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- PDB-7znj: Structure of an ALYREF-exon junction complex hexamer -

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Basic information

Entry
Database: PDB / ID: 7znj
TitleStructure of an ALYREF-exon junction complex hexamer
Components
  • Eukaryotic initiation factor 4A-III, N-terminally processed
  • Maltose/maltodextrin-binding periplasmic protein,THO complex subunit 4
  • Protein mago nashi homolog
  • RNA
  • RNA-binding protein 8A
KeywordsGENE REGULATION / transcription-exort complex / TREX / splicing / exon junction complex / EJC / RNA export / RNA binding proteins
Function / homology
Function and homology information


exon-exon junction subcomplex mago-y14 / transcription export complex / negative regulation of selenocysteine incorporation / regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / cellular response to selenite ion / C5-methylcytidine-containing RNA reader activity / 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 ...exon-exon junction subcomplex mago-y14 / transcription export complex / negative regulation of selenocysteine incorporation / regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / cellular response to selenite ion / C5-methylcytidine-containing RNA reader activity / 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 / Deadenylation of mRNA / regulation of mRNA processing / selenocysteine insertion sequence binding / poly(A) binding / Transport of the SLBP independent Mature mRNA / M-decay: degradation of maternal mRNAs by maternally stored factors / Transport of the SLBP Dependant Mature mRNA / mRNA 3'-end processing / Transport of Mature mRNA Derived from an Intronless Transcript / U2-type catalytic step 1 spliceosome / embryonic cranial skeleton morphogenesis / Transport of Mature mRNA derived from an Intron-Containing Transcript / RNA export from nucleus / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / RNA Polymerase II Transcription Termination / exploration behavior / regulation of alternative mRNA splicing, via spliceosome / associative learning / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / mRNA export from nucleus / ribonucleoprotein complex binding / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / 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 processing / ISG15 antiviral mechanism / Regulation of expression of SLITs and ROBOs / mRNA splicing, via spliceosome / osteoblast differentiation / RNA stem-loop binding / rRNA processing / regulation of translation / outer membrane-bounded periplasmic space / postsynapse / RNA helicase activity / negative regulation of translation / RNA helicase / nuclear speck / mRNA binding / neuronal cell body / glutamatergic synapse / dendrite / nucleolus / ATP hydrolysis activity / RNA binding / extracellular exosome / nucleoplasm / ATP binding / membrane / nucleus / cytoplasm / cytosol
Similarity search - Function
Chromatin target of PRMT1 protein, C-terminal / C-terminal duplication domain of Friend of PRMT1 / C-terminal duplication domain of Friend of PRMT1 / 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 ...Chromatin target of PRMT1 protein, C-terminal / C-terminal duplication domain of Friend of PRMT1 / C-terminal duplication domain of Friend of PRMT1 / 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. / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / 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 nucleoside triphosphate hydrolase
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / RNA / Maltose/maltodextrin-binding periplasmic protein / Eukaryotic initiation factor 4A-III / Protein mago nashi homolog / THO complex subunit 4 / RNA-binding protein 8A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.4 Å
AuthorsPacheco-Fiallos, F.B. / Vorlaender, M.K. / Plaschka, C.
Funding supportEuropean Union, 2items
OrganizationGrant numberCountry
European Research Council (ERC)European Union
European Molecular Biology Organization (EMBO)623-2020European Union
CitationJournal: Nature / Year: 2023
Title: mRNA recognition and packaging by the human transcription-export complex.
Authors: Belén Pacheco-Fiallos / Matthias K Vorländer / Daria Riabov-Bassat / Laura Fin / Francis J O'Reilly / Farja I Ayala / Ulla Schellhaas / Juri Rappsilber / Clemens Plaschka /
Abstract: Newly made mRNAs are processed and packaged into mature ribonucleoprotein complexes (mRNPs) and are recognized by the essential transcription-export complex (TREX) for nuclear export. However, the ...Newly made mRNAs are processed and packaged into mature ribonucleoprotein complexes (mRNPs) and are recognized by the essential transcription-export complex (TREX) for nuclear export. However, the mechanisms of mRNP recognition and three-dimensional mRNP organization are poorly understood. Here we report cryo-electron microscopy and tomography structures of reconstituted and endogenous human mRNPs bound to the 2-MDa TREX complex. We show that mRNPs are recognized through multivalent interactions between the TREX subunit ALYREF and mRNP-bound exon junction complexes. Exon junction complexes can multimerize through ALYREF, which suggests a mechanism for mRNP organization. Endogenous mRNPs form compact globules that are coated by multiple TREX complexes. These results reveal how TREX may simultaneously recognize, compact and protect mRNAs to promote their packaging for nuclear export. The organization of mRNP globules provides a framework to understand how mRNP architecture facilitates mRNA biogenesis and export.
History
DepositionApr 21, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 12, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 19, 2023Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2May 3, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3May 17, 2023Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.4May 24, 2023Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Eukaryotic initiation factor 4A-III, N-terminally processed
B: Protein mago nashi homolog
C: RNA-binding protein 8A
D: Maltose/maltodextrin-binding periplasmic protein,THO complex subunit 4
E: RNA
a: Eukaryotic initiation factor 4A-III, N-terminally processed
b: Protein mago nashi homolog
c: RNA-binding protein 8A
d: Maltose/maltodextrin-binding periplasmic protein,THO complex subunit 4
e: RNA
F: Eukaryotic initiation factor 4A-III, N-terminally processed
G: Protein mago nashi homolog
H: RNA-binding protein 8A
I: Maltose/maltodextrin-binding periplasmic protein,THO complex subunit 4
J: RNA
f: Eukaryotic initiation factor 4A-III, N-terminally processed
g: Protein mago nashi homolog
h: RNA-binding protein 8A
i: Maltose/maltodextrin-binding periplasmic protein,THO complex subunit 4
j: RNA
K: Eukaryotic initiation factor 4A-III, N-terminally processed
L: Protein mago nashi homolog
M: RNA-binding protein 8A
N: Maltose/maltodextrin-binding periplasmic protein,THO complex subunit 4
O: RNA
k: Eukaryotic initiation factor 4A-III, N-terminally processed
l: Protein mago nashi homolog
m: RNA-binding protein 8A
n: Maltose/maltodextrin-binding periplasmic protein,THO complex subunit 4
o: RNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)787,80542
Polymers784,62230
Non-polymers3,18312
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area73650 Å2
ΔGint-365 kcal/mol
Surface area172650 Å2

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Components

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Protein , 4 types, 24 molecules AaFfKkBbGgLlCcHhMmDdIiNn

#1: Protein
Eukaryotic initiation factor 4A-III, N-terminally processed


Mass: 43819.367 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EIF4A3, DDX48, KIAA0111 / Production host: Escherichia coli (E. coli) / References: UniProt: P38919
#2: Protein
Protein mago nashi homolog


Mass: 17189.625 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MAGOH, MAGOHA / Production host: Escherichia coli (E. coli) / References: UniProt: P61326
#3: Protein
RNA-binding protein 8A / Binder of OVCA1-1 / BOV-1 / RNA-binding motif protein 8A / RNA-binding protein Y14 / Ribonucleoprotein RBM8A


Mass: 10370.525 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RBM8A, RBM8, HSPC114, MDS014 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y5S9
#4: Protein
Maltose/maltodextrin-binding periplasmic protein,THO complex subunit 4 / MMBP / Maltodextrin-binding protein / Maltose-binding protein / MBP / Tho4 / Ally of AML-1 and LEF- ...MMBP / Maltodextrin-binding protein / Maltose-binding protein / MBP / Tho4 / Ally of AML-1 and LEF-1 / Aly/REF export factor / Transcriptional coactivator Aly/REF / bZIP-enhancing factor BEF


Mass: 57598.855 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: malE, Z5632, ECs5017, ALYREF, ALY, BEF, THOC4 / Production host: Escherichia coli (E. coli) / References: UniProt: P0AEY0, UniProt: Q86V81

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RNA chain , 1 types, 6 molecules EeJjOo

#5: RNA chain
RNA


Mass: 1792.037 Da / Num. of mol.: 6 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Non-polymers , 2 types, 12 molecules

#6: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#7: Chemical
ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM

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Details

Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Hexameric complex between the TREX subunit ALYREF and the exon junction complex
Type: COMPLEX
Details: Assembled with truncated MBP-tagged ALYREF (residues 55-183)
Entity ID: #1-#5 / Source: RECOMBINANT
Molecular weightValue: 0.65 MDa / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.9
SpecimenConc.: 1.7 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 600 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

Software
NameVersionClassification
phenix.real_space_refine1.20.1_4487refinement
PHENIX1.20.1_4487refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: D3 (2x3 fold dihedral)
3D reconstructionResolution: 2.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1564602 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 16.44 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.003135814
ELECTRON MICROSCOPYf_angle_d0.713748522
ELECTRON MICROSCOPYf_chiral_restr0.04575382
ELECTRON MICROSCOPYf_plane_restr0.00526150
ELECTRON MICROSCOPYf_dihedral_angle_d7.31055148

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