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Yorodumi- PDB-1zse: RNA stemloop from bacteriophage Qbeta complexed with an N87S muta... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1zse | ||||||
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Title | RNA stemloop from bacteriophage Qbeta complexed with an N87S mutant MS2 Capsid | ||||||
Components |
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Keywords | RNA/VIRUS/VIRAL PROTEIN / capsid / complex (capsid protein - rna hairpin) / hairpin / levivirus / virus/viral protein/rna / RNA-VIRUS-VIRAL PROTEIN COMPLEX | ||||||
Function / homology | Function and homology information negative regulation of viral translation / T=3 icosahedral viral capsid / regulation of translation / structural molecule activity / RNA binding / identical protein binding Similarity search - Function | ||||||
Biological species | Enterobacterio phage MS2 (virus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å | ||||||
Authors | Horn, W.T. / Tars, K. / Grahn, E. / Helgstrand, C. / Baron, A.J. / Lago, H. / Adams, C.J. / Peabody, D.S. / Phillips, S.E.V. / Stonehouse, N.J. ...Horn, W.T. / Tars, K. / Grahn, E. / Helgstrand, C. / Baron, A.J. / Lago, H. / Adams, C.J. / Peabody, D.S. / Phillips, S.E.V. / Stonehouse, N.J. / Liljas, L. / Stockley, P.G. | ||||||
Citation | Journal: Structure / Year: 2006 Title: Structural Basis of RNA Binding Discrimination between Bacteriophages Qbeta and MS2 Authors: Horn, W.T. / Tars, K. / Grahn, E. / Helgstrand, C. / Baron, A.J. / Lago, H. / Adams, C.J. / Peabody, D.S. / Phillips, S.E.V. / Stonehouse, N.J. / Liljas, L. / Stockley, P.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1zse.cif.gz | 96.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1zse.ent.gz | 71.6 KB | Display | PDB format |
PDBx/mmJSON format | 1zse.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zs/1zse ftp://data.pdbj.org/pub/pdb/validation_reports/zs/1zse | HTTPS FTP |
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-Related structure data
Related structure data | 2b2dC 2b2eC 2b2gC 2bnyC 2bq5C 2bs0C 2bs1C 2ms2S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Symmetry | Point symmetry: (Hermann–Mauguin notation: 532 / Schoenflies symbol: I (icosahedral)) | |||||||||||||||||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: RNA chain | Mass: 6391.863 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: SYNTHESISED RNA STEMLOOP | ||
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#2: Protein | Mass: 13711.438 Da / Num. of mol.: 3 / Mutation: N87S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterobacterio phage MS2 (virus) / Genus: LevivirusEmesvirus / Species: Enterobacteria phage MS2Bacteriophage MS2 / Production host: Escherichia coli (E. coli) / References: UniProt: P03612 #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 4 |
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-Sample preparation
Crystal grow | Temperature: 303 K / Method: vapor diffusion, hanging drop / pH: 7.4 Details: MS2 COATPROTEIN IN 1.25% OR 1.5% PEG 8K, 0.4M SODIUM PHOSPHATE BUFFER, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 303K | ||||||||||||||||||||||||
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Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX14.1 / Wavelength: 1.488 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 26, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.488 Å / Relative weight: 1 |
Reflection | Resolution: 3→30 Å / Num. all: 200773 / Num. obs: 141000 / % possible obs: 70.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.6 % / Rsym value: 0.205 / Net I/σ(I): 3.1 |
Reflection shell | Resolution: 3.02→3.22 Å / Redundancy: 1.9 % / Mean I/σ(I) obs: 1.5 / Rsym value: 0.482 / % possible all: 70.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2MS2 Resolution: 3→30 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber Details: The waters listed in remark 525 are ncs symmetry related waters which are in hydrogen bonding distance to protein or RNA when the biological molecule is generated. NCS symmetry related B ...Details: The waters listed in remark 525 are ncs symmetry related waters which are in hydrogen bonding distance to protein or RNA when the biological molecule is generated. NCS symmetry related B chain instead of the chain used for the actual refinement has been included so that the protein-RNA interactions between the AB dimer and the R chain RNA are clear without generating the NCS symmetry related 'B' chain.
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3→30 Å
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Refine LS restraints |
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