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Yorodumi- PDB-6pzq: Structure of the human respiratory syncytial virus M2-1 protein i... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6pzq | ||||||
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Title | Structure of the human respiratory syncytial virus M2-1 protein in complex with a short positive-sense gene-end RNA | ||||||
Components |
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Keywords | METAL BINDING PROTEIN/RNA / HRSV M2-1 RNA complex / RNA BINDING PROTEIN / METAL BINDING PROTEIN-RNA complex | ||||||
Function / homology | Function and homology information regulation of viral transcription / Respiratory syncytial virus genome transcription / Translation of respiratory syncytial virus mRNAs / Respiratory syncytial virus genome replication / RSV-host interactions / Assembly and release of respiratory syncytial virus (RSV) virions / Maturation of hRSV A proteins / viral transcription / Respiratory syncytial virus (RSV) attachment and entry / virion component ...regulation of viral transcription / Respiratory syncytial virus genome transcription / Translation of respiratory syncytial virus mRNAs / Respiratory syncytial virus genome replication / RSV-host interactions / Assembly and release of respiratory syncytial virus (RSV) virions / Maturation of hRSV A proteins / viral transcription / Respiratory syncytial virus (RSV) attachment and entry / virion component / transcription antitermination / host cell cytoplasm / host cell nucleus / structural molecule activity / RNA binding / metal ion binding Similarity search - Function | ||||||
Biological species | Human respiratory syncytial virus A Human respiratory syncytial virus A2 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.703 Å | ||||||
Authors | Gao, Y. / Cao, D. / Liang, B. | ||||||
Funding support | United States, 1items
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Citation | Journal: Structure / Year: 2020 Title: Structure of the Human Respiratory Syncytial Virus M2-1 Protein in Complex with a Short Positive-Sense Gene-End RNA. Authors: Gao, Y. / Cao, D. / Pawnikar, S. / John, K.P. / Ahn, H.M. / Hill, S. / Ha, J.M. / Parikh, P. / Ogilvie, C. / Swain, A. / Yang, A. / Bell, A. / Salazar, A. / Miao, Y. / Liang, B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6pzq.cif.gz | 263.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6pzq.ent.gz | 212.9 KB | Display | PDB format |
PDBx/mmJSON format | 6pzq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pz/6pzq ftp://data.pdbj.org/pub/pdb/validation_reports/pz/6pzq | HTTPS FTP |
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-Related structure data
Related structure data | 4c3bS S: Starting model for refinement |
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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
#1: Protein | Mass: 22216.404 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human respiratory syncytial virus A (strain A2) Strain: A2 / Gene: M2-1 / Production host: Escherichia coli (E. coli) / References: UniProt: P04545 #2: RNA chain | Mass: 2206.363 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Human respiratory syncytial virus A2 #3: Chemical | ChemComp-ZN / #4: Water | ChemComp-HOH / | 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: 2.57 Å3/Da / Density % sol: 52.1 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop Details: 0.2 M magnesium chloride hexahydrate, 0.1 M Tris pH 8.5, 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: 22-ID / Wavelength: 1 Å |
Detector | Type: MAR CCD 130 mm / Detector: CCD / Date: Apr 15, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.703→94.75 Å / Num. obs: 25701 / % possible obs: 99.8 % / Redundancy: 24.3 % / Biso Wilson estimate: 89.84 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.127 / Rpim(I) all: 0.027 / Rrim(I) all: 0.132 / Net I/σ(I): 13.3 |
Reflection shell | Resolution: 2.703→2.85 Å / Redundancy: 26 % / Num. unique obs: 3673 / Rpim(I) all: 0.39 / % possible all: 100 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4C3B Resolution: 2.703→63.517 Å / SU ML: 0.44 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 33.07 / Stereochemistry target values: ML
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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 max: 211.15 Å2 / Biso mean: 104.4578 Å2 / Biso min: 36.64 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.703→63.517 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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