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Yorodumi- PDB-2vop: Crystal structure of N-terminal domains of Human La protein compl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2vop | ||||||
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Title | Crystal structure of N-terminal domains of Human La protein complexed with RNA oligomer AUUUU | ||||||
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 export from nucleus / tRNA modification / 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 export from nucleus / tRNA modification / RNA Polymerase III Abortive And Retractive Initiation / tRNA 5'-leader removal / poly(U) RNA binding / sequence-specific mRNA binding / tRNA processing / positive regulation of translation / cytoplasmic stress granule / tRNA binding / chromosome, telomeric region / 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: 2.8 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 | 2vop.cif.gz | 53.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2vop.ent.gz | 36.8 KB | Display | PDB format |
PDBx/mmJSON format | 2vop.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2vop_validation.pdf.gz | 464.8 KB | Display | wwPDB validaton report |
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Full document | 2vop_full_validation.pdf.gz | 470.4 KB | Display | |
Data in XML | 2vop_validation.xml.gz | 10.1 KB | Display | |
Data in CIF | 2vop_validation.cif.gz | 12.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vo/2vop ftp://data.pdbj.org/pub/pdb/validation_reports/vo/2vop | HTTPS FTP |
-Related structure data
Related structure data | 2vodC 2vonC 2vooC 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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Unit cell |
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-Components
#1: Protein | Mass: 22529.809 Da / Num. of mol.: 1 / 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 | ||
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#2: RNA chain | Mass: 1508.912 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) | ||
#3: Chemical | Sequence details | FIRST TWO RESIDUES ARE FROM VECTOR (GS) REMAINING SEQUENCE CORRESPOND | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.15 Å3/Da / Density % sol: 70.16 % / Description: NONE |
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-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: Jul 12, 2006 / 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: 2.8→63 Å / Num. obs: 8894 / % possible obs: 98.3 % / Observed criterion σ(I): 0 / Redundancy: 2.4 % / Biso Wilson estimate: 76.5 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 6.2 |
Reflection shell | Resolution: 2.8→2.95 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 1.9 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1ZH5 Resolution: 2.8→48.24 Å / Rfactor Rfree error: 0.013 / Data cutoff high absF: 1603544.48 / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 56.5 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→48.24 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.98 Å / Total num. of bins used: 6
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