7ZNJ | pdb_00007znj

Structure of an ALYREF-exon junction complex hexamer

PDB DOI: https://doi.org/10.2210/pdb7ZNJ/pdb
NAKB: 7ZNJ
EM Map EMD-14803: EMDB EMDataResource

Classification: GENE REGULATION
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2022-04-21 Released: 2023-04-12
Deposition Author(s): Pacheco-Fiallos, F.B., Vorlaender, M.K., Plaschka, C.
Funding Organization(s): European Research Council (ERC), European Molecular Biology Organization (EMBO)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.40 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.6 of the entry. See complete history.

Literature

mRNA recognition and packaging by the human transcription-export complex.

Pacheco-Fiallos, B., Vorlander, M.K., Riabov-Bassat, D., Fin, L., O'Reilly, F.J., Ayala, F.I., Schellhaas, U., Rappsilber, J., Plaschka, C.

(2023) Nature 616: 828-835

PubMed: 37020021 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s41586-023-05904-0
Primary Citation Related Structures:
7ZNJ, 7ZNK, 7ZNL

PubMed 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 ^1,2. However, the mechanisms of mRNP recognition and three-dimensional mRNP organization are poorly understood ³. 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.

Organizational Affiliation

Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria.

Macromolecule Content

Total Structure Weight: 787.81 kDa
Atom Count: 35,088
Modeled Residue Count: 4,278
Deposited Residue Count: 6,912
Unique protein chains: 4
Unique nucleic acid chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Eukaryotic initiation factor 4A-III, N-terminally processed	A F [auth a] K [auth F] P [auth f] U [auth K] A, F [auth a], K [auth F], P [auth f], U [auth K], Z [auth k]	382	Homo sapiens	Mutation(s): 0 Gene Names: EIF4A3, DDX48, KIAA0111 EC: 3.6.4.13
UniProt & NIH Common Fund Data Resources
Find proteins for P38919 (Homo sapiens) Explore P38919 Go to UniProtKB: P38919
PHAROS: P38919 GTEx: ENSG00000141543
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P38919
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein mago nashi homolog	AA [auth l] B G [auth b] L [auth G] Q [auth g] AA [auth l], B, G [auth b], L [auth G], Q [auth g], V [auth L]	146	Homo sapiens	Mutation(s): 0 Gene Names: MAGOH, MAGOHA
UniProt & NIH Common Fund Data Resources
Find proteins for P61326 (Homo sapiens) Explore P61326 Go to UniProtKB: P61326
PHAROS: P61326 GTEx: ENSG00000162385
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P61326
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
RNA-binding protein 8A	BA [auth m] C H [auth c] M [auth H] R [auth h] BA [auth m], C, H [auth c], M [auth H], R [auth h], W [auth M]	91	Homo sapiens	Mutation(s): 0 Gene Names: RBM8A, RBM8, HSPC114, MDS014
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y5S9 (Homo sapiens) Explore Q9Y5S9 Go to UniProtKB: Q9Y5S9
PHAROS: Q9Y5S9 GTEx: ENSG00000265241
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9Y5S9
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Reference Sequence

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| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Maltose/maltodextrin-binding periplasmic protein,THO complex subunit 4	CA [auth n] D I [auth d] N [auth I] S [auth i] CA [auth n], D, I [auth d], N [auth I], S [auth i], X [auth N]	527	Homo sapiens	Mutation(s): 0 Gene Names: malE, Z5632, ECs5017, ALYREF, ALY, BEF, THOC4
UniProt & NIH Common Fund Data Resources
Find proteins for P0AEY0 (Escherichia coli O157:H7) Explore P0AEY0 Go to UniProtKB: P0AEY0
Find proteins for Q86V81 (Homo sapiens) Explore Q86V81 Go to UniProtKB: Q86V81
PHAROS: Q86V81
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Groups	Q86V81 P0AEY0
Sequence Annotations Expand
Reference Sequence

Find similar nucleic acids by: Sequence

Molecule	Chains	Length	Organism
Entity ID: 5
RNA	DA [auth o] E J [auth e] O [auth J] T [auth j] DA [auth o], E, J [auth e], O [auth J], T [auth j], Y [auth O]	6	Homo sapiens
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ANP Query on ANP Download:Ideal Coordinates CCD File SDF format, chain HA [auth a] SDF format, chain PA [auth k] SDF format, chain NA [auth K] SDF format, chain LA [auth f] SDF format, chain JA [auth F] SDF format, chain FA [auth A] MOL2 format, chain HA [auth a] MOL2 format, chain PA [auth k] MOL2 format, chain NA [auth K] MOL2 format, chain LA [auth f] MOL2 format, chain JA [auth F] MOL2 format, chain FA [auth A] mmCIF format, chain HA [auth a] mmCIF format, chain PA [auth k] mmCIF format, chain NA [auth K] mmCIF format, chain LA [auth f] mmCIF format, chain JA [auth F] mmCIF format, chain FA [auth A]	FA [auth A] HA [auth a] JA [auth F] LA [auth f] NA [auth K] FA [auth A], HA [auth a], JA [auth F], LA [auth f], NA [auth K], PA [auth k]	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER C₁₀ H₁₇ N₆ O₁₂ P₃ PVKSNHVPLWYQGJ-KQYNXXCUSA-N		Interactions Focus chain FA [auth A] Focus chain HA [auth a] Focus chain JA [auth F] Focus chain LA [auth f] Focus chain NA [auth K] Focus chain PA [auth k] Interactions & Density Focus chain FA [auth A] Focus chain HA [auth a] Focus chain JA [auth F] Focus chain LA [auth f] Focus chain NA [auth K] Focus chain PA [auth k]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain OA [auth k] SDF format, chain MA [auth K] SDF format, chain KA [auth f] SDF format, chain IA [auth F] SDF format, chain GA [auth a] SDF format, chain EA [auth A] MOL2 format, chain OA [auth k] MOL2 format, chain MA [auth K] MOL2 format, chain KA [auth f] MOL2 format, chain IA [auth F] MOL2 format, chain GA [auth a] MOL2 format, chain EA [auth A] mmCIF format, chain OA [auth k] mmCIF format, chain MA [auth K] mmCIF format, chain KA [auth f] mmCIF format, chain IA [auth F] mmCIF format, chain GA [auth a] mmCIF format, chain EA [auth A]	EA [auth A] GA [auth a] IA [auth F] KA [auth f] MA [auth K] EA [auth A], GA [auth a], IA [auth F], KA [auth f], MA [auth K], OA [auth k]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain EA [auth A] Focus chain GA [auth a] Focus chain IA [auth F] Focus chain KA [auth f] Focus chain MA [auth K] Focus chain OA [auth k] Interactions & Density Focus chain EA [auth A] Focus chain GA [auth a] Focus chain IA [auth F] Focus chain KA [auth f] Focus chain MA [auth K] Focus chain OA [auth k]