+Open data
-Basic information
Entry | Database: PDB / ID: 7p3a | |||||||||
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Title | N-terminal domain of CGI-99 | |||||||||
Components | RNA transcription, translation and transport factor proteinTranscription (biology) | |||||||||
Keywords | UNKNOWN FUNCTION / calponin homology domain / hCLE / RTRAF / c14orf166 | |||||||||
Function / homology | Function and homology information tRNA-splicing ligase complex / RNA transport / tRNA splicing, via endonucleolytic cleavage and ligation / tRNA processing in the nucleus / RNA polymerase II complex binding / negative regulation of protein kinase activity / mitotic spindle / centrosome / perinuclear region of cytoplasm / positive regulation of transcription by RNA polymerase II ...tRNA-splicing ligase complex / RNA transport / tRNA splicing, via endonucleolytic cleavage and ligation / tRNA processing in the nucleus / RNA polymerase II complex binding / negative regulation of protein kinase activity / mitotic spindle / centrosome / perinuclear region of cytoplasm / positive regulation of transcription by RNA polymerase II / RNA binding / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å | |||||||||
Authors | Kroupova, A. / Jinek, M. | |||||||||
Funding support | Switzerland, 2items
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Citation | Journal: Elife / Year: 2021 Title: Molecular architecture of the human tRNA ligase complex. Authors: Kroupova, A. / Ackle, F. / Asanovic, I. / Weitzer, S. / Boneberg, F.M. / Faini, M. / Leitner, A. / Chui, A. / Aebersold, R. / Martinez, J. / Jinek, M. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7p3a.cif.gz | 98.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7p3a.ent.gz | 74.7 KB | Display | PDB format |
PDBx/mmJSON format | 7p3a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p3/7p3a ftp://data.pdbj.org/pub/pdb/validation_reports/p3/7p3a | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
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-Components
#1: Protein | Mass: 12506.033 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: SNA is the affinity tag cleavage scar / Source: (gene. exp.) Homo sapiens (human) / Gene: RTRAF, C14orf166, CGI-99 / Plasmid: pET His6 TEV LIC cloning vector (1B) / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y224 #2: Chemical | ChemComp-IPA / #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 2.57 Å3/Da / Density % sol: 52.15 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 100 mM HEPES pH 7.5, 200 mM magnesium chloride, 20% isopropanol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.0084 Å |
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Mar 14, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0084 Å / Relative weight: 1 |
Reflection | Resolution: 2→45.86 Å / Num. obs: 17246 / % possible obs: 99.9 % / Redundancy: 20.2 % / Biso Wilson estimate: 30.79 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.142 / Rpim(I) all: 0.032 / Net I/σ(I): 18.6 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 19.3 % / Rmerge(I) obs: 1.53 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 3450 / CC1/2: 0.74 / Rpim(I) all: 0.354 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2→45.86 Å / SU ML: 0.251 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.5107 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.91 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→45.86 Å
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Refine LS restraints |
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LS refinement shell |
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