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- PDB-1u1l: Crystal Structure of UP1 Complexed With d(TTAGGGTT PRN GGG); A Hu... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1u1l | ||||||
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Title | Crystal Structure of UP1 Complexed With d(TTAGGGTT PRN GGG); A Human Telomeric Repeat Containing nebularine | ||||||
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![]() | TRANSPORT PROTEIN/DNA / protein-DNA complex / UP1 / human telomeric repeat / hTR / TR2-A(9)NEB / RRM / RNA Recognition Motif / PRN / nebularine / hnRNP A1 / TRANSPORT PROTEIN-DNA COMPLEX | ||||||
Function / homology | ![]() cellular response to sodium arsenite / SARS-CoV-1-host interactions / import into nucleus / telomeric repeat-containing RNA binding / pre-mRNA binding / G-rich strand telomeric DNA 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 / pre-mRNA binding / G-rich strand telomeric DNA binding / nuclear export / RNA export from nucleus / miRNA binding / FGFR2 alternative splicing / regulation of alternative mRNA splicing, via spliceosome / SARS-CoV-1 modulates host translation machinery / regulation of RNA splicing / Processing of Capped Intron-Containing Pre-mRNA / negative regulation of telomere maintenance via telomerase / mRNA transport / cellular response to glucose starvation / positive regulation of telomere maintenance via telomerase / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / mRNA 3'-UTR binding / spliceosomal complex / mRNA splicing, via spliceosome / single-stranded DNA binding / single-stranded RNA binding / ribonucleoprotein complex / protein domain specific binding / DNA binding / RNA binding / extracellular exosome / nucleoplasm / identical protein binding / membrane / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Myers, J.C. / Shamoo, Y. | ||||||
![]() | ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 59.4 KB | Display | ![]() |
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PDB format | ![]() | 41.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 433.3 KB | Display | ![]() |
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Full document | ![]() | 435.3 KB | Display | |
Data in XML | ![]() | 10.9 KB | Display | |
Data in CIF | ![]() | 14.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1u1kC ![]() 1u1mC ![]() 1u1nC ![]() 1u1oC ![]() 1u1pC ![]() 1u1qC ![]() 1u1rC ![]() 2up1S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: DNA chain | Mass: 3454.254 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: Oligonucleotide d(TTAGGGTT PRN GGG) based on human telomeric repeat d(TTAGGG)n |
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#2: Protein | Mass: 22303.082 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.266 Å3/Da / Density % sol: 44.71 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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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 |
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-Data collection
Diffraction | Mean temperature: 103 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU JUPITER / Detector: CCD / Date: Oct 28, 2001 / Details: osmic mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→20 Å / Num. all: 16172 / Num. obs: 14752 / % possible obs: 91.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.91 % / Biso Wilson estimate: 25.7 Å2 / Rmerge(I) obs: 0.062 / Rsym value: 0.062 / Net I/σ(I): 9.9 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 2.36 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 1.7 / Num. unique all: 1222 / % possible all: 87.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2UP1 Resolution: 2→19.9 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 348143.41 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 41.8669 Å2 / ksol: 0.370304 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→19.9 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.07 Å / Rfactor Rfree error: 0.044 / Total num. of bins used: 10
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Xplor file |
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