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- PDB-9kur: Crystal structure of mAb nCoV400Fab with SARS-CoV-2 N-CTD Complex -

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Basic information

Entry
Database: PDB / ID: 9kur
TitleCrystal structure of mAb nCoV400Fab with SARS-CoV-2 N-CTD Complex
Components
  • 400Fab Heavy chain
  • 400Fab Light chain
  • Nucleoprotein
KeywordsVIRAL PROTEIN / Coronavirus / SARS-CoV-2 / Nucleocapsid protein / C-terminal dimerization domain
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 ...: / 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 / NOD1/2 Signaling Pathway / TAK1-dependent IKK and NF-kappa-B activation / 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 / viral nucleocapsid / Transcription of SARS-CoV-2 sgRNAs / host cell endoplasmic reticulum-Golgi intermediate compartment / Translation of Structural Proteins / Virion Assembly and Release / host extracellular space / host cell Golgi apparatus / 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
Biological speciesSevere acute respiratory syndrome coronavirus 2
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.06 Å
AuthorsXue, S.J. / Chen, S.D.
Funding support China, 3items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2022YFC2304200 China
National Natural Science Foundation of China (NSFC)92269106 China
National Natural Science Foundation of China (NSFC)32171192 China
CitationJournal: Commun Biol / Year: 2025
Title: Structural basis of a human antibody targeting SARS-CoV-2 nucleocapsid protein dimerization domain and interfering with RNA-binding.
Authors: Xue, S. / He, S. / Huang, Z. / Yang, M. / Hu, G. / Chen, X. / Chen, Q. / Zhou, W. / Lin, S. / Chen, S.
History
DepositionDec 4, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Oct 15, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nucleoprotein
B: Nucleoprotein
H: 400Fab Heavy chain
L: 400Fab Light chain
D: 400Fab Light chain
G: 400Fab Heavy chain


Theoretical massNumber of molelcules
Total (without water)121,8956
Polymers121,8956
Non-polymers00
Water14,052780
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16380 Å2
ΔGint-87 kcal/mol
Surface area47640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.408, 74.222, 96.510
Angle α, β, γ (deg.)106.63, 103.63, 96.07
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 13084.662 Da / Num. of mol.: 2 / Fragment: CoV N 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: Antibody 400Fab Heavy chain


Mass: 24939.816 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Antibody 400Fab Light chain


Mass: 22923.246 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 780 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.6 Å3/Da / Density % sol: 52.74 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop / Details: 0.2 M sodium formate, 16% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 7, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.06→88.8 Å / Num. obs: 74510 / % possible obs: 98 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.101 / Net I/σ(I): 14.5
Reflection shellResolution: 2.06→2.1 Å / Rmerge(I) obs: 0.576 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 11057

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PDB_EXTRACTdata extraction
DIALSdata reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7DE1,6TCN

7de1

6tcn


Resolution: 2.06→24.98 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 26.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2494 3507 4.73 %
Rwork0.1993 --
obs0.2016 74158 97.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.06→24.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8311 0 0 783 9094
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0028547
X-RAY DIFFRACTIONf_angle_d0.611644
X-RAY DIFFRACTIONf_dihedral_angle_d5.351186
X-RAY DIFFRACTIONf_chiral_restr0.0431294
X-RAY DIFFRACTIONf_plane_restr0.0051495
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.06-2.090.35451390.34292681X-RAY DIFFRACTION94
2.09-2.120.31061470.27872829X-RAY DIFFRACTION97
2.12-2.150.29551480.25752787X-RAY DIFFRACTION97
2.15-2.180.28221430.24292822X-RAY DIFFRACTION97
2.18-2.220.30771570.24522773X-RAY DIFFRACTION97
2.22-2.260.32691330.28992693X-RAY DIFFRACTION93
2.26-2.30.271400.24172850X-RAY DIFFRACTION97
2.3-2.340.281400.22322770X-RAY DIFFRACTION98
2.34-2.390.30341260.22472851X-RAY DIFFRACTION98
2.39-2.440.28781330.22762836X-RAY DIFFRACTION98
2.44-2.50.27291470.23342809X-RAY DIFFRACTION98
2.5-2.560.27941490.23272872X-RAY DIFFRACTION98
2.56-2.630.30281400.22862795X-RAY DIFFRACTION98
2.63-2.710.27061360.2312838X-RAY DIFFRACTION97
2.71-2.80.28581550.22042807X-RAY DIFFRACTION98
2.8-2.890.28831510.22382828X-RAY DIFFRACTION98
2.89-3.010.28781230.21352870X-RAY DIFFRACTION98
3.01-3.150.27141220.20052877X-RAY DIFFRACTION99
3.15-3.310.24831280.20222851X-RAY DIFFRACTION99
3.31-3.520.24511490.19012860X-RAY DIFFRACTION98
3.52-3.790.2481700.182818X-RAY DIFFRACTION99
3.79-4.170.19811530.15932866X-RAY DIFFRACTION99
4.17-4.770.1721300.13622880X-RAY DIFFRACTION99
4.77-60.19091320.16112892X-RAY DIFFRACTION99
6-24.980.19361160.16462896X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -20.0896 Å / Origin y: 19.0769 Å / Origin z: -35.4333 Å
111213212223313233
T0.163 Å20.0199 Å2-0.0021 Å2-0.1851 Å20.0044 Å2--0.1699 Å2
L0.4879 °20.1356 °20.012 °2-0.3164 °20.0272 °2--0.1838 °2
S-0.0189 Å °0.111 Å °-0 Å °-0.0301 Å °0.0323 Å °0.0198 Å °-0.0046 Å °0.0209 Å °-0.0167 Å °
Refinement TLS groupSelection details: all

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