[English] 日本語
Yorodumi- PDB-1u1r: Crystal Structure of UP1 Complexed With d(TTAGGGTTAG(2PR)G); A Hu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1u1r | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of UP1 Complexed With d(TTAGGGTTAG(2PR)G); A Human Telomeric Repeat Containing 2-aminopurine | ||||||
Components |
| ||||||
Keywords | TRANSPORT PROTEIN/DNA / protein-DNA complex / UP1 / human telomeric repeat / hTR / TR2-G(11)2PR / RRM / RNA Recognition Motif / 2PR / 2-aminopurine / hnRNP A1 / TRANSPORT PROTEIN-DNA COMPLEX | ||||||
Function / homology | Function and homology information cellular response to sodium arsenite / SARS-CoV-1-host interactions / import into nucleus / telomeric repeat-containing RNA binding / G-rich strand telomeric DNA binding / pre-mRNA binding / nuclear export / RNA export from nucleus / miRNA binding / FGFR2 alternative splicing ...cellular response to sodium arsenite / SARS-CoV-1-host interactions / import into nucleus / telomeric repeat-containing RNA binding / G-rich strand telomeric DNA binding / pre-mRNA binding / nuclear export / RNA export from nucleus / miRNA binding / FGFR2 alternative splicing / regulation of alternative mRNA splicing, via spliceosome / intracellular non-membrane-bounded organelle / SARS-CoV-1 modulates host translation machinery / regulation of RNA splicing / negative regulation of telomere maintenance via telomerase / Processing of Capped Intron-Containing Pre-mRNA / mRNA transport / cellular response to glucose starvation / localization / positive regulation of telomere maintenance via telomerase / catalytic step 2 spliceosome / molecular condensate scaffold activity / mRNA Splicing - Major Pathway / mRNA 3'-UTR binding / spliceosomal complex / mRNA splicing, via spliceosome / single-stranded DNA binding / amyloid fibril formation / single-stranded RNA binding / ribonucleoprotein complex / protein domain specific binding / DNA binding / RNA binding / extracellular exosome / nucleoplasm / membrane / identical protein binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Myers, J.C. / Shamoo, Y. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2004 Title: Human UP1 as a Model for Understanding Purine Recognition in the Family of Proteins Containing the RNA Recognition Motif (RRM). Authors: Myers, J.C. / Shamoo, Y. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1u1r.cif.gz | 62.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1u1r.ent.gz | 43 KB | Display | PDB format |
PDBx/mmJSON format | 1u1r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u1/1u1r ftp://data.pdbj.org/pub/pdb/validation_reports/u1/1u1r | HTTPS FTP |
---|
-Related structure data
Related structure data | 1u1kC 1u1lC 1u1mC 1u1nC 1u1oC 1u1pC 1u1qC 2up1S S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: DNA chain | Mass: 3453.270 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: Oligonucleotide d(TTAGGGTTAG (2PR) G) based on human telomeric repeat d(TTAGGG)n |
---|---|
#2: Protein | Mass: 22303.082 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HNRPA1 / Plasmid: pYS45 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3 / References: UniProt: P09651 |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.245 Å3/Da / Density % sol: 44.19 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 283 K / Method: vapor diffusion, hanging drop / pH: 8.1 Details: ammonium phosphate, glycerol, Tris, sodium chloride, MES, EDTA, beta-mercaptoethanol , pH 8.1, VAPOR DIFFUSION, HANGING DROP, temperature 283.0K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
|
-Data collection
Diffraction | Mean temperature: 103 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.9764 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 29, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9764 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→20 Å / Num. all: 21785 / Num. obs: 20583 / % possible obs: 94.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.89 % / Biso Wilson estimate: 32.2 Å2 / Rmerge(I) obs: 0.051 / Rsym value: 0.051 / Net I/σ(I): 13.3 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 4.98 % / Rmerge(I) obs: 0.05 / Mean I/σ(I) obs: 3.3 / Num. unique all: 2114 / % possible all: 68.8 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2UP1 Resolution: 1.8→18.98 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 578210.87 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 56.3918 Å2 / ksol: 0.401491 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 40.1 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→18.98 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.8→1.86 Å / Rfactor Rfree error: 0.043 / Total num. of bins used: 10
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
|