+Open data
-Basic information
Entry | Database: PDB / ID: 5lxy | ||||||
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Title | Structure of the minimal RBM7 - ZCCHC8 Complex | ||||||
Components |
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Keywords | RNA BINDING PROTEIN / NEXT Complex RRM RBM7 ZCCHC8 | ||||||
Function / homology | Function and homology information : / snRNA catabolic process / TRAMP complex / snRNA binding / regulation of alternative mRNA splicing, via spliceosome / pre-mRNA intronic binding / 14-3-3 protein binding / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / meiotic cell cycle ...: / snRNA catabolic process / TRAMP complex / snRNA binding / regulation of alternative mRNA splicing, via spliceosome / pre-mRNA intronic binding / 14-3-3 protein binding / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / meiotic cell cycle / mRNA splicing, via spliceosome / single-stranded RNA binding / nuclear body / RNA binding / zinc ion binding / nucleoplasm / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å | ||||||
Authors | Falk, S. / Finogenova, K. / Benda, C. / Conti, E. | ||||||
Citation | Journal: Nat Commun / Year: 2016 Title: Structure of the RBM7-ZCCHC8 core of the NEXT complex reveals connections to splicing factors. Authors: Falk, S. / Finogenova, K. / Melko, M. / Benda, C. / Lykke-Andersen, S. / Jensen, T.H. / Conti, E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5lxy.cif.gz | 155.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5lxy.ent.gz | 118.4 KB | Display | PDB format |
PDBx/mmJSON format | 5lxy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5lxy_validation.pdf.gz | 546.8 KB | Display | wwPDB validaton report |
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Full document | 5lxy_full_validation.pdf.gz | 558.9 KB | Display | |
Data in XML | 5lxy_validation.xml.gz | 27.4 KB | Display | |
Data in CIF | 5lxy_validation.cif.gz | 38 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lx/5lxy ftp://data.pdbj.org/pub/pdb/validation_reports/lx/5lxy | HTTPS FTP |
-Related structure data
Related structure data | 5lxrSC 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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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 10032.661 Da / Num. of mol.: 7 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RBM7 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y580 #2: Protein/peptide | Mass: 5097.909 Da / Num. of mol.: 7 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ZCCHC8 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6NZY4 #3: Chemical | ChemComp-BR / #4: Water | ChemComp-HOH / | |
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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: 2.9 Å3/Da / Density % sol: 57.3 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.1 M Bis-Tris-Propane 0.2 M NaBr 0.1 M Sodium malonate 20% (w/v) PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 26, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.85→71.79 Å / Num. obs: 24933 / % possible obs: 99.8 % / Redundancy: 3.2 % / CC1/2: 0.995 / Rmerge(I) obs: 0.061 / Net I/σ(I): 8.1 |
Reflection shell | Resolution: 2.85→2.92 Å / CC1/2: 0.62 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5LXR Resolution: 2.85→71.79 Å / Cor.coef. Fo:Fc: 0.866 / Cor.coef. Fo:Fc free: 0.829 / Cross valid method: THROUGHOUT / σ(F): 0 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Displacement parameters | Biso max: 244.62 Å2 / Biso min: 32.73 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.85→71.79 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.85→2.924 Å /
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