+Open data
-Basic information
Entry | Database: PDB / ID: 6msf | ||||||
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Title | F6 APTAMER MS2 COAT PROTEIN COMPLEX | ||||||
Components |
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Keywords | Virus/RNA / VIRAL COAT PROTEIN-RNA COMPLEX / RNA APTAMER / RNA STEM LOOP / BACTERIOPHAGE MS2 / Icosahedral virus / Virus-RNA 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 / DIFFERENCE FOURIER / Resolution: 2.8 Å | ||||||
Authors | Convery, M.A. / Rowsell, S. / Stonehouse, N.J. / Ellington, A.D. / Hirao, I. / Murray, J.B. / Peabody, D.S. / Phillips, S.E.V. / Stockley, P.G. | ||||||
Citation | Journal: Nat.Struct.Biol. / Year: 1998 Title: Crystal structure of an RNA aptamer-protein complex at 2.8 A resolution. Authors: Convery, M.A. / Rowsell, S. / Stonehouse, N.J. / Ellington, A.D. / Hirao, I. / Murray, J.B. / Peabody, D.S. / Phillips, S.E. / Stockley, P.G. #1: Journal: J.Mol.Biol. / Year: 1997 Title: The Three-Dimensional Structures of Two Complexes between Recombinant MS2 Capsids and RNA Operator Fragments Reveal Sequence-Specific Protein-RNA Interactions Authors: Valegard, K. / Murray, J.B. / Stonehouse, N.J. / Van Den Worm, S. / Stockley, P.G. / Liljas, L. #2: Journal: Nature / Year: 1994 Title: Crystal Structure of an RNA Bacteriophage Coat Protein-Operator Complex Authors: Valegard, K. / Murray, J.B. / Stockley, P.G. / Stonehouse, N.J. / Liljas, L. #3: Journal: J.Mol.Biol. / Year: 1993 Title: The Refined Structure of Bacteriophage MS2 at 2.8 A Resolution Authors: Golmohammadi, R. / Valegard, K. / Fridborg, K. / Liljas, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6msf.cif.gz | 96.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6msf.ent.gz | 76.5 KB | Display | PDB format |
PDBx/mmJSON format | 6msf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6msf_validation.pdf.gz | 469.9 KB | Display | wwPDB validaton report |
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Full document | 6msf_full_validation.pdf.gz | 475.9 KB | Display | |
Data in XML | 6msf_validation.xml.gz | 17.2 KB | Display | |
Data in CIF | 6msf_validation.cif.gz | 23.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ms/6msf ftp://data.pdbj.org/pub/pdb/validation_reports/ms/6msf | HTTPS FTP |
-Related structure data
Related structure data | 2ms2S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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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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Details | THE COMPLETE PARTICLE CAN BE GENERATED BY APPLYING THE NCS MATRICES TO THE COORDINATES AND THEN APPLYING THE CRYSTALLOGRAPHIC SYMMETRY OPERATORS. |
-Components
#1: RNA chain | Mass: 4461.724 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: FAMILY 6 CONSENSUS SEQUENCE FROM IN VITRO SELECTION | ||
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#2: RNA chain | Mass: 3176.948 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: FAMILY 6 CONSENSUS SEQUENCE FROM IN VITRO SELECTION | ||
#3: Protein | Mass: 13738.464 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterobacterio phage MS2 (virus) / Genus: Levivirus / Species: Enterobacteria phage MS2 / Gene: COAT PROTEIN / Production host: Escherichia coli (E. coli) / Strain (production host): TG1 / References: UniProt: P03612 #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 7 |
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-Sample preparation
Crystal | Density % sol: 80 % Description: ADDITIONAL DATA WERE COLLECTED AT ESRF STATION ID2. | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 7.4 Details: PROTEIN IN 1.25% OR 1.5% PEG 8000, 0.1M NA PHOSPHATE PH 7.4 AND 0.02% NA AZIDE WAS EQUILIBRATED AGAINST 0.35M OR 0.4M NA PHOSPHATE PH 7.4, 0.02% NA AZIDE AT 30O OR 37O C. WASHED CRYSTALS ...Details: PROTEIN IN 1.25% OR 1.5% PEG 8000, 0.1M NA PHOSPHATE PH 7.4 AND 0.02% NA AZIDE WAS EQUILIBRATED AGAINST 0.35M OR 0.4M NA PHOSPHATE PH 7.4, 0.02% NA AZIDE AT 30O OR 37O C. WASHED CRYSTALS WERE SOAKED IN 2MG/ML RNA. | ||||||||||||||||||||||||||||||
Crystal | *PLUS | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 30 ℃ / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 278 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX9.6 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 1, 1997 / Details: MIRROR |
Radiation | Monochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2.8→36 Å / Num. obs: 169875 / % possible obs: 68 % / Redundancy: 1.8 % / Biso Wilson estimate: 45.9 Å2 / Rmerge(I) obs: 0.186 / Net I/σ(I): 3 |
Reflection shell | Resolution: 2.8→2.95 Å / Redundancy: 1.3 % / Rmerge(I) obs: 0.369 / % possible all: 43 |
Reflection | *PLUS Highest resolution: 2.8 Å / Lowest resolution: 36 Å / % possible obs: 68 % / Redundancy: 1.8 % / Num. measured all: 313760 / Biso Wilson estimate: 45.9 Å2 |
Reflection shell | *PLUS Highest resolution: 2.8 Å / Lowest resolution: 2.95 Å / % possible obs: 42.8 % / Redundancy: 1.3 % |
-Processing
Software |
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Refinement | Method to determine structure: DIFFERENCE FOURIER Starting model: PDB ENTRY 2MS2 Resolution: 2.8→36 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 33.6 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.8→36 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: CONSTRAINED | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.8→2.98 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.86 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.8 Å / Lowest resolution: 36 Å / σ(F): 0 / % reflection Rfree: 4 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 33.6 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS % reflection Rfree: 3.9 % |