9HFL | pdb_00009hfl

Cryo-EM structure of the human snRNA export complex comprising CBC-PHAX-CRM1-RanGTP and capped-RNA


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.62 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural basis for the synergistic assembly of the snRNA export complex.

Dubiez, E.Garland, W.Finderup Brask, M.Boeri Erba, E.Heick Jensen, T.Kadlec, J.Cusack, S.

(2025) Nat Struct Mol Biol 32: 1555-1566

  • DOI: https://doi.org/10.1038/s41594-025-01595-5
  • Primary Citation of Related Structures:  
    9HFL

  • PubMed Abstract: 

    The nuclear cap-binding complex (CBC) and its partner Arsenite-Resistance Protein 2 (ARS2) regulate the fate of RNA polymerase II transcripts via mutually exclusive interactions with RNA effectors. One such effector is PHAX, which mediates the nuclear export of U-rich small nuclear RNAs (snRNAs). Here we present the cryo-electron microscopy structure of the human snRNA export complex comprising phosphorylated PHAX, CBC, CRM1-RanGTP and capped RNA. The central region of PHAX bridges CBC to the export factor CRM1-RanGTP, while also reinforcing cap dinucleotide binding. Additionally, PHAX interacts with a distant region of CRM1, facilitating contacts of the essential phosphorylated region of PHAX with the prominent basic surface of RanGTP. CBC engagement within the snRNA export complex is incompatible with its binding to other RNA effectors such as ALYREF or NCBP3. We demonstrate that snRNA export complex formation requires synergistic binding of all its components, which in turn displaces ARS2 from CBC and commits the complex for export.


  • Organizational Affiliation
    • Université Grenoble Alpes, CNRS, CEA, IBS, Grenoble, France.

Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Exportin-11,071Homo sapiensMutation(s): 0 
Gene Names: XPO1CRM1
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Find proteins for O14980 (Homo sapiens)
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Go to UniProtKB:  O14980
PHAROS:  O14980
GTEx:  ENSG00000082898 
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UniProt GroupO14980
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
GTP-binding nuclear protein Ran216Homo sapiensMutation(s): 1 
Gene Names: RANARA24OK/SW-cl.81
EC: 3.6.5
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Find proteins for P62826 (Homo sapiens)
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PHAROS:  P62826
GTEx:  ENSG00000132341 
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UniProt GroupP62826
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Nuclear cap-binding protein subunit 1790Homo sapiensMutation(s): 0 
Gene Names: NCBP1CBP80NCBP
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Find proteins for Q09161 (Homo sapiens)
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PHAROS:  Q09161
GTEx:  ENSG00000136937 
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UniProt GroupQ09161
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Nuclear cap-binding protein subunit 2156Homo sapiensMutation(s): 0 
Gene Names: NCBP2CBP20PIG55
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Find proteins for P52298 (Homo sapiens)
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PHAROS:  P52298
GTEx:  ENSG00000114503 
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UniProt GroupP52298
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Phosphorylated adapter RNA export proteinE [auth N],
F [auth P]
394Homo sapiensMutation(s): 0 
Gene Names: PHAXRNUXA
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Find proteins for Q9H814 (Homo sapiens)
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Go to UniProtKB:  Q9H814
PHAROS:  Q9H814
GTEx:  ENSG00000164902 
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UniProt GroupQ9H814
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  • Reference Sequence

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Entity ID: 6
MoleculeChains LengthOrganismImage
RNA (5'-D(*(ADM))-R(P*A)-3')G [auth R]14Homo sapiens
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.62 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Agence Nationale de la Recherche (ANR)France--

Revision History  (Full details and data files)

  • Version 1.0: 2025-07-16
    Type: Initial release
  • Version 1.1: 2025-08-27
    Changes: Data collection, Database references