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Yorodumi- PDB-7n3d: Crystal Structure of Human Fab S24-1564 in the complex with the N... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7n3d | ||||||
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Title | Crystal Structure of Human Fab S24-1564 in the complex with the N-terminal Domain of Nucleocapsid protein from SARS CoV-2 | ||||||
Components |
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Keywords | VIRAL 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 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 | ||||||
Biological species | Homo sapiens (human) Severe acute respiratory syndrome coronavirus 2 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.53 Å | ||||||
Authors | Kim, 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
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Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7n3d.cif.gz | 291.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7n3d.ent.gz | 194.8 KB | Display | PDB format |
PDBx/mmJSON format | 7n3d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n3/7n3d ftp://data.pdbj.org/pub/pdb/validation_reports/n3/7n3d | HTTPS FTP |
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-Related structure data
Related structure data | 6vyoC 6wkpC 7n3cC 7strC 7stsC 7sueC 5kkuS 5o4gS 6iebS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules C
#3: Protein | 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 | 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) |
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#2: Antibody | 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) |
-Non-polymers , 3 types, 407 molecules
#4: Chemical | ChemComp-EDO / #5: Chemical | ChemComp-CL / #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.29 Å3/Da / Density % sol: 46.35 % |
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Crystal grow | Temperature: 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 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9789 Å |
Detector | Type: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Feb 2, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9789 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDBIDs 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
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.84 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.53→39.51 Å
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Refine LS restraints |
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LS refinement shell |
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