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- PDB-2j0s: The crystal structure of the Exon Junction Complex at 2.2 A resolution -
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Open data
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Basic information
Entry | Database: PDB / ID: 2j0s | ||||||
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Title | The crystal structure of the Exon Junction Complex at 2.2 A resolution | ||||||
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![]() | HYDROLASE / MRNA PROCESSING / PHOSPHORYLATION / RRNA PROCESSING / MRNA SPLICING / MRNA TRANSPORT / NUCLEAR PROTEIN / ALTERNATIVE SPLICING / NONSENSE-MEDIATED MRNA DECAY / DEAD-BOX HELICASE / NUCLEOTIDE-BINDING / ATP-BINDING / DNA-BINDING / RNA-BINDING / COILED COIL / EJC / HELICASE / TRANSPORT / ACETYLATION | ||||||
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 / intracellular mRNA localization / negative regulation of excitatory postsynaptic potential / Z-decay: degradation of maternal mRNAs by zygotically expressed factors / regulation of mRNA processing ...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 / intracellular mRNA localization / negative regulation of excitatory postsynaptic potential / Z-decay: degradation of maternal mRNAs by zygotically expressed factors / regulation of mRNA processing / selenocysteine insertion sequence binding / Deadenylation of mRNA / 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 / RNA Polymerase II Transcription Termination / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / 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 / 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 / RNA stem-loop binding / 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 / identical protein binding / membrane / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Bono, F. / Ebert, J. / Lorentzen, E. / Conti, E. | ||||||
![]() | ![]() Title: The Crystal Structure of the Exon Junction Complex Reveals How It Mantains a Stable Grip on Mrna Authors: Bono, F. / Ebert, J. / Lorentzen, E. / Conti, E. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 164 KB | Display | ![]() |
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PDB format | ![]() | 124.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 812.1 KB | Display | ![]() |
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Full document | ![]() | 820.7 KB | Display | |
Data in XML | ![]() | 16.4 KB | Display | |
Data in CIF | ![]() | 26.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2j0qC ![]() 2j0uC ![]() 1fukS ![]() 1fuuS ![]() 1p27S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein , 4 types, 4 molecules ACDT
#1: Protein | Mass: 46799.766 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Protein | Mass: 17189.625 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
#3: Protein | Mass: 10216.358 Da / Num. of mol.: 1 / Fragment: RESIDUES 66-154 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
#5: Protein | Mass: 17713.482 Da / Num. of mol.: 1 / Fragment: RESIDUES 137-286 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
-RNA chain , 1 types, 1 molecules E
#4: RNA chain | Mass: 4547.529 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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-Non-polymers , 3 types, 346 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/ANP.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ANP.gif)
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#6: Chemical | ChemComp-MG / |
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#7: Chemical | ChemComp-ANP / |
#8: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.05 Å3/Da / Density % sol: 59.7 % |
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Crystal grow | Details: 8% PEG 6000, 100 MM MGCL2, 100 MM MES PH 6.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jun 17, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. obs: 58631 / % possible obs: 98.9 % / Observed criterion σ(I): 2.5 / Redundancy: 3.6 % / Rmerge(I) obs: 0.08 / Rsym value: 0.08 / Net I/σ(I): 11.1 |
Reflection shell | Resolution: 2.2→2.3 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 2.5 / Rsym value: 0.54 / % possible all: 95.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1FUU, 1FUK, 1P27 Resolution: 2.21→43.73 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.944 / SU B: 9.503 / SU ML: 0.133 / Cross valid method: THROUGHOUT / ESU R: 0.178 / ESU R Free: 0.158 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 43.99 Å2
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Refinement step | Cycle: LAST / Resolution: 2.21→43.73 Å
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Refine LS restraints |
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