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- PDB-7c22: Crystal structure of the C-terminal domain of SARS-CoV-2 nucleoca... -

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Basic information

Entry
Database: PDB / ID: 7c22
TitleCrystal structure of the C-terminal domain of SARS-CoV-2 nucleocapsid protein
ComponentsNucleoprotein
KeywordsVIRAL PROTEIN / Coronavirus / nucleocapsid / SARS-CoV-2 / dimerization.
Function / homology
Function and homology information


cytoplasmic capsid assembly / response to host immune response / viral RNA genome packaging / negative regulation of interferon-beta production / Maturation of nucleoprotein / 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 ...cytoplasmic capsid assembly / response to host immune response / viral RNA genome packaging / negative regulation of interferon-beta production / Maturation of nucleoprotein / 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 / 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 / RNA stem-loop binding / viral capsid / Interferon alpha/beta signaling / PIP3 activates AKT signaling / Transcription of SARS-CoV-2 sgRNAs / host cell endoplasmic reticulum-Golgi intermediate compartment / viral nucleocapsid / host cell Golgi apparatus / 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 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 / DI(HYDROXYETHYL)ETHER / Nucleoprotein
Similarity search - Component
Biological speciesSevere acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsZhou, R.J. / Zeng, R. / Lei, J.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)2020YFS0010/HX2019nCoV039 China
CitationJournal: Mol Biomed / Year: 2020
Title: Structural characterization of the C-terminal domain of SARS-CoV-2 nucleocapsid protein.
Authors: Zhou, R. / Zeng, R. / von Brunn, A. / Lei, J.
History
DepositionMay 7, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 20, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 12, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Oct 28, 2020Group: Database references / Category: citation / Item: _citation.country / _citation.journal_volume
Revision 1.3Mar 10, 2021Group: Structure summary / Category: entity_name_com / Item: _entity_name_com.name
Revision 1.4Feb 16, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Nov 29, 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

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Assembly

Deposited unit
A: Nucleoprotein
B: Nucleoprotein
C: Nucleoprotein
D: Nucleoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,7207
Polymers53,4964
Non-polymers2243
Water7,116395
1
A: Nucleoprotein
B: Nucleoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,9134
Polymers26,7482
Non-polymers1652
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5480 Å2
ΔGint-34 kcal/mol
Surface area11460 Å2
MethodPISA
2
C: Nucleoprotein
D: Nucleoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,8073
Polymers26,7482
Non-polymers591
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5560 Å2
ΔGint-30 kcal/mol
Surface area11740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.763, 49.458, 68.819
Angle α, β, γ (deg.)106.790, 90.050, 97.790
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 13374.036 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Production host: Escherichia coli (E. coli) / References: UniProt: P0DTC9
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 395 / 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: 2.69 Å3/Da / Density % sol: 54.24 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.2M Ammonium acetate, 0.1M Sodium acetate pH 4.6, 30% PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 3, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2→19.82 Å / Num. obs: 35328 / % possible obs: 95.6 % / Redundancy: 3.5 % / CC1/2: 0.995 / Rmerge(I) obs: 0.107 / Rpim(I) all: 0.065 / Net I/σ(I): 5.9
Reflection shellResolution: 2→2.05 Å / Rmerge(I) obs: 0.639 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 2636 / CC1/2: 0.752 / Rpim(I) all: 0.391 / % possible all: 96

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2CJR

2cjr


Resolution: 2→19.82 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.925 / SU B: 5.932 / SU ML: 0.153 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.184 / ESU R Free: 0.169
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY SF file contains friedel pairs under I/F minus and I/F plus columns.
RfactorNum. reflection% reflectionSelection details
Rfree0.2382 1667 4.7 %RANDOM
Rwork0.1887 ---
obs0.191 33660 95.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 91.64 Å2 / Biso mean: 24.603 Å2 / Biso min: 12.49 Å2
Baniso -1Baniso -2Baniso -3
1--2.1 Å20.27 Å20.14 Å2
2--3.4 Å2-0.45 Å2
3----1.04 Å2
Refinement stepCycle: final / Resolution: 2→19.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3536 0 15 395 3946
Biso mean--50.28 33.13 -
Num. residues----442
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0133679
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173349
X-RAY DIFFRACTIONr_angle_refined_deg1.4371.6694977
X-RAY DIFFRACTIONr_angle_other_deg1.3061.5867811
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5765452
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.35422.277202
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.29115628
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.691524
X-RAY DIFFRACTIONr_chiral_restr0.0690.2481
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024155
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02805
LS refinement shellResolution: 2→2.052 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3 108 -
Rwork0.273 2523 -
all-2631 -
obs--95.99 %

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