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- PDB-7cr5: Complex structure of a human monoclonal antibody with SARS-CoV-2 ... -

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Basic information

Entry
Database: PDB / ID: 7cr5
TitleComplex structure of a human monoclonal antibody with SARS-CoV-2 nucleocapsid protein NTD
Components
  • Nucleoprotein
  • monoclonal antibody chain H
  • monoclonal antibody chain L
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / Human monoclonal antibody / SARS-CoV-2 / nucleocapsid protein / Complex / 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: 2.08 Å
AuthorsChen, S. / Kang, S.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31770801 China
CitationJournal: Nat Commun / Year: 2021
Title: A SARS-CoV-2 antibody curbs viral nucleocapsid protein-induced complement hyperactivation.
Authors: Kang, S. / Yang, M. / He, S. / Wang, Y. / Chen, X. / Chen, Y.Q. / Hong, Z. / Liu, J. / Jiang, G. / Chen, Q. / Zhou, Z. / Zhou, Z. / Huang, Z. / Huang, X. / He, H. / Zheng, W. / Liao, H.X. / ...Authors: Kang, S. / Yang, M. / He, S. / Wang, Y. / Chen, X. / Chen, Y.Q. / Hong, Z. / Liu, J. / Jiang, G. / Chen, Q. / Zhou, Z. / Zhou, Z. / Huang, Z. / Huang, X. / He, H. / Zheng, W. / Liao, H.X. / Xiao, F. / Shan, H. / Chen, S.
History
DepositionAug 12, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 24, 2021Provider: repository / Type: Initial release
Revision 1.1May 26, 2021Group: 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
Revision 1.2Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nucleoprotein
H: monoclonal antibody chain H
L: monoclonal antibody chain L
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,0384
Polymers61,9733
Non-polymers651
Water4,594255
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5210 Å2
ΔGint-61 kcal/mol
Surface area25790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)154.065, 52.596, 85.299
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z

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Components

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


Mass: 14750.459 Da / Num. of mol.: 1
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 monoclonal antibody chain H


Mass: 24122.855 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Antibody monoclonal antibody chain L


Mass: 23099.518 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 255 / 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: 2.83 Å3/Da / Density % sol: 56.52 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion / pH: 7.2
Details: 0.01M Calcium chloride dihydrate, 0.05 M Sodium cacodylate trihydrate (pH 7.2) ,1.675M Ammonium sulfate, 0.5mM spermine

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 16, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.08→50 Å / Num. obs: 41759 / % possible obs: 99.9 % / Redundancy: 12.1 % / Biso Wilson estimate: 33.33 Å2 / CC1/2: 0.979 / CC star: 0.995 / Rmerge(I) obs: 0.22 / Rpim(I) all: 0.064 / Rrim(I) all: 0.23 / Χ2: 1.215 / Net I/av σ(I): 16.7 / Net I/σ(I): 13.18
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 8.4 % / Rmerge(I) obs: 1.331 / Mean I/σ(I) obs: 1.64 / Num. unique obs: 2023 / CC1/2: 0.782 / CC star: 0.937 / Rrim(I) all: 1.405 / Χ2: 0.449 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PHENIX1.17.1_3660refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6M3M,6TCN

6m3m

6tcn


Resolution: 2.08→28.58 Å / SU ML: 0.2646 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 25.0681
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.222 1998 4.8 %
Rwork0.1908 39668 -
obs0.1923 41666 98.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 35.6 Å2
Refinement stepCycle: LAST / Resolution: 2.08→28.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4179 0 1 255 4435
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00764284
X-RAY DIFFRACTIONf_angle_d0.87595836
X-RAY DIFFRACTIONf_chiral_restr0.054642
X-RAY DIFFRACTIONf_plane_restr0.0055754
X-RAY DIFFRACTIONf_dihedral_angle_d9.5991597
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.08-2.140.34371150.26992276X-RAY DIFFRACTION80.51
2.14-2.190.28961430.25692838X-RAY DIFFRACTION99.6
2.19-2.260.25621410.23412802X-RAY DIFFRACTION99.83
2.26-2.330.30861420.22952843X-RAY DIFFRACTION99.9
2.33-2.410.28431440.22772831X-RAY DIFFRACTION99.9
2.41-2.510.25271440.22032872X-RAY DIFFRACTION99.97
2.51-2.630.29941410.21372819X-RAY DIFFRACTION99.97
2.63-2.760.24841440.21322862X-RAY DIFFRACTION100
2.76-2.940.23641440.21272866X-RAY DIFFRACTION99.97
2.94-3.160.27241440.20732854X-RAY DIFFRACTION100
3.16-3.480.24911470.19672894X-RAY DIFFRACTION99.93
3.48-3.980.1931460.17182897X-RAY DIFFRACTION100
3.98-5.010.1421480.14072943X-RAY DIFFRACTION100
5.01-28.580.18361550.1713071X-RAY DIFFRACTION99.57

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