[English] 日本語
![](img/lk-miru.gif)
- PDB-2hyi: Structure of the human exon junction complex with a trapped DEAD-... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 2hyi | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of the human exon junction complex with a trapped DEAD-box helicase bound to RNA | ||||||
![]() |
| ||||||
![]() | hydrolase/RNA binding protein/RNA / exon junction / splicing / mRNA processing / translation / DEAD-box ATPase / nonsense mediated decay / hydrolase-RNA binding protein-RNA COMPLEX | ||||||
Function / homology | ![]() exon-exon junction subcomplex mago-y14 / negative regulation of selenocysteine incorporation / regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / cellular response to selenite ion / exon-exon junction complex / regulation of translation at postsynapse, modulating synaptic transmission / Z-decay: degradation of maternal mRNAs by zygotically expressed factors / negative regulation of excitatory postsynaptic potential / intracellular mRNA localization / Deadenylation of mRNA ...exon-exon junction subcomplex mago-y14 / negative regulation of selenocysteine incorporation / regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / cellular response to selenite ion / exon-exon junction complex / regulation of translation at postsynapse, modulating synaptic transmission / Z-decay: degradation of maternal mRNAs by zygotically expressed factors / negative regulation of excitatory postsynaptic potential / intracellular mRNA localization / Deadenylation of mRNA / regulation of mRNA processing / selenocysteine insertion sequence binding / poly(A) binding / M-decay: degradation of maternal mRNAs by maternally stored factors / mRNA 3'-end processing / U2-type catalytic step 1 spliceosome / embryonic cranial skeleton morphogenesis / Transport of Mature mRNA derived from an Intron-Containing Transcript / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / RNA Polymerase II Transcription Termination / exploration behavior / regulation of alternative mRNA splicing, via spliceosome / associative learning / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / mRNA export from nucleus / ribonucleoprotein complex binding / cellular response to brain-derived neurotrophic factor stimulus / RNA stem-loop binding / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / RNA splicing / positive regulation of translation / response to organic cyclic compound / ISG15 antiviral mechanism / Regulation of expression of SLITs and ROBOs / mRNA splicing, via spliceosome / cytoplasmic stress granule / rRNA processing / regulation of translation / postsynapse / nuclear membrane / RNA helicase activity / negative regulation of translation / RNA helicase / nuclear speck / mRNA binding / neuronal cell body / glutamatergic synapse / ubiquitin protein ligase binding / dendrite / nucleolus / perinuclear region of cytoplasm / enzyme binding / ATP hydrolysis activity / RNA binding / nucleoplasm / ATP binding / membrane / identical protein binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Andersen, C.B.F. / Le Hir, H. / Andersen, G.R. | ||||||
![]() | ![]() Title: Structure of the exon junction core complex with a trapped DEAD-box ATPase bound to RNA. Authors: Andersen, C.B.F. / Ballut, L. / Johansen, J.S. / Chamieh, H. / Nielsen, K.H. / Oliveira, C.L. / Pedersen, J.S. / Seraphin, B. / Le Hir, H. / Andersen, G.R. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 307.8 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 245 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 60.3 KB | Display | |
Data in CIF | ![]() | 85.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
Unit cell |
|
-
Components
-RNA chain , 1 types, 2 molecules FL
#1: RNA chain | Mass: 1792.037 Da / Num. of mol.: 2 / Fragment: mRNA mimick / Source method: obtained synthetically |
---|
-Protein , 4 types, 8 molecules AGBHCIDJ
#2: Protein | Mass: 17189.625 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #3: Protein | Mass: 10370.526 Da / Num. of mol.: 2 / Fragment: N-terminal deletion mutant Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #4: Protein | Mass: 47173.230 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P38919, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides #5: Protein | Mass: 9435.402 Da / Num. of mol.: 2 / Fragment: Selor fragment Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
---|
-Non-polymers , 3 types, 664 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/ANP.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ANP.gif)
![](data/chem/img/HOH.gif)
#6: Chemical | #7: Chemical | #8: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3.25 Å3/Da / Density % sol: 62.15 % | ||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 297 K / Method: vapor diffusion / pH: 8.8 Details: 7% PEG3350 50 mM Tris 200 mM NaAcetate, pH 8.8, VAPOR DIFFUSION, temperature 297K | ||||||||||||||||||||||||||||||||
Components of the solutions |
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 2, 2006 |
Radiation | Monochromator: Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9464 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→20 Å / Num. all: 98109 / Num. obs: 97913 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.75 % / Rsym value: 0.064 / Net I/σ(I): 14.24 |
Reflection shell | Resolution: 2.3→2.4 Å / Redundancy: 4.78 % / Mean I/σ(I) obs: 3.22 / Rsym value: 0.527 / % possible all: 99.9 |
-
Processing
Software |
| ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]()
| ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→20 Å
|