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- PDB-2j0s: The crystal structure of the Exon Junction Complex at 2.2 A resolution -

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Basic information

Entry
Database: PDB / ID: 2j0s
TitleThe crystal structure of the Exon Junction Complex at 2.2 A resolution
Components
  • 5'-R(*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP *UP*UP*UP*UP*U)-3'
  • ATP-DEPENDENT RNA HELICASE DDX48
  • PROTEIN CASC3
  • PROTEIN MAGO NASHI HOMOLOG
  • RNA-BINDING PROTEIN 8A
KeywordsHYDROLASE / 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
Function and homology information


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 / selenocysteine insertion sequence binding / exon-exon junction complex / regulation of translation at postsynapse, modulating synaptic transmission / negative regulation of excitatory postsynaptic potential / intracellular mRNA localization / Z-decay: degradation of maternal mRNAs by zygotically expressed factors ...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 / selenocysteine insertion sequence binding / exon-exon junction complex / regulation of translation at postsynapse, modulating synaptic transmission / negative regulation of excitatory postsynaptic potential / intracellular mRNA localization / Z-decay: degradation of maternal mRNAs by zygotically expressed factors / regulation of mRNA processing / Deadenylation of mRNA / M-decay: degradation of maternal mRNAs by maternally stored factors / poly(A) binding / embryonic cranial skeleton morphogenesis / mRNA 3'-end processing / U2-type catalytic step 1 spliceosome / Transport of Mature mRNA derived from an Intron-Containing Transcript / RNA Polymerase II Transcription Termination / exploration behavior / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / regulation of alternative mRNA splicing, via spliceosome / associative learning / mRNA export from nucleus / ribonucleoprotein complex binding / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / 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 / mRNA splicing, via spliceosome / ISG15 antiviral mechanism / Regulation of expression of SLITs and ROBOs / cytoplasmic stress granule / RNA stem-loop binding / rRNA processing / regulation of translation / nuclear membrane / postsynapse / 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 / cytosol / cytoplasm
Similarity search - Function
Mago nashi protein / Mago nashi / CASC3/Barentsz eIF4AIII binding / CASC3/Barentsz eIF4AIII binding / Btz domain / Mago nashi protein / RNA-binding motif protein 8 / RBM8, RNA recognition motif / Mago nashi superfamily / Mago nashi protein ...Mago nashi protein / Mago nashi / CASC3/Barentsz eIF4AIII binding / CASC3/Barentsz eIF4AIII binding / Btz domain / Mago nashi protein / RNA-binding motif protein 8 / RBM8, RNA recognition motif / Mago nashi superfamily / Mago nashi protein / DEAD-box subfamily ATP-dependent helicases signature. / RNA helicase, DEAD-box type, Q motif / ATP-dependent RNA helicase DEAD-box, conserved site / DEAD-box RNA helicase Q motif profile. / RRM (RNA recognition motif) domain / DEAD/DEAH box helicase domain / DEAD/DEAH box helicase / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / Helicase conserved C-terminal domain / RNA-binding domain superfamily / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / P-loop containing nucleotide triphosphate hydrolases / Nucleotide-binding alpha-beta plait domain superfamily / Alpha-Beta Plaits / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / RNA / RNA (> 10) / Protein CASC3 / Eukaryotic initiation factor 4A-III / Protein mago nashi homolog / RNA-binding protein 8A
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.21 Å
AuthorsBono, F. / Ebert, J. / Lorentzen, E. / Conti, E.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2006
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
DepositionAug 4, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 6, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ATP-DEPENDENT RNA HELICASE DDX48
C: PROTEIN MAGO NASHI HOMOLOG
D: RNA-BINDING PROTEIN 8A
E: 5'-R(*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP *UP*UP*UP*UP*U)-3'
T: PROTEIN CASC3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,9977
Polymers96,4675
Non-polymers5312
Water6,197344
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)169.440, 169.440, 71.040
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number172
Space group name H-MP64

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Components

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Protein , 4 types, 4 molecules ACDT

#1: Protein ATP-DEPENDENT RNA HELICASE DDX48 / EIF4AIII RNA-HELICASE / DEAD BOX PROTEIN 48 / EUKARYOTIC INITIATION FACTOR 4A-LIKE NUK-34 / NUCLEAR ...EIF4AIII RNA-HELICASE / DEAD BOX PROTEIN 48 / EUKARYOTIC INITIATION FACTOR 4A-LIKE NUK-34 / NUCLEAR MATRIX PROTEIN 265 / HNMP 265 / EUKARYOTIC TRANSLATION INITIATION FACTOR 4A ISOFORM 3


Mass: 46799.766 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P38919
#2: Protein PROTEIN MAGO NASHI HOMOLOG


Mass: 17189.625 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P61326
#3: Protein RNA-BINDING PROTEIN 8A / RNA-BINDING MOTIF PROTEIN 8A / RIBONUCLEOPROTEIN RBM8A / RNA-BINDING PROTEIN Y14 / BINDER OF OVCA1-1 / BOV-1


Mass: 10216.358 Da / Num. of mol.: 1 / Fragment: RESIDUES 66-154
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9Y5S9
#5: Protein PROTEIN CASC3 / BARENTSZ / CANCER SUSCEPTIBILITY CANDIDATE GENE 3 PROTEIN / METASTATIC LYMPH NODE PROTEIN 51 / BTZ ...BARENTSZ / CANCER SUSCEPTIBILITY CANDIDATE GENE 3 PROTEIN / METASTATIC LYMPH NODE PROTEIN 51 / BTZ / MLN 51 PROTEIN / BARENTSZ PROTEIN


Mass: 17713.482 Da / Num. of mol.: 1 / Fragment: RESIDUES 137-286
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O15234

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RNA chain , 1 types, 1 molecules E

#4: RNA chain 5'-R(*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP *UP*UP*UP*UP*U)-3'


Mass: 4547.529 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Non-polymers , 3 types, 346 molecules

#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#7: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 344 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.05 Å3/Da / Density % sol: 59.7 %
Crystal growDetails: 8% PEG 6000, 100 MM MGCL2, 100 MM MES PH 6.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.98
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 17, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 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

Software
NameVersionClassification
REFMAC5.2.0005refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1FUU, 1FUK, 1P27

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
RfactorNum. reflection% reflectionSelection details
Rfree0.216 2932 5 %RANDOM
Rwork0.185 ---
obs0.187 55698 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 43.99 Å2
Baniso -1Baniso -2Baniso -3
1--0.33 Å2-0.16 Å20 Å2
2---0.33 Å20 Å2
3---0.49 Å2
Refinement stepCycle: LAST / Resolution: 2.21→43.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5359 121 32 344 5856
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0225691
X-RAY DIFFRACTIONr_bond_other_d0.0010.025108
X-RAY DIFFRACTIONr_angle_refined_deg1.4931.9917738
X-RAY DIFFRACTIONr_angle_other_deg0.843311882
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4565683
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.3123.978279
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.90215985
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7941544
X-RAY DIFFRACTIONr_chiral_restr0.0850.2858
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.026235
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021155
X-RAY DIFFRACTIONr_nbd_refined0.1950.21117
X-RAY DIFFRACTIONr_nbd_other0.1910.25408
X-RAY DIFFRACTIONr_nbtor_refined0.1780.22688
X-RAY DIFFRACTIONr_nbtor_other0.0880.23217
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2250.2332
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0390.21
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1110.216
X-RAY DIFFRACTIONr_symmetry_vdw_other0.270.253
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1480.29
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8061.53634
X-RAY DIFFRACTIONr_mcbond_other0.1511.51373
X-RAY DIFFRACTIONr_mcangle_it1.14825413
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.74632585
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.7244.52314
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.21→2.26 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.363 210 -
Rwork0.301 3982 -
obs--100 %

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