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- PDB-9ezb: SARS-CoV-2 Nucleocapsid N-terminal domain (NTD) mutant P67S -

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Basic information

Entry
Database: PDB / ID: 9ezb
TitleSARS-CoV-2 Nucleocapsid N-terminal domain (NTD) mutant P67S
ComponentsNucleoprotein
KeywordsVIRAL PROTEIN / SARS-CoV-2 / Nucelocapsid / N-terminal domain / Omicron BA.1.20
Function / homology
Function and homology information


response to host immune response / viral RNA genome packaging / negative regulation of interferon-beta production / poly(U) RNA binding / 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 ...response to host immune response / viral RNA genome packaging / negative regulation of interferon-beta production / poly(U) RNA binding / 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 / NOD1/2 Signaling Pathway / 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 / 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
DI(HYDROXYETHYL)ETHER / Nucleoprotein
Similarity search - Component
Biological speciesSevere acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsDhamotharan, K. / Schlundt, A. / Guenther, S.
Funding support Germany, 4items
OrganizationGrant numberCountry
German Research Foundation (DFG)SCHL2062/2-1 and 2-2 Germany
German Research Foundation (DFG)161793742 Germany
Other governmentGoethe-Corona-Funds
Other governmentJohanna Quandt Young Academy at Goethe (stipend number 2019/AS01)
CitationJournal: Nat Commun / Year: 2024
Title: A core network in the SARS-CoV-2 nucleocapsid NTD mediates structural integrity and selective RNA-binding.
Authors: Dhamotharan, K. / Korn, S.M. / Wacker, A. / Becker, M.A. / Gunther, S. / Schwalbe, H. / Schlundt, A.
History
DepositionApr 11, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 20, 2024Provider: repository / Type: Initial release
Revision 1.1Dec 11, 2024Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
Revision 1.2Dec 18, 2024Group: 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

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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)59,6806
Polymers59,5384
Non-polymers1422
Water7,855436
1
A: Nucleoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,9202
Polymers14,8851
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Nucleoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,9912
Polymers14,8851
Non-polymers1061
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Nucleoprotein


Theoretical massNumber of molelcules
Total (without water)14,8851
Polymers14,8851
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Nucleoprotein


Theoretical massNumber of molelcules
Total (without water)14,8851
Polymers14,8851
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.789, 92.466, 96.393
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 14884.554 Da / Num. of mol.: 4 / Mutation: P67S
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-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl / 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.: 436 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.21 Å3/Da / Density % sol: 44.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 150mM Sodium Chloride 28% PEG Smear Medium / PH range: 8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.97598 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 20, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97598 Å / Relative weight: 1
ReflectionResolution: 1.6→96.39 Å / Num. obs: 69831 / % possible obs: 99.7 % / Redundancy: 10.3 % / Biso Wilson estimate: 27.7 Å2 / CC1/2: 0.996 / Χ2: 0.89 / Net I/av σ(I): 2.15 / Net I/σ(I): 11.2
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 9.7 % / Mean I/σ(I) obs: 2.2 / Num. unique obs: 3345 / CC1/2: 0.819 / Χ2: 0.48 / % possible all: 97.1

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Processing

Software
NameVersionClassification
BUSTER2.10.4refinement
REFMAC5.8.0425refinement
PDB-REDO8.06refinement
Coot0.9.8.8model building
BUCCANEER3.5.2model building
Aimless0.7.13data scaling
pointless1.12.15data scaling
STARANISO2.3.74data scaling
autoPROC1.1.7data reduction
XDSBUILT 20230630data reduction
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→16.12 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.94 / SU R Cruickshank DPI: 0.121 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.106 / SU Rfree Blow DPI: 0.098 / SU Rfree Cruickshank DPI: 0.095
RfactorNum. reflection% reflectionSelection details
Rfree0.2372 3462 -RANDOM
Rwork0.2196 ---
obs0.2204 69694 99.6 %-
Displacement parametersBiso mean: 45.39 Å2
Baniso -1Baniso -2Baniso -3
1-2.2139 Å20 Å20 Å2
2---8.6091 Å20 Å2
3---6.3952 Å2
Refine analyzeLuzzati coordinate error obs: 0.23 Å
Refinement stepCycle: LAST / Resolution: 1.6→16.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3931 0 8 436 4375
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.017884HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0214185HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2283SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes1274HARMONIC5
X-RAY DIFFRACTIONt_it4045HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion512SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact6903SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion4.06
X-RAY DIFFRACTIONt_other_torsion13.69
LS refinement shellResolution: 1.6→1.61 Å
RfactorNum. reflection% reflection
Rfree0.2635 72 -
Rwork0.2555 --
obs0.2559 1394 98.1 %
Refinement TLS params.

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)
11.3986-0.189-0.67741.3260.16783.77430.06660.1298-0.04230.1298-0.09620.0326-0.04230.03260.0296-0.0065-0.0435-0.0168-0.06020.0299-0.0464.8871-1.4994-7.651
21.12510.62930.01664.4062-1.10792.08230.1720.4571-0.54420.4571-0.0263-0.0675-0.5442-0.0675-0.14560.14570.03230.0542-0.10210.03240.019310.569416.7589-27.2459
32.8516-0.6682-0.40021.9742-0.14033.0204-0.085-0.07520.4904-0.0752-0.06930.23070.49040.23070.1543-0.00940.06390.0351-0.0630.06180.102522.378-13.6359-31.1922
43.7006-0.20181.46871.7022-0.18612.32510.0937-0.14990.0892-0.1499-0.01910.11950.08920.1195-0.0747-0.0850.0157-0.01180.1595-0.0237-0.0527-10.399-5.0233-36.1266
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A48 - 174
2X-RAY DIFFRACTION2{ B|* }B50 - 173
3X-RAY DIFFRACTION3{ C|* }C48 - 174
4X-RAY DIFFRACTION4{ D|* }D48 - 174
5X-RAY DIFFRACTION4{ D|* }D201

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