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Yorodumi- PDB-2von: Crystal structure of N-terminal domains of Human La protein compl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2von | ||||||
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Title | Crystal structure of N-terminal domains of Human La protein complexed with RNA oligomer AUAAUUU | ||||||
Components |
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Keywords | RNA BINDING PROTEIN / RNA-BINDING PROTEIN / RNA RECOGNITION MOTIF / SYSTEMIC LUPUS ERYTHEMATOSUS / PHOSPHOPROTEIN / RNA MATURATION / NUCLEUS / LA MOTIF / RNA-BINDING / POLYMORPHISM | ||||||
Function / homology | Function and homology information nuclear histone mRNA catabolic process / histone mRNA metabolic process / tRNA 3'-end processing / protein localization to cytoplasmic stress granule / RNA Polymerase III Transcription Termination / IRES-dependent viral translational initiation / tRNA modification / tRNA export from nucleus / RNA Polymerase III Abortive And Retractive Initiation / tRNA 5'-leader removal ...nuclear histone mRNA catabolic process / histone mRNA metabolic process / tRNA 3'-end processing / protein localization to cytoplasmic stress granule / RNA Polymerase III Transcription Termination / IRES-dependent viral translational initiation / tRNA modification / tRNA export from nucleus / RNA Polymerase III Abortive And Retractive Initiation / tRNA 5'-leader removal / sequence-specific mRNA binding / poly(U) RNA binding / tRNA processing / positive regulation of translation / cytoplasmic stress granule / chromosome, telomeric region / tRNA binding / ribonucleoprotein complex / mRNA binding / RNA binding / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Kotik-Kogan, O. / Valentine, E.R. / Sanfelice, D. / Conte, M.R. / Curry, S. | ||||||
Citation | Journal: Structure / Year: 2008 Title: Structural Analysis Reveals Conformational Plasticity in the Recognition of RNA 3' Ends by the Human La Protein. Authors: Kotik-Kogan, O. / Valentine, E.R. / Sanfelice, D. / Conte, M.R. / Curry, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2von.cif.gz | 99.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2von.ent.gz | 74.9 KB | Display | PDB format |
PDBx/mmJSON format | 2von.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2von_validation.pdf.gz | 460 KB | Display | wwPDB validaton report |
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Full document | 2von_full_validation.pdf.gz | 467.6 KB | Display | |
Data in XML | 2von_validation.xml.gz | 18.7 KB | Display | |
Data in CIF | 2von_validation.cif.gz | 26.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vo/2von ftp://data.pdbj.org/pub/pdb/validation_reports/vo/2von | HTTPS FTP |
-Related structure data
Related structure data | 2vodC 2vooC 2vopC 1zh5S 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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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.6489, 0.0117, -0.7608), Vector: |
-Components
#1: Protein | Mass: 22529.809 Da / Num. of mol.: 2 / Fragment: N-TERMINAL DOMAIN, RESIDUES 4-194 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PETM11 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P05455 #2: RNA chain | Mass: 2167.323 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) #3: Water | ChemComp-HOH / | Sequence details | FIRST TWO RESIDUES ARE FROM VECTOR (GS) REMAINING SEQUENCE CORRESPOND | |
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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: 2.63 Å3/Da / Density % sol: 52.79 % / Description: NONE |
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Crystal grow | Method: vapor diffusion, sitting drop Details: 0.2 M NaCl, 0.1 M phosphate citrate (pH 5.0), 22% (v/w) PEG 8000, 0.01 M taurine. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.62 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Sep 13, 2007 / Details: SINGLE SILICON (111) MONOCHROMATOR |
Radiation | Monochromator: SINGLE SILICON (111) MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.62 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→43 Å / Num. obs: 27637 / % possible obs: 90.4 % / Observed criterion σ(I): 0 / Redundancy: 1.7 % / Biso Wilson estimate: 8.4 Å2 / Rmerge(I) obs: 0.084 / Net I/σ(I): 7.5 |
Reflection shell | Resolution: 2.1→2.21 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.223 / Mean I/σ(I) obs: 4.1 / % possible all: 92.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1ZH5 Resolution: 2.1→43 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1804074.3 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MLF
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Displacement parameters | Biso mean: 23.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.1→43 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.23 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
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Xplor file | Serial no: 1 / Param file: ION.ED-12.PARAM / Topol file: ION.ED-12.TOP |