+Open data
-Basic information
Entry | Database: PDB / ID: 1m5o | ||||||
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Title | Transition State Stabilization by a Catalytic RNA | ||||||
Components |
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Keywords | TRANSLATION/RNA / HAIRPIN RIBOZYME / CATALYTIC RNA / U1A RNA BINDING PROTEIN / Vandate / transition state mimic / TRANSLATION-RNA COMPLEX | ||||||
Function / homology | Function and homology information U1 snRNP binding / U1 snRNP / U1 snRNA binding / U4/U6 x U5 tri-snRNP complex / mRNA Splicing - Major Pathway / spliceosomal complex / mRNA splicing, via spliceosome / DNA binding / RNA binding / nucleoplasm ...U1 snRNP binding / U1 snRNP / U1 snRNA binding / U4/U6 x U5 tri-snRNP complex / mRNA Splicing - Major Pathway / spliceosomal complex / mRNA splicing, via spliceosome / DNA binding / RNA binding / nucleoplasm / identical protein binding / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Rupert, P.B. / Massey, A.P. / Sigurdsson, S.T. / Ferre-D'Amare, A.R. | ||||||
Citation | Journal: Science / Year: 2002 Title: Transition state stabilization by a catalytic RNA Authors: Rupert, P.B. / Massey, A.P. / Sigurdsson, S.T. / Ferre-D'Amare, A.R. #1: Journal: Nature / Year: 2001 Title: Crystal structure of a hairpin ribozyme-inhibitor complex with implications for catalysis Authors: Rupert, P.B. / Ferre-D'Amare, A.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1m5o.cif.gz | 183.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1m5o.ent.gz | 137.3 KB | Display | PDB format |
PDBx/mmJSON format | 1m5o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m5/1m5o ftp://data.pdbj.org/pub/pdb/validation_reports/m5/1m5o | HTTPS FTP |
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-Related structure data
Related structure data | 1m5pC 1m5vC 1hp6 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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1 |
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2 |
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Unit cell |
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-Components
#1: RNA chain | Mass: 6681.896 Da / Num. of mol.: 2 / Source method: obtained synthetically Details: THIS SEQUENCE OCCURS NATURALLY IN SATELLITE TOBACCO RINGSPOT VIRUS #2: RNA chain | Mass: 29809.795 Da / Num. of mol.: 2 / Source method: obtained synthetically Details: THIS SEQUENCE OCCURS NATURALLY IN SATELLITE TOBACCO RINGSPOT VIRUS #3: Protein | Mass: 11498.472 Da / Num. of mol.: 2 / Fragment: U1A RNA BINDING DOMAIN / Mutation: Y31H,Q36R Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SNRPA / Production host: Escherichia coli (E. coli) / References: UniProt: P09012 #4: Chemical | ChemComp-CA / #5: Water | ChemComp-HOH / | |
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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: 2.94 Å3/Da / Density % sol: 58.15 % | ||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 300 K / Method: vapor diffusion, sitting drop / pH: 5 Details: MPD, calcium Chloride, ammonium chloride, meta-ammonium vanadate, pH 5.0, VAPOR DIFFUSION, SITTING DROP at 300K | ||||||||||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 150 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 10, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→20 Å / Num. all: 57194 / Num. obs: 57194 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 34.6 Å2 / Rsym value: 0.064 / Net I/σ(I): 22.9 |
Reflection shell | Resolution: 2.2→2.28 Å / Mean I/σ(I) obs: 1.9 / Rsym value: 0.489 / % possible all: 99 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1HP6 1hp6 Resolution: 2.2→20 Å / Rfactor Rfree error: 0.004 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 Stereochemistry target values: Engh & Huber, Parkinson et al.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 52.9379 Å2 / ksol: 0.32267 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 81.4 Å2
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Refine analyze | Luzzati coordinate error free: 0.39 Å / Luzzati sigma a free: 0.46 Å | ||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.34 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
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Xplor file |
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