[English] 日本語
Yorodumi- PDB-8g91: LaM domain of human LARP1 in complex with Rp phosphorothioate iso... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8g91 | ||||||
---|---|---|---|---|---|---|---|
Title | LaM domain of human LARP1 in complex with Rp phosphorothioate isomer of AAAAA(SRA) RNA | ||||||
Components |
| ||||||
Keywords | RNA BINDING PROTEIN/RNA / Winged helix fold / RNA binding domain / RNA BINDING PROTEIN / RNA BINDING PROTEIN-RNA complex | ||||||
Function / homology | RNA / Isoform 2 of La-related protein 1 Function and homology information | ||||||
Biological species | Homo sapiens (human) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å | ||||||
Authors | Kozlov, G. / Jiang, J. / Gehring, K. | ||||||
Funding support | Canada, 1items
| ||||||
Citation | Journal: To Be Published Title: Structural insights into RNA binding by the LaM domain of LARP1 Authors: Kozlov, G. / Jiang, J. / Noronha, A.M. / Wilds, C.J. / Gehring, K. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8g91.cif.gz | 69.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8g91.ent.gz | 41 KB | Display | PDB format |
PDBx/mmJSON format | 8g91.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8g91_validation.pdf.gz | 463.8 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 8g91_full_validation.pdf.gz | 464.4 KB | Display | |
Data in XML | 8g91_validation.xml.gz | 7.8 KB | Display | |
Data in CIF | 8g91_validation.cif.gz | 10.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g9/8g91 ftp://data.pdbj.org/pub/pdb/validation_reports/g9/8g91 | HTTPS FTP |
-Related structure data
Related structure data | 8g90C C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
| ||||||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 11806.507 Da / Num. of mol.: 1 / Fragment: Residues 323-410 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: LARP1, KIAA0731, LARP / Production host: Escherichia coli (E. coli) / References: UniProt: Q6PKG0-3 |
---|---|
#2: RNA chain | Mass: 1946.343 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#3: Chemical | ChemComp-GOL / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.38 Å3/Da / Density % sol: 48.27 % |
---|---|
Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop Details: 0.1 M ammonium acetate, 0.1 M Bis-Tris pH 5.5, 17% PEG 10000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.95371 Å |
Detector | Type: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Jul 29, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95371 Å / Relative weight: 1 |
Reflection | Resolution: 1.2→50 Å / Num. obs: 41809 / % possible obs: 99.4 % / Redundancy: 20 % / Biso Wilson estimate: 13.23 Å2 / CC1/2: 0.999 / Net I/σ(I): 42.4 |
Reflection shell | Resolution: 1.2→1.22 Å / Redundancy: 10.3 % / Mean I/σ(I) obs: 1.2 / Num. unique obs: 3876 / CC1/2: 0.592 / % possible all: 96.6 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.2→35.06 Å / SU ML: 0.1507 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 16.9635 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.97 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.2→35.06 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group | Refine-ID: X-RAY DIFFRACTION
|