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Yorodumi- PDB-6u54: Anti-Zaire ebolavirus Nucleoprotein Single Domain Antibody Zaire ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6u54 | ||||||||||||
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Title | Anti-Zaire ebolavirus Nucleoprotein Single Domain Antibody Zaire C (ZC) Complexed with Zaire ebolavirus Nucleoprotein C-terminal Domain 634-739 | ||||||||||||
Components |
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Keywords | IMMUNE SYSTEM / Antibody / nanobody / Ebola / filovirus | ||||||||||||
Function / homology | Ebola nucleoprotein / Ebola nucleoprotein / viral RNA genome packaging / helical viral capsid / viral nucleocapsid / host cell cytoplasm / ribonucleoprotein complex / RNA binding / Nucleoprotein Function and homology information | ||||||||||||
Biological species | Lama glama (llama) Zaire ebolavirus | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||||||||
Authors | Taylor, A.B. / Sherwood, L.J. / Hart, P.J. / Hayhurst, A. | ||||||||||||
Funding support | United States, 3items
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Citation | Journal: J.Mol.Biol. / Year: 2019 Title: Paratope Duality and Gullying are Among the Atypical Recognition Mechanisms Used by a Trio of Nanobodies to Differentiate Ebolavirus Nucleoproteins. Authors: Sherwood, L.J. / Taylor, A.B. / Hart, P.J. / Hayhurst, A. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6u54.cif.gz | 109.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6u54.ent.gz | 79.1 KB | Display | PDB format |
PDBx/mmJSON format | 6u54.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u5/6u54 ftp://data.pdbj.org/pub/pdb/validation_reports/u5/6u54 | HTTPS FTP |
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-Related structure data
Related structure data | 6u50C 6u51SC 6u52C 6u53C 6u55C 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 on special symmetry positions |
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-Components
#1: Antibody | Mass: 12334.829 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Semi-synthetic single pot library Nomad 1 based upon Lama glama Source: (gene. exp.) Lama glama (llama) / Plasmid: pecan219 / Production host: Escherichia coli (E. coli) |
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#2: Protein | Mass: 14136.546 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: C-terminal domain (residues 634-739) / Source: (gene. exp.) Zaire ebolavirus (strain Kikwit-95) / Strain: Kikwit-95 / Gene: NP / Plasmid: pecan236/237 / Production host: Escherichia coli (E. coli) / References: UniProt: O72142 |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.77 Å3/Da / Density % sol: 55.59 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop Details: 1.1 M malonic acid, 0.15 M ammonium citrate tribasic, 0.072 M succinic acid, 0.18 M DL-malic acid, 0.24 M sodium acetate, 0.3 M sodium formate, 0.096 M ammonium tartrate dibasic PH range: 7 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 21, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→57.71 Å / Num. obs: 38012 / % possible obs: 96.2 % / Redundancy: 4.2 % / Biso Wilson estimate: 28.48 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.025 / Rrim(I) all: 0.054 / Net I/σ(I): 13.5 |
Reflection shell | Resolution: 1.6→1.69 Å / Redundancy: 4.2 % / Mean I/σ(I) obs: 0.8 / Num. unique obs: 5651 / CC1/2: 0.499 / Rpim(I) all: 0.902 / Rrim(I) all: 1.886 / % possible all: 98.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6U51 Resolution: 1.6→57.71 Å / SU ML: 0.2169 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 25.5724
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.64 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→57.71 Å
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Refine LS restraints |
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LS refinement shell |
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