRACTIONr_nbtor_refined0.1790.22653
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0840.22273
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1860.2544
X-RAY DIFFRACTIONr_metal_ion_refined0.0940.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1520.241
X-RAY DIFFRACTIONr_nbd_other0.2240.2163
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1670.233
X-RAY DIFFRACTIONr_mcbond_it1.7811.8082678
X-RAY DIFFRACTIONr_mcbond_other1.7811.8082677
X-RAY DIFFRACTIONr_mcangle_it2.8112.6933359
X-RAY DIFFRACTIONr_mcangle_other2.8112.6933360
X-RAY DIFFRACTIONr_scbond_it2.7332.2282904
X-RAY DIFFRACTIONr_scbond_other2.7322.2292905
X-RAY DIFFRACTIONr_scangle_it4.3053.1914185
X-RAY DIFFRACTIONr_scangle_other4.3043.1924186
X-RAY DIFFRACTIONr_lrange_it6.13522.726591
X-RAY DIFFRACTIONr_lrange_other5.96221.9526394
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.733-1.7780.3432560.33248590.33351950.7210.73298.46010.327
1.778-1.8270.2922540.28948410.28950960.8150.81999.98040.28
1.827-1.880.292470.25546870.25749340.850.8571000.241
1.88-1.9370.282400.22445490.22747900.8770.89799.97910.206
1.937-2.0010.2722340.20944470.21346810.8840.9041000.185
2.001-2.0710.2392270.19643170.19845450.9140.92599.9780.172
2.071-2.1490.2272160.18340990.18543150.9260.9361000.159
2.149-2.2360.2072100.1739910.17142010.9380.9491000.146
2.236-2.3360.2052020.15938540.16240560.9440.9551000.138
2.336-2.4490.2071940.15736770.15938720.9430.95999.97420.133
2.449-2.5810.2151850.16235070.16436920.9410.9531000.139
2.581-2.7370.1841750.15633340.15735090.9530.9591000.134
2.737-2.9250.1851640.14931240.15132900.9550.96399.93920.131
2.925-3.1590.2231540.15329110.15730650.9430.9581000.137
3.159-3.4580.191420.15727090.15828510.9530.9611000.142
3.458-3.8630.1841300.14324590.14525900.9630.97199.96140.135
3.863-4.4550.161150.12922000.1323150.9730.9771000.125
4.455-5.4430.19990.15518820.15719810.9720.9751000.15
5.443-7.6390.239790.18914850.19115640.950.9611000.178
7.639-43.980.209480.1729110.1749600.9590.96799.89580.175

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