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- PDB-7n3d: Crystal Structure of Human Fab S24-1564 in the complex with the N... -

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Basic information

Entry
Database: PDB / ID: 7n3d
TitleCrystal Structure of Human Fab S24-1564 in the complex with the N-terminal Domain of Nucleocapsid protein from SARS CoV-2
Components
  • (S24-1564 Fab ...) x 2
  • Nucleoprotein
KeywordsVIRAL PROTEIN / SARS Coronavirus 2 / Nucleocapsid protein / Human antibody Fab / COVID-19 / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
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. / Immunoglobulins ...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. / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
Severe acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.53 Å
AuthorsKim, Y. / Maltseva, N. / Tesar, C. / Jedrzejczak, R. / Dugan, H. / Stamper, C. / Wilson, P. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Iscience / Year: 2024
Title: Epitopes recognition of SARS-CoV-2 nucleocapsid RNA binding domain by human monoclonal antibodies.
Authors: Kim, Y. / Maltseva, N. / Tesar, C. / Jedrzejczak, R. / Endres, M. / Ma, H. / Dugan, H.L. / Stamper, C.T. / Chang, C. / Li, L. / Changrob, S. / Zheng, N.Y. / Huang, M. / Ramanathan, A. / ...Authors: Kim, Y. / Maltseva, N. / Tesar, C. / Jedrzejczak, R. / Endres, M. / Ma, H. / Dugan, H.L. / Stamper, C.T. / Chang, C. / Li, L. / Changrob, S. / Zheng, N.Y. / Huang, M. / Ramanathan, A. / Wilson, P. / Michalska, K. / Joachimiak, A.
History
DepositionMay 31, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 7, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 28, 2021Group: Database references / Structure summary / Category: citation / struct / Item: _citation.title / _struct.title
Revision 1.2Oct 18, 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
Revision 1.3Feb 28, 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
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: S24-1564 Fab heavy chain
L: S24-1564 Fab light chain
C: Nucleoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,31616
Polymers61,6693
Non-polymers64713
Water7,098394
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7450 Å2
ΔGint-56 kcal/mol
Surface area23940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.927, 67.318, 86.087
Angle α, β, γ (deg.)90.000, 106.643, 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

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Protein , 1 types, 1 molecules C

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


Mass: 14303.961 Da / Num. of mol.: 1 / Fragment: CoV N NTD domain, residues 47-173
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): gold / References: UniProt: P0DTC9

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Antibody , 2 types, 2 molecules HL

#1: Antibody S24-1564 Fab heavy chain


Mass: 23950.830 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
#2: Antibody S24-1564 Fab light chain


Mass: 23413.963 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo sapiens (human)

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Non-polymers , 3 types, 407 molecules

#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 394 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
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: 2.29 Å3/Da / Density % sol: 46.35 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M Magnesium chloride hexahydrate, 0.1 M HEPES pH 7.5, 25% w/v Polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9789 Å
DetectorType: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Feb 2, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 1.52→50 Å / Num. obs: 81619 / % possible obs: 95.9 % / Redundancy: 4.4 % / Biso Wilson estimate: 21.23 Å2 / CC1/2: 0.986 / Rmerge(I) obs: 0.114 / Net I/σ(I): 22
Reflection shellResolution: 1.53→1.56 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.834 / Mean I/σ(I) obs: 0.96 / Num. unique obs: 2795 / CC1/2: 0.412 / % possible all: 66.2

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Processing

Software
NameVersionClassification
PHENIX1.19_4092refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDBIDs 5KKU, 5O4G, 6IEB

5kku

5o4g

6ieb


Resolution: 1.53→39.51 Å / SU ML: 0.1753 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 20.7602
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1902 3930 4.82 %
Rwork0.1572 77630 -
obs0.1588 81560 95.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.84 Å2
Refinement stepCycle: LAST / Resolution: 1.53→39.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4164 0 34 394 4592
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00944640
X-RAY DIFFRACTIONf_angle_d1.0156351
X-RAY DIFFRACTIONf_chiral_restr0.0634695
X-RAY DIFFRACTIONf_plane_restr0.0078838
X-RAY DIFFRACTIONf_dihedral_angle_d13.4671695
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.52-1.540.3202800.26721471X-RAY DIFFRACTION50.77
1.54-1.560.27411150.27092033X-RAY DIFFRACTION70.89
1.56-1.580.3044920.26322451X-RAY DIFFRACTION83.54
1.58-1.60.30871420.24642646X-RAY DIFFRACTION90.76
1.6-1.620.30281110.23462763X-RAY DIFFRACTION94.6
1.62-1.650.32351330.24162810X-RAY DIFFRACTION96.43
1.65-1.670.31331560.20772806X-RAY DIFFRACTION98.27
1.67-1.70.25711470.19042885X-RAY DIFFRACTION98.67
1.7-1.730.22761560.17792851X-RAY DIFFRACTION98.82
1.73-1.760.21351170.15952912X-RAY DIFFRACTION99.12
1.76-1.80.22221440.15472891X-RAY DIFFRACTION98.86
1.8-1.830.20731470.1482838X-RAY DIFFRACTION98.51
1.83-1.870.18551490.14112885X-RAY DIFFRACTION99.48
1.87-1.920.19161480.13692901X-RAY DIFFRACTION99.64
1.92-1.960.20071320.14212920X-RAY DIFFRACTION99.32
1.96-2.020.17741520.13682847X-RAY DIFFRACTION99.37
2.02-2.080.16981380.14792871X-RAY DIFFRACTION99.01
2.08-2.140.18941640.14042881X-RAY DIFFRACTION98.67
2.14-2.220.1891450.13812881X-RAY DIFFRACTION98.09
2.22-2.310.17471680.14252850X-RAY DIFFRACTION99.57
2.31-2.410.18981310.14412931X-RAY DIFFRACTION99.64
2.41-2.540.19611680.15642890X-RAY DIFFRACTION99.51
2.54-2.70.20511410.15732858X-RAY DIFFRACTION98.55
2.7-2.910.18581400.16842870X-RAY DIFFRACTION97.89
2.91-3.20.18211680.16182915X-RAY DIFFRACTION99.48
3.2-3.660.19921490.15362905X-RAY DIFFRACTION99.61
3.66-4.610.13791530.142893X-RAY DIFFRACTION98.26
4.61-39.510.18291440.15962975X-RAY DIFFRACTION98.67

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