+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-3279 | |||||||||
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Title | Electron microscopy of human RNA helicase DHX34 | |||||||||
Map data | Reconstruction of DHX34 | |||||||||
Sample |
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Keywords | NMD / SMG1 / SMG8 / SMG9 / PIKK / DHX34 / RNA degradation / RNA helicase | |||||||||
Function / homology | Function and homology information RNA helicase activity => GO:0003724 / RNA binding => GO:0003723 / negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / positive regulation of phosphorylation / nuclear-transcribed mRNA catabolic process / RNA processing / RNA helicase activity / RNA helicase / protein-containing complex binding ...RNA helicase activity => GO:0003724 / RNA binding => GO:0003723 / negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / positive regulation of phosphorylation / nuclear-transcribed mRNA catabolic process / RNA processing / RNA helicase activity / RNA helicase / protein-containing complex binding / ATP hydrolysis activity / RNA binding / ATP binding / membrane / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / negative staining / Resolution: 24.23 Å | |||||||||
Authors | Melero R / Hug N / Lopez-Perrote A / Yamashita A / Caceres J / Llorca O | |||||||||
Citation | Journal: Nat Commun / Year: 2016 Title: The RNA helicase DHX34 functions as a scaffold for SMG1-mediated UPF1 phosphorylation. Authors: Roberto Melero / Nele Hug / Andrés López-Perrote / Akio Yamashita / Javier F Cáceres / Oscar Llorca / Abstract: Nonsense-mediated decay (NMD) is a messenger RNA quality-control pathway triggered by SMG1-mediated phosphorylation of the NMD factor UPF1. In recent times, the RNA helicase DHX34 was found to ...Nonsense-mediated decay (NMD) is a messenger RNA quality-control pathway triggered by SMG1-mediated phosphorylation of the NMD factor UPF1. In recent times, the RNA helicase DHX34 was found to promote mRNP remodelling, leading to activation of NMD. Here we demonstrate the mechanism by which DHX34 functions in concert with SMG1. DHX34 comprises two distinct structural units, a core that binds UPF1 and a protruding carboxy-terminal domain (CTD) that binds the SMG1 kinase, as shown using truncated forms of DHX34 and electron microscopy of the SMG1-DHX34 complex. Truncation of the DHX34 CTD does not affect binding to UPF1; however, it compromises DHX34 binding to SMG1 to affect UPF1 phosphorylation and hence abrogate NMD. Altogether, these data suggest the existence of a complex comprising SMG1, UPF1 and DHX34, with DHX34 functioning as a scaffold for UPF1 and SMG1. This complex promotes UPF1 phosphorylation leading to functional NMD. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_3279.map.gz | 1.3 MB | EMDB map data format | |
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Header (meta data) | emd-3279-v30.xml emd-3279.xml | 10.1 KB 10.1 KB | Display Display | EMDB header |
Images | EMD-3279_DHX34.png | 76.5 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-3279 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-3279 | HTTPS FTP |
-Validation report
Summary document | emd_3279_validation.pdf.gz | 219.4 KB | Display | EMDB validaton report |
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Full document | emd_3279_full_validation.pdf.gz | 218.5 KB | Display | |
Data in XML | emd_3279_validation.xml.gz | 4.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3279 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3279 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_3279.map.gz / Format: CCP4 / Size: 1.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Reconstruction of DHX34 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 5.68 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : DHX34
Entire | Name: DHX34 |
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Components |
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-Supramolecule #1000: DHX34
Supramolecule | Name: DHX34 / type: sample / ID: 1000 / Oligomeric state: Monomeric DHX34 / Number unique components: 1 |
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Molecular weight | Theoretical: 128 KDa |
-Macromolecule #1: DHX34
Macromolecule | Name: DHX34 / type: protein_or_peptide / ID: 1 / Name.synonym: DHX34 / Number of copies: 1 / Oligomeric state: Monomer / Recombinant expression: Yes |
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Source (natural) | Organism: Homo sapiens (human) / synonym: Human |
Molecular weight | Theoretical: 128 KDa |
Recombinant expression | Organism: Homo sapiens (human) / Recombinant cell: 293T cells |
Sequence | UniProtKB: Probable ATP-dependent RNA helicase DHX34 GO: cytoplasm, membrane, ATP binding, RNA helicase activity => GO:0003724, RNA binding => GO:0003723, negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay, ...GO: cytoplasm, membrane, ATP binding, RNA helicase activity => GO:0003724, RNA binding => GO:0003723, negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay, nuclear-transcribed mRNA catabolic process, nuclear-transcribed mRNA catabolic process, nonsense-mediated decay, RNA processing InterPro: DEAD-box helicase, OB fold, Helicase-associated domain, Helicase superfamily 1/2, ATP-binding domain, Helicase, C-terminal, P-loop containing nucleoside triphosphate hydrolase, INTERPRO: IPR015880 |
-Experimental details
-Structure determination
Method | negative staining |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.01 mg/mL |
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Buffer | pH: 7.5 Details: 10 mM HEPES-KOH, 150 mM NaCl, 20% (v/v) glycerol, 10 mM MgCl2 |
Staining | Type: NEGATIVE / Details: 1% uranyl formate |
Grid | Details: 400 mesh grid with thin carbon support, glow discharged |
Vitrification | Cryogen name: NONE / Instrument: OTHER |
-Electron microscopy
Microscope | JEOL 1230 |
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Alignment procedure | Legacy - Astigmatism: Objective lens astigmatism was corrected using a TVIPS F416 CMOS and the EM-MENU software (TVIPS) |
Date | Feb 17, 2012 |
Image recording | Category: CCD / Film or detector model: TVIPS TEMCAM-F416 (4k x 4k) / Digitization - Sampling interval: 15.6 µm / Average electron dose: 15 e/Å2 Details: Using a TVIPS F416 CMOS and the EM-TOOLS software (TVIPS) Bits/pixel: 16 |
Electron beam | Acceleration voltage: 100 kV / Electron source: TUNGSTEN HAIRPIN |
Electron optics | Calibrated magnification: 54926 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.9 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 40000 |
Sample stage | Specimen holder model: JEOL |
-Image processing
CTF correction | Details: Each micrograph using BSOFT |
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Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 24.23 Å / Resolution method: OTHER / Software - Name: EMAN, EMAN2, Xmipp / Number images used: 12316 |