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- EMDB-14803: Structure of an ALYREF-exon junction complex hexamer -

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Basic information

Entry
Database: EMDB / ID: EMD-14803
TitleStructure of an ALYREF-exon junction complex hexamer
Map dataLocally sharpened ALYREF(55-183)-EJC-RNA map
Sample
  • Complex: Hexameric complex between the TREX subunit ALYREF and the exon junction complex
    • Protein or peptide: Eukaryotic initiation factor 4A-III, N-terminally processed
    • Protein or peptide: Protein mago nashi homolog
    • Protein or peptide: RNA-binding protein 8A
    • Protein or peptide: Maltose/maltodextrin-binding periplasmic protein,THO complex subunit 4
    • RNA: RNA
  • Ligand: MAGNESIUM ION
  • Ligand: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
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 / transcription export complex / cellular response to selenite ion / C5-methylcytidine-containing RNA reader activity / exon-exon junction complex / selenocysteine insertion sequence binding / regulation of translation at postsynapse, modulating synaptic transmission / negative regulation of excitatory postsynaptic potential ...exon-exon junction subcomplex mago-y14 / negative regulation of selenocysteine incorporation / regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / transcription export complex / cellular response to selenite ion / C5-methylcytidine-containing RNA reader activity / exon-exon junction complex / selenocysteine insertion sequence binding / 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 / Transport of the SLBP independent Mature mRNA / Transport of the SLBP Dependant Mature mRNA / poly(A) binding / M-decay: degradation of maternal mRNAs by maternally stored factors / mRNA 3'-end processing / Transport of Mature mRNA Derived from an Intronless Transcript / U2-type catalytic step 1 spliceosome / embryonic cranial skeleton morphogenesis / RNA export from nucleus / 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 / maltose binding / maltose transport / maltodextrin transmembrane transport / associative learning / carbohydrate transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / mRNA export from nucleus / ribonucleoprotein complex binding / RNA stem-loop 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 / mRNA processing / Regulation of expression of SLITs and ROBOs / mRNA splicing, via spliceosome / osteoblast differentiation / 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 / cytosol / cytoplasm
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
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.4 Å
AuthorsPacheco-Fiallos FB / Vorlaender MK / Plaschka C
Funding supportEuropean Union, 2 items
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, 2022-
Header (metadata) releaseApr 12, 2023-
Map releaseApr 12, 2023-
UpdateMay 24, 2023-
Current statusMay 24, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_14803.png

Downloads & links

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Map

FileDownload / File: emd_14803.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationLocally sharpened ALYREF(55-183)-EJC-RNA map
Voxel sizeX=Y=Z: 0.945 Å
Density
Contour LevelBy AUTHOR: 0.5
Minimum - Maximum-2.6168554 - 4.556373
Average (Standard dev.)0.0028653864 (±0.078886375)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 302.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_14803_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Globally sharpened ALYREF(55-183)-EJC-RNA map

Fileemd_14803_additional_1.map
AnnotationGlobally sharpened ALYREF(55-183)-EJC-RNA map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Unsharpened ALYREF(55-183)-EJC-RNA map

Fileemd_14803_additional_2.map
AnnotationUnsharpened ALYREF(55-183)-EJC-RNA map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: ALYREF(55-183)-EJC-RNA half map

Fileemd_14803_half_map_1.map
AnnotationALYREF(55-183)-EJC-RNA half map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: ALYREF(55-183)-EJC-RNA half map

Fileemd_14803_half_map_2.map
AnnotationALYREF(55-183)-EJC-RNA half map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Hexameric complex between the TREX subunit ALYREF and the exon ju...

EntireName: Hexameric complex between the TREX subunit ALYREF and the exon junction complex
Components
  • Complex: Hexameric complex between the TREX subunit ALYREF and the exon junction complex
    • Protein or peptide: Eukaryotic initiation factor 4A-III, N-terminally processed
    • Protein or peptide: Protein mago nashi homolog
    • Protein or peptide: RNA-binding protein 8A
    • Protein or peptide: Maltose/maltodextrin-binding periplasmic protein,THO complex subunit 4
    • RNA: RNA
  • Ligand: MAGNESIUM ION
  • Ligand: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER

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Supramolecule #1: Hexameric complex between the TREX subunit ALYREF and the exon ju...

SupramoleculeName: Hexameric complex between the TREX subunit ALYREF and the exon junction complex
type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: #1-#5
Details: Assembled with truncated MBP-tagged ALYREF (residues 55-183)
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 650 KDa

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

MacromoleculeName: Eukaryotic initiation factor 4A-III, N-terminally processed
type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 43.819367 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MTKVEFETSE EVDVTPTFDT MGLREDLLRG IYAYGFEKPS AIQQRAIKQI IKGRDVIAQS QSGTGKTATF SISVLQCLDI QVRETQALI LAPTRELAVQ IQKGLLALGD YMNVQCHACI GGTNVGEDIR KLDYGQHVVA GTPGRVFDMI RRRSLRTRAI K MLVLDEAD ...String:
MTKVEFETSE EVDVTPTFDT MGLREDLLRG IYAYGFEKPS AIQQRAIKQI IKGRDVIAQS QSGTGKTATF SISVLQCLDI QVRETQALI LAPTRELAVQ IQKGLLALGD YMNVQCHACI GGTNVGEDIR KLDYGQHVVA GTPGRVFDMI RRRSLRTRAI K MLVLDEAD EMLNKGFKEQ IYDVYRYLPP ATQVVLISAT LPHEILEMTN KFMTDPIRIL VKRDELTLEG IKQFFVAVER EE WKFDTLC DLYDTLTITQ AVIFCNTKRK VDWLTEKMRE ANFTVSSMHG DMPQKERESI MKEFRSGASR VLISTDVWAR GLD VPQVSL IINYDLPNNR ELYIHRIGRS GRYGRKGVAI NFVKNDDIRI LRDIEQYYST QIDEMP

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Macromolecule #2: Protein mago nashi homolog

MacromoleculeName: Protein mago nashi homolog / type: protein_or_peptide / ID: 2 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 17.189625 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MESDFYLRYY VGHKGKFGHE FLEFEFRPDG KLRYANNSNY KNDVMIRKEA YVHKSVMEEL KRIIDDSEIT KEDDALWPPP DRVGRQELE IVIGDEHISF TTSKIGSLID VNQSKDPEGL RVFYYLVQDL KCLVFSLIGL HFKIKPI

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Macromolecule #3: RNA-binding protein 8A

MacromoleculeName: RNA-binding protein 8A / type: protein_or_peptide / ID: 3 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 10.370525 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
GPQRSVEGWI LFVTGVHEEA TEEDIHDKFA EYGEIKNIHL NLDRRTGYLK GYTLVEYETY KEAQAAMEGL NGQDLMGQPI SVDWCFVRG PP

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Macromolecule #4: Maltose/maltodextrin-binding periplasmic protein,THO complex subunit 4

MacromoleculeName: Maltose/maltodextrin-binding periplasmic protein,THO complex subunit 4
type: protein_or_peptide / ID: 4 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 57.598855 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MQLSHHHHHH HHHHSSGMKI EEGKLVIWIN GDKGYNGLAE VGKKFEKDTG IKVTVEHPDK LEEKFPQVAA TGDGPDIIFW AHDRFGGYA QSGLLAEITP DKAFQDKLYP FTWDAVRYNG KLIAYPIAVE ALSLIYNKDL LPNPPKTWEE IPALDKELKA K GKSALMFN ...String:
MQLSHHHHHH HHHHSSGMKI EEGKLVIWIN GDKGYNGLAE VGKKFEKDTG IKVTVEHPDK LEEKFPQVAA TGDGPDIIFW AHDRFGGYA QSGLLAEITP DKAFQDKLYP FTWDAVRYNG KLIAYPIAVE ALSLIYNKDL LPNPPKTWEE IPALDKELKA K GKSALMFN LQEPYFTWPL IAADGGYAFK YENGKYDIKD VGVDNAGAKA GLTFLVDLIK NKHMNADTDY SIAEAAFNKG ET AMTINGP WAWSNIDTSK VNYGVTVLPT FKGQPSKPFV GVLSAGINAA SPNKELAKEF LENYLLTDEG LEAVNKDKPL GAV ALKSYE EELAKDPRIA ATMENAQKGE IMPNIPQMSA FWYAVRTAVI NAASGRQTVD EALKDAQTSS GLEVLFQGPG SSGI RNRPA IARGAAGGGG RNRPAPYSRP KQLPDKWQHD LFDSGFGGGA GVETGGKLLV SNLDFGVSDA DIQELFAEFG TLKKA AVHY DRSGRSLGTA DVHFERKADA LKAMKQYNGV PLDGRPMNIQ LVT

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Macromolecule #5: RNA

MacromoleculeName: RNA / type: rna / ID: 5 / Number of copies: 6
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 1.792037 KDa
SequenceString:
UUUUUU

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Macromolecule #6: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 6 / Number of copies: 6 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #7: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER

MacromoleculeName: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / type: ligand / ID: 7 / Number of copies: 6 / Formula: ANP
Molecular weightTheoretical: 506.196 Da
Chemical component information

ChemComp-ANP:
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / AMP-PNP, energy-carrying molecule analogue*YM

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration1.7 mg/mL
BufferpH: 7.9
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.6 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 40.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionApplied symmetry - Point group: D3 (2x3 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 2.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 1564602
FSC plot (resolution estimation)

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