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- PDB-3ex7: The crystal structure of EJC in its transition state -

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Basic information

Entry
Database: PDB / ID: 3ex7
TitleThe crystal structure of EJC in its transition state
Components
  • Eukaryotic initiation factor 4A-III
  • Protein CASC3
  • Protein mago nashi homolog
  • RNA (5'-R(*UP*UP*UP*UP*UP*U)-3')
  • RNA-binding protein 8A
Keywordshydrolase/RNA binding protein/RNA / PROTEIN-RNA COMPLEX / mRNA processing / mRNA splicing / mRNA transport / Nonsense-mediated mRNA decay / Nucleus / RNA-binding / Spliceosome / Transport / Alternative splicing / Cytoplasm / Phosphoprotein / Acetylation / ATP-binding / Helicase / Hydrolase / Nucleotide-binding / rRNA processing / Coiled coil / 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
ADENOSINE-5'-DIPHOSPHATE / ALUMINUM FLUORIDE / 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: 2.301 Å
AuthorsAndersen, G.R. / Nielsen, K.H.
CitationJournal: Rna / Year: 2009
Title: Mechanism of ATP turnover inhibition in the EJC
Authors: Nielsen, K.H. / Chamieh, H. / Andersen, C.B. / Fredslund, F. / Hamborg, K. / Le Hir, H. / Andersen, G.R.
History
DepositionOct 16, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 9, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / software / 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 / _software.name / _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
A: Protein mago nashi homolog
B: RNA-binding protein 8A
C: Eukaryotic initiation factor 4A-III
D: Protein CASC3
E: Protein mago nashi homolog
G: RNA-binding protein 8A
H: Eukaryotic initiation factor 4A-III
I: Protein CASC3
F: RNA (5'-R(*UP*UP*UP*UP*UP*U)-3')
J: RNA (5'-R(*UP*UP*UP*UP*UP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)197,20516
Polymers196,13410
Non-polymers1,0716
Water6,846380
1
A: Protein mago nashi homolog
B: RNA-binding protein 8A
C: Eukaryotic initiation factor 4A-III
D: Protein CASC3
F: RNA (5'-R(*UP*UP*UP*UP*UP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,6038
Polymers98,0675
Non-polymers5353
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13540 Å2
ΔGint-60 kcal/mol
Surface area28010 Å2
MethodPISA
2
E: Protein mago nashi homolog
G: RNA-binding protein 8A
H: Eukaryotic initiation factor 4A-III
I: Protein CASC3
J: RNA (5'-R(*UP*UP*UP*UP*UP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,6038
Polymers98,0675
Non-polymers5353
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13450 Å2
ΔGint-57 kcal/mol
Surface area28070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)182.040, 100.750, 145.880
Angle α, β, γ (deg.)90.000, 112.080, 90.000
Int Tables number5
Space group name H-MC121

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Components

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Protein , 4 types, 8 molecules AEBGCHDI

#1: 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: pET30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P61326
#2: Protein RNA-binding protein 8A / RNA-binding motif protein 8A / Ribonucleoprotein RBM8A / RNA-binding protein Y14 / Binder of OVCA1-1 / BOV-1


Mass: 14637.176 Da / Num. of mol.: 2 / Fragment: UNP residues 51-174
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RBM8A / Plasmid: pET30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q9Y5S9
#3: Protein Eukaryotic initiation factor 4A-III / Eukaryotic translation initiation factor 4A isoform 3 / ATP-dependent RNA helicase eIF4A-3 / ATP- ...Eukaryotic translation initiation factor 4A isoform 3 / ATP-dependent RNA helicase eIF4A-3 / ATP-dependent RNA helicase DDX48 / DEAD box protein 48 / Eukaryotic initiation factor 4A-like NUK-34 / Nuclear matrix protein 265 / hNMP 265


Mass: 47173.230 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EIF4A3 / Plasmid: pET30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: P38919, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides
#4: Protein Protein CASC3 / Cancer susceptibility candidate gene 3 protein / Metastatic lymph node protein 51 / Protein MLN 51 ...Cancer susceptibility candidate gene 3 protein / Metastatic lymph node protein 51 / Protein MLN 51 / Protein barentsz / Btz


Mass: 17275.068 Da / Num. of mol.: 2 / Fragment: UNP residues 138-283
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CASC3 / Plasmid: pET30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: O15234

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RNA chain , 1 types, 2 molecules FJ

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


Mass: 1792.037 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: poly Uracil (Sigma)

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Non-polymers , 4 types, 386 molecules

#6: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#7: Chemical ChemComp-AF3 / ALUMINUM FLUORIDE / Aluminium fluoride


Mass: 83.977 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: AlF3
#8: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 380 / 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: 3.16 Å3/Da / Density % sol: 61.08 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.8
Details: 7% PEG 3350, 50mM Tris HCl pH 8.8, 200mM NaAcetate, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 335011
2Tris11
3NaAcetate11
4H2O11
5PEG 335012
6Tris12
7NaAcetate12
8H2O12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.91745 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 19, 2006
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91745 Å / Relative weight: 1
ReflectionResolution: 2.3→40 Å / Num. all: 108638 / Num. obs: 107635 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.6 % / Biso Wilson estimate: 34.55 Å2 / Rsym value: 0.108 / Net I/σ(I): 11.35
Reflection shellResolution: 2.3→2.4 Å / Redundancy: 4.6 % / Mean I/σ(I) obs: 2.58 / Num. unique all: 12443 / Rsym value: 0.666 / % possible all: 96

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Processing

Software
NameVersionClassificationNB
PHENIXrefinement
PDB_EXTRACT3.006data extraction
ADSCQuantumdata collection
XDSdata reduction
XSCALEdata scaling
BEASTphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2HYI

2hyi


Resolution: 2.301→39.065 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.804 / SU ML: 0.34 / Cross valid method: Througout / σ(F): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.251 2144 1.99 %RANDOM
Rwork0.206 ---
all0.207 108360 --
obs0.207 107634 99.33 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 57.702 Å2 / ksol: 0.354 e/Å3
Displacement parametersBiso max: 275.05 Å2 / Biso mean: 67.293 Å2 / Biso min: 12.96 Å2
Baniso -1Baniso -2Baniso -3
1--7.574 Å20 Å21.778 Å2
2--22.507 Å20 Å2
3----14.934 Å2
Refinement stepCycle: LAST / Resolution: 2.301→39.065 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11178 234 64 380 11856
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00911733
X-RAY DIFFRACTIONf_angle_d1.21515896
X-RAY DIFFRACTIONf_chiral_restr0.0771736
X-RAY DIFFRACTIONf_plane_restr0.0052018
X-RAY DIFFRACTIONf_dihedral_angle_d18.5364429
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.301-2.3550.3521560.2996705686195
2.355-2.4140.3221510.286992714399
2.414-2.4790.321300.2587046717699
2.479-2.5520.2931390.2456982712199
2.552-2.6340.2891480.24270107158100
2.634-2.7280.2651440.22570507194100
2.728-2.8370.2631410.21969967137100
2.837-2.9660.2791540.21770667220100
2.966-3.1230.2821380.22270227160100
3.123-3.3180.2581520.21170557207100
3.318-3.5740.2361290.19470957224100
3.574-3.9340.2341420.17470747216100
3.934-4.5020.1781200.15471327252100
4.502-5.6690.1891590.16771137272100
5.669-39.0710.2611410.2087152729399
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.1131-0.0457-0.05020.1212-0.00060.0790.01730.082-0.0093-0.0264-0.0889-0.01560.07820.0798-00.22540.01560.00510.1188-0.03370.2238-12.51747.50192.1101
20.03930.00450.01350.04210.04220.0151-0.0770.2820.0180.08560.02780.05310.0862-0.232700.2441-0.1606-0.00340.1655-0.08890.229-31.0671-6.32643.5805
30.25250.1206-0.3170.11310.00550.36140.0126-0.03860.0115-0.0126-0.0115-0.05630.0047-0.1647-00.15750.0024-0.0160.1018-0.0150.1697-28.670117.626429.9669
40.009-0.02980.04820.08260.02930.0376-0.0205-0.14710.1741-0.00390.1031-0.1065-0.0324-0.013500.27270.02380.00180.3472-0.03190.2629-23.712125.723742.9424
50.02210.0091-0.0094-0.0111-0.01130.03930.14360.0269-0.22110.03740.0759-0.18650.1040.043400.634-0.74090.11621.6537-0.12740.113312.467132.264770.3123
60.00230.0044-0.00240.0042-0.00340.00160.0597-0.02360.01470.0626-0.0404-0.04590.00380.004600.33560.00350.07040.3681-0.06030.3374-23.347931.731136.6648
70.0026-0.00340.0134-0.00540.00790.02020.05210.03050.02770.0574-0.0701-0.030.02470.039501.0239-0.66510.04331.6831-0.22970.492430.458147.447769.6306
80.07880.11210.1113-0.32930.4523-0.03550.1657-0.23980.0408-0.2015-0.4313-0.12420.1334-0.124200.1987-0.2287-0.04280.5643-0.2010.237318.874237.525237.6029
90.0270.1120.0835-0.01290.14240.04540.0646-0.21840.0887-0.3714-0.2597-0.11660.33570.1012-00.0874-0.3014-0.10940.4999-0.26050.233612.922629.479226.1066
100.0060.00760.0044-0.00310.00190.0008-0.0543-0.0334-0.02060.0165-0.00990.0838-0.0038-0.0146-00.432-0.11410.04450.8201-0.24950.5387.538332.378626.9142
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B
3X-RAY DIFFRACTION3chain C
4X-RAY DIFFRACTION4chain D
5X-RAY DIFFRACTION5chain E
6X-RAY DIFFRACTION6chain F
7X-RAY DIFFRACTION7chain G
8X-RAY DIFFRACTION8chain H
9X-RAY DIFFRACTION9chain I
10X-RAY DIFFRACTION10chain J

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