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- PDB-7ylb: Two monobodies recognizing the conserved epitopes of SARS-CoV-2 N... -

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Basic information

Entry
Database: PDB / ID: 7ylb
TitleTwo monobodies recognizing the conserved epitopes of SARS-CoV-2 N antigen applicable to the broad COVID-19 diagnosis
Components
  • NC2
  • Nucleoprotein
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / Engineered 10Fn3 / SARS-CoV-2 N / Monobody / VIRAL PROTEIN / 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 / RNA stem-loop binding / Maturation of nucleoprotein / positive regulation of NLRP3 inflammasome complex assembly / intracellular non-membrane-bounded organelle / CD28 dependent PI3K/Akt signaling / MHC class I protein binding ...cytoplasmic capsid assembly / viral RNA genome packaging / response to host immune response / negative regulation of interferon-beta production / RNA stem-loop binding / Maturation of nucleoprotein / positive regulation of NLRP3 inflammasome complex assembly / intracellular non-membrane-bounded organelle / CD28 dependent PI3K/Akt signaling / MHC class I protein binding / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / molecular condensate scaffold activity / protein sequestering activity / VEGFR2 mediated vascular permeability / 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 / 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, N-terminal / Coronavirus nucleocapsid / Nucleocapsid protein, C-terminal
Similarity search - Domain/homology
Biological speciesSevere acute respiratory syndrome coronavirus 2
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.41 Å
AuthorsHu, M. / Du, Y. / Sun, R. / Hao, Q.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Two monobodies recognizing the conserved epitopes of SARS-CoV-2 N antigen applicable to the broad COVID-19 diagnosis
Authors: Hu, M. / Du, Y. / Sun, R. / Hao, Q.
History
DepositionJul 26, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 6, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Nucleoprotein
D: Nucleoprotein
F: NC2
A: Nucleoprotein
B: Nucleoprotein
E: NC2
G: Nucleoprotein
H: Nucleoprotein
I: NC2
J: Nucleoprotein
K: Nucleoprotein
L: NC2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,42016
Polymers150,03612
Non-polymers3844
Water0
1
C: Nucleoprotein
D: Nucleoprotein
F: NC2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,6054
Polymers37,5093
Non-polymers961
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7620 Å2
ΔGint-61 kcal/mol
Surface area15470 Å2
MethodPISA
2
A: Nucleoprotein
B: Nucleoprotein
E: NC2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,6054
Polymers37,5093
Non-polymers961
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7670 Å2
ΔGint-62 kcal/mol
Surface area15550 Å2
MethodPISA
3
G: Nucleoprotein
H: Nucleoprotein
I: NC2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,6054
Polymers37,5093
Non-polymers961
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7650 Å2
ΔGint-61 kcal/mol
Surface area15620 Å2
MethodPISA
4
J: Nucleoprotein
K: Nucleoprotein
L: NC2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,6054
Polymers37,5093
Non-polymers961
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7680 Å2
ΔGint-59 kcal/mol
Surface area15560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)143.081, 48.458, 143.247
Angle α, β, γ (deg.)90.000, 105.160, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 13562.218 Da / Num. of mol.: 8 / Fragment: CTD
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: Protein
NC2


Mass: 10384.603 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
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: 3.19 Å3/Da / Density % sol: 61.5 %
Crystal growTemperature: 293.15 K / Method: evaporation / Details: 0.2M K2SO4, 18% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 5, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.41→138.261 Å / Num. obs: 74632 / % possible obs: 99.8 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.186 / Net I/σ(I): 7.6
Reflection shellResolution: 2.41→2.45 Å / Rmerge(I) obs: 0.945 / Num. unique obs: 3673

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Processing

Software
NameVersionClassification
REFMAC5.8.0266refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6YUN, 1FNA

6yun

1fna


Resolution: 2.41→138.261 Å / Cor.coef. Fo:Fc: 0.889 / Cor.coef. Fo:Fc free: 0.821 / SU B: 12.799 / SU ML: 0.293 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.361 / ESU R Free: 0.296 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.3259 3709 5 %RANDOM
Rwork0.2671 ---
obs0.27 70911 99.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 137.72 Å2 / Biso mean: 41.358 Å2 / Biso min: 15.18 Å2
Baniso -1Baniso -2Baniso -3
1--2.35 Å2-0 Å21.52 Å2
2---4.21 Å2-0 Å2
3---4.99 Å2
Refinement stepCycle: final / Resolution: 2.41→138.261 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9719 0 20 0 9739
Biso mean--42.41 --
Num. residues----1221
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0129996
X-RAY DIFFRACTIONr_angle_refined_deg1.6751.65413547
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.85751205
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.56221.801522
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.684151635
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8561564
X-RAY DIFFRACTIONr_chiral_restr0.1320.21313
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.027736
LS refinement shellResolution: 2.41→2.468 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.365 262 -
Rwork0.346 5193 -
obs--100 %

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