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- PDB-2hyi: Structure of the human exon junction complex with a trapped DEAD-... -

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Basic information

Entry
Database: PDB / ID: 2hyi
TitleStructure of the human exon junction complex with a trapped DEAD-box helicase bound to RNA
Components
  • 5'-R(*UP*UP*UP*UP*UP*U)-3'
  • Probable ATP-dependent RNA helicase DDX48
  • Protein CASC3
  • Protein mago nashi homolog
  • RNA-binding protein 8A
Keywordshydrolase/RNA binding protein/RNA / exon junction / splicing / mRNA processing / translation / DEAD-box ATPase / nonsense mediated decay / hydrolase-RNA binding protein-RNA COMPLEX
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 / intracellular mRNA localization / regulation of translation at postsynapse, modulating synaptic transmission / negative regulation of excitatory postsynaptic potential / 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 / intracellular mRNA localization / regulation of translation at postsynapse, modulating synaptic transmission / negative regulation of excitatory postsynaptic potential / Z-decay: degradation of maternal mRNAs by zygotically expressed factors / regulation of mRNA processing / Deadenylation of mRNA / U2-type catalytic step 1 spliceosome / poly(A) binding / M-decay: degradation of maternal mRNAs by maternally stored factors / RNA stem-loop binding / mRNA 3'-end processing / 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) / ribonucleoprotein complex binding / mRNA export from nucleus / 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 / mRNA splicing, via spliceosome / rRNA processing / Regulation of expression of SLITs and ROBOs / cytoplasmic stress granule / regulation of translation / postsynapse / nuclear membrane / negative regulation of translation / RNA helicase activity / RNA helicase / nuclear speck / mRNA binding / dendrite / neuronal cell body / glutamatergic synapse / ubiquitin protein ligase binding / 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
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. / ATP-dependent RNA helicase DEAD-box, conserved site / RNA helicase, DEAD-box type, Q motif / DEAD-box RNA helicase Q motif profile. / RRM (RNA recognition motif) domain / DEAD/DEAH box helicase / DEAD/DEAH box helicase domain / 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 / Nucleotide-binding alpha-beta plait domain superfamily / P-loop containing nucleotide triphosphate hydrolases / Alpha-Beta Plaits / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / RNA / 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: 2.3 Å
AuthorsAndersen, C.B.F. / Le Hir, H. / Andersen, G.R.
CitationJournal: Science / Year: 2006
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
DepositionAug 6, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 15, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
F: 5'-R(*UP*UP*UP*UP*UP*U)-3'
L: 5'-R(*UP*UP*UP*UP*UP*U)-3'
A: Protein mago nashi homolog
B: RNA-binding protein 8A
C: Probable ATP-dependent RNA helicase DDX48
D: Protein CASC3
G: Protein mago nashi homolog
H: RNA-binding protein 8A
I: Probable ATP-dependent RNA helicase DDX48
J: Protein CASC3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)172,98314
Polymers171,92210
Non-polymers1,0614
Water11,890660
1
F: 5'-R(*UP*UP*UP*UP*UP*U)-3'
A: Protein mago nashi homolog
B: RNA-binding protein 8A
C: Probable ATP-dependent RNA helicase DDX48
D: Protein CASC3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,4917
Polymers85,9615
Non-polymers5312
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
L: 5'-R(*UP*UP*UP*UP*UP*U)-3'
G: Protein mago nashi homolog
H: RNA-binding protein 8A
I: Probable ATP-dependent RNA helicase DDX48
J: Protein CASC3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,4917
Polymers85,9615
Non-polymers5312
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)185.830, 88.260, 145.770
Angle α, β, γ (deg.)90.00, 110.77, 90.00
Int Tables number5
Space group name H-MC121

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Components

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RNA chain , 1 types, 2 molecules FL

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


Mass: 1792.037 Da / Num. of mol.: 2 / Fragment: mRNA mimick / Source method: obtained synthetically

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Protein , 4 types, 8 molecules AGBHCIDJ

#2: Protein Protein mago nashi homolog


Mass: 17189.625 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MAGOH / Plasmid: pET28A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 rosetta / 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: 10370.526 Da / Num. of mol.: 2 / Fragment: N-terminal deletion mutant
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RBM8A, RBM8 / Plasmid: pET28A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 rosetta / References: UniProt: Q9Y5S9
#4: Protein Probable ATP-dependent RNA helicase DDX48 / DEAD box protein 48 / Eukaryotic initiation factor 4A-like NUK-34 / Nuclear matrix protein 265 / ...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: 47173.230 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DDX48, EIF4A3, KIAA0111 / Plasmid: pET28A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 rosetta
References: UniProt: P38919, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides
#5: Protein Protein CASC3 / Cancer susceptibility candidate gene 3 protein / Metastatic lymph node protein 51 / MLN 51 protein ...Cancer susceptibility candidate gene 3 protein / Metastatic lymph node protein 51 / MLN 51 protein / Barentsz protein / Btz


Mass: 9435.402 Da / Num. of mol.: 2 / Fragment: Selor fragment
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CASC3, MLN51 / Plasmid: pET28A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 rosetta / References: UniProt: O15234

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Non-polymers , 3 types, 664 molecules

#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#7: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 660 / 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: 3.25 Å3/Da / Density % sol: 62.15 %
Crystal growTemperature: 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
IDNameCrystal-IDSol-ID
1PEG335011
2Tris11
3NaAcetate11
4H2O11
5PEG335012
6NaAcetate12
7H2O12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9464 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 2, 2006
RadiationMonochromator: Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9464 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 2.3→2.4 Å / Redundancy: 4.78 % / Mean I/σ(I) obs: 3.22 / Rsym value: 0.527 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHASERphasing
CNS1.1refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→20 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.231 1948 random
Rwork0.212 --
all0.213 97913 -
obs0.213 97913 -
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11075 234 64 660 12033

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