+Open data
-Basic information
Entry | Database: PDB / ID: 3zhe | ||||||
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Title | Structure of the C. elegans SMG5-SMG7 complex | ||||||
Components |
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Keywords | MRNA-BINDING PROTEIN / NMD / PHOSPHO-PEPTIDE BINDING DOMAINS | ||||||
Function / homology | Function and homology information : / embryonic genitalia morphogenesis / regulatory ncRNA-mediated post-transcriptional gene silencing => GO:0035194 / DEAD/H-box RNA helicase binding / protein phosphatase regulator activity / regulation of telomere maintenance via telomerase / telomerase holoenzyme complex / telomerase RNA binding / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / telomeric DNA binding ...: / embryonic genitalia morphogenesis / regulatory ncRNA-mediated post-transcriptional gene silencing => GO:0035194 / DEAD/H-box RNA helicase binding / protein phosphatase regulator activity / regulation of telomere maintenance via telomerase / telomerase holoenzyme complex / telomerase RNA binding / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / telomeric DNA binding / telomere maintenance via telomerase / RNA nuclease activity / protein phosphatase 2A binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | CAENORHABDITIS ELEGANS (invertebrata) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 3 Å | ||||||
Authors | Jonas, S. / Weichenrieder, O. / Izaurralde, E. | ||||||
Citation | Journal: Genes Dev. / Year: 2013 Title: An Unusual Arrangement of Two 14-3-3-Like Domains in the Smg5-Smg7 Heterodimer is Required for Efficient Nonsense-Mediated Mrna Decay. Authors: Jonas, S. / Weichenrieder, O. / Izaurralde, E. | ||||||
History |
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Remark 650 | HELIX DETERMINATION METHOD: AUTHOR PROVIDED. | ||||||
Remark 700 | SHEET DETERMINATION METHOD: AUTHOR PROVIDED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3zhe.cif.gz | 617.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3zhe.ent.gz | 519 KB | Display | PDB format |
PDBx/mmJSON format | 3zhe.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3zhe_validation.pdf.gz | 451 KB | Display | wwPDB validaton report |
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Full document | 3zhe_full_validation.pdf.gz | 465.5 KB | Display | |
Data in XML | 3zhe_validation.xml.gz | 51.2 KB | Display | |
Data in CIF | 3zhe_validation.cif.gz | 69.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zh/3zhe ftp://data.pdbj.org/pub/pdb/validation_reports/zh/3zhe | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 49004.523 Da / Num. of mol.: 2 / Fragment: 14-3-3 AND ALPHA-HELICAL DOMAINS, RESIDUES 1-420 Source method: isolated from a genetically manipulated source Source: (gene. exp.) CAENORHABDITIS ELEGANS (invertebrata) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): STAR / References: UniProt: G5ECF1 #2: Protein | Mass: 45868.605 Da / Num. of mol.: 2 / Fragment: 14-3-3 AND ALPHA-HELICAL DOMAINS, RESIDUES 1-395 Source method: isolated from a genetically manipulated source Source: (gene. exp.) CAENORHABDITIS ELEGANS (invertebrata) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): STAR / References: UniProt: G5EF47 |
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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: 3.82 Å3/Da / Density % sol: 68 % / Description: NONE |
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Crystal grow | pH: 5 Details: 0.1 M SODIUM CITRATE (PH 5.0), 8% (W/V) PEG 8000, 10% GLYCEROL, 500 MM NACL, 60 MM (NH4)2SO4, 4 MM DTT AND 2 MM TCEP |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9793 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 18, 2011 / Details: MIRRORS |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 3→50 Å / Num. obs: 55840 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 6.8 % / Biso Wilson estimate: 94.31 Å2 / Rsym value: 0.08 / Net I/σ(I): 14.5 |
Reflection shell | Resolution: 3→3.2 Å / Redundancy: 6.9 % / Mean I/σ(I) obs: 2.37 / Rsym value: 0.73 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MIRAS Starting model: NONE Resolution: 3→49.337 Å / SU ML: 0.38 / σ(F): 1.99 / Phase error: 32.14 / Stereochemistry target values: ML
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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: 105 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3→49.337 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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