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- PDB-7n0r: Structure of the SARS-CoV-2 N protein RNA-binding domain bound to... -

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Basic information

Entry
Database: PDB / ID: 7n0r
TitleStructure of the SARS-CoV-2 N protein RNA-binding domain bound to single-domain antibody C2
Components
  • Nucleoprotein
  • Single-domain antibody C2
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / SARS-CoV-2 / nanobody / nucleocapsid / VIRUS / VIRAL PROTEIN-IMMUNE SYSTEM 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
Biological speciesSevere acute respiratory syndrome coronavirus 2
Lama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.42 Å
AuthorsYe, Q. / Corbett, K.D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM128464 United States
Citation
Journal: Front Immunol / Year: 2021
Title: Structural Basis for SARS-CoV-2 Nucleocapsid Protein Recognition by Single-Domain Antibodies.
Authors: Ye, Q. / Lu, S. / Corbett, K.D.
#1: Journal: Biorxiv / Year: 2021
Title: Structural basis for SARS-CoV-2 Nucleocapsid protein recognition by single-domain antibodies.
Authors: Ye, Q. / Lu, S. / Corbett, K.D.
History
DepositionMay 25, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 2, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 1, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Feb 9, 2022Group: Database references / Category: citation / citation_author
Revision 1.3Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / pdbx_initial_refinement_model
Item: _citation.journal_id_ISSN

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nucleoprotein
B: Nucleoprotein
C: Single-domain antibody C2
D: Single-domain antibody C2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,5467
Polymers57,2584
Non-polymers2883
Water12,412689
1
A: Nucleoprotein
C: Single-domain antibody C2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,7253
Polymers28,6292
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1720 Å2
ΔGint-18 kcal/mol
Surface area12700 Å2
MethodPISA
2
B: Nucleoprotein
D: Single-domain antibody C2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,8214
Polymers28,6292
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1840 Å2
ΔGint-26 kcal/mol
Surface area12650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.668, 77.120, 71.932
Angle α, β, γ (deg.)90.000, 95.140, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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


Mass: 14144.752 Da / Num. of mol.: 2 / Fragment: RNA-binding domain
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: Antibody Single-domain antibody C2


Mass: 14484.096 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli)
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 689 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.25 Å3/Da / Density % sol: 45.37 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Tris-HCl pH 8.5, 0.2 M LiSO4, and 20% PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 11, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.42→77.12 Å / Num. obs: 95122 / % possible obs: 99.1 % / Redundancy: 6.7 % / Biso Wilson estimate: 17.22 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.037 / Rpim(I) all: 0.016 / Net I/σ(I): 25.7
Reflection shellResolution: 1.42→1.44 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.257 / Mean I/σ(I) obs: 4.5 / Num. unique obs: 4475 / CC1/2: 0.976 / Rpim(I) all: 0.121 / % possible all: 94.4

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Processing

Software
NameVersionClassification
PHENIX1.19_4092refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7CDZ

7cdz


Resolution: 1.42→52.49 Å / SU ML: 0.1302 / Cross valid method: FREE R-VALUE / σ(F): 0.31 / Phase error: 15.1893
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1662 4628 4.87 %
Rwork0.1405 90421 -
obs0.1417 95049 99.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 22.58 Å2
Refinement stepCycle: LAST / Resolution: 1.42→52.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3818 0 15 689 4522
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00793984
X-RAY DIFFRACTIONf_angle_d0.96365417
X-RAY DIFFRACTIONf_chiral_restr0.0774558
X-RAY DIFFRACTIONf_plane_restr0.0082715
X-RAY DIFFRACTIONf_dihedral_angle_d11.83821433
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.42-1.430.19811440.16892762X-RAY DIFFRACTION92.52
1.43-1.450.23211580.15453025X-RAY DIFFRACTION99.07
1.45-1.470.16961500.14623023X-RAY DIFFRACTION99.03
1.47-1.490.20091590.14832958X-RAY DIFFRACTION98.7
1.49-1.510.18541790.14253042X-RAY DIFFRACTION99.02
1.51-1.530.18361520.13972938X-RAY DIFFRACTION98.6
1.53-1.550.17581750.13572992X-RAY DIFFRACTION98.45
1.55-1.570.1781500.13622931X-RAY DIFFRACTION97.53
1.57-1.60.17521420.13882965X-RAY DIFFRACTION97.03
1.6-1.620.18331390.14163004X-RAY DIFFRACTION99.9
1.62-1.650.171610.14023080X-RAY DIFFRACTION99.97
1.65-1.680.2421420.16523056X-RAY DIFFRACTION100
1.68-1.710.20721590.16133008X-RAY DIFFRACTION99.91
1.71-1.750.19371530.15763036X-RAY DIFFRACTION99.97
1.75-1.790.18611430.14733046X-RAY DIFFRACTION99.94
1.79-1.830.18161380.13623014X-RAY DIFFRACTION99.81
1.83-1.870.17141450.13133089X-RAY DIFFRACTION99.75
1.87-1.920.15891510.12492997X-RAY DIFFRACTION99.56
1.92-1.980.15251730.1293016X-RAY DIFFRACTION99.63
1.98-2.050.14761420.12743041X-RAY DIFFRACTION99.13
2.05-2.120.16571610.13343003X-RAY DIFFRACTION99.09
2.12-2.20.16291540.12422992X-RAY DIFFRACTION98.22
2.2-2.30.15981480.13243034X-RAY DIFFRACTION99.87
2.3-2.420.15181580.13773040X-RAY DIFFRACTION99.84
2.43-2.580.15851500.13913091X-RAY DIFFRACTION99.78
2.58-2.780.16741370.13783031X-RAY DIFFRACTION99.72
2.78-3.060.16221750.14333004X-RAY DIFFRACTION99.78
3.06-3.50.14451370.14073089X-RAY DIFFRACTION99.35
3.5-4.410.14781680.12883009X-RAY DIFFRACTION98.42
4.41-52.490.18551850.16743105X-RAY DIFFRACTION99.73

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