[English] 日本語
Yorodumi
- PDB-9hfl: Cryo-EM structure of the human snRNA export complex comprising CB... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9hfl
TitleCryo-EM structure of the human snRNA export complex comprising CBC-PHAX-CRM1-RanGTP and capped-RNA
Components
  • (Nuclear cap-binding protein subunit ...) x 2
  • Exportin-1
  • GTP-binding nuclear protein Ran
  • Phosphorylated adapter RNA export protein
  • RNA (5'-D(*(ADM))-R(P*A)-3')
KeywordsRNA BINDING PROTEIN / snRNA export / Exportin / Cap-binding / Co-transcriptional regulation
Function / homology
Function and homology information


mRNA cap binding complex binding / positive regulation of RNA binding / snRNA export from nucleus / nuclear cap binding complex / histone mRNA metabolic process / RNA cap binding complex / mRNA metabolic process / cellular response to triglyceride / RNA stabilization / cellular response to salt ...mRNA cap binding complex binding / positive regulation of RNA binding / snRNA export from nucleus / nuclear cap binding complex / histone mRNA metabolic process / RNA cap binding complex / mRNA metabolic process / cellular response to triglyceride / RNA stabilization / cellular response to salt / positive regulation of RNA export from nucleus / HuR (ELAVL1) binds and stabilizes mRNA / positive regulation of mRNA 3'-end processing / cap-dependent translational initiation / annulate lamellae / Processing of Intronless Pre-mRNAs / regulation of proteasomal ubiquitin-dependent protein catabolic process / RNA cap binding / snRNA binding / pre-miRNA export from nucleus / RNA nuclear export complex / snRNA import into nucleus / regulation of mRNA processing / primary miRNA processing / miRNA-mediated post-transcriptional gene silencing / manchette / nuclear export signal receptor activity / regulation of centrosome duplication / cellular response to mineralocorticoid stimulus / SLBP independent Processing of Histone Pre-mRNAs / SLBP Dependent Processing of Replication-Dependent Histone Pre-mRNAs / regulatory ncRNA-mediated post-transcriptional gene silencing / Regulation of cholesterol biosynthesis by SREBP (SREBF) / RNA 7-methylguanosine cap binding / Transport of the SLBP independent Mature mRNA / importin-alpha family protein binding / Transport of the SLBP Dependant Mature mRNA / alternative mRNA splicing, via spliceosome / regulation of protein export from nucleus / mRNA 3'-end processing / Transport of Mature mRNA Derived from an Intronless Transcript / positive regulation of mRNA splicing, via spliceosome / Rev-mediated nuclear export of HIV RNA / Nuclear import of Rev protein / mRNA 3'-end processing / protein localization to nucleolus / mRNA cis splicing, via spliceosome / NEP/NS2 Interacts with the Cellular Export Machinery / Transport of Mature mRNA derived from an Intron-Containing Transcript / tRNA processing in the nucleus / GTP metabolic process / RNA catabolic process / Postmitotic nuclear pore complex (NPC) reformation / RNA Polymerase II Transcription Termination / Abortive elongation of HIV-1 transcript in the absence of Tat / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / regulation of translational initiation / FGFR2 alternative splicing / nucleocytoplasmic transport / MicroRNA (miRNA) biogenesis / Signaling by FGFR2 IIIa TM / DNA metabolic process / Formation of the Early Elongation Complex / Formation of the HIV-1 Early Elongation Complex / mRNA Capping / Maturation of hRSV A proteins / spliceosomal complex assembly / mRNA Splicing - Minor Pathway / dynein intermediate chain binding / Processing of Capped Intron-Containing Pre-mRNA / mitotic sister chromatid segregation / RNA polymerase II transcribes snRNA genes / 7-methylguanosine mRNA capping / viral process / spermatid development / ribosomal large subunit export from nucleus / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / protein localization to nucleus / positive regulation of protein binding / sperm flagellum / toxic substance binding / nuclear pore / mRNA export from nucleus / Formation of HIV-1 elongation complex containing HIV-1 Tat / Cajal body / Formation of HIV elongation complex in the absence of HIV Tat / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / ribosomal subunit export from nucleus / Cyclin A/B1/B2 associated events during G2/M transition / Formation of RNA Pol II elongation complex / ribosomal small subunit export from nucleus / NPAS4 regulates expression of target genes / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / RNA Polymerase II Pre-transcription Events / centriole / Transcriptional and post-translational regulation of MITF-M expression and activity / Mitotic Prometaphase / mRNA Splicing - Major Pathway / EML4 and NUDC in mitotic spindle formation
Similarity search - Function
Phosphorylated adapter RNA export protein / Phosphorylated adapter RNA export protein, RNA-binding domain / Phosphorylated adapter RNA export protein, RNA-binding domain superfamily / Phosphorylated adapter RNA export protein, RNA-binding domain / MIF4G-like, type 1 / MIF4G-like, type 2 / Nuclear cap-binding protein subunit 1 / MIF4G like / MIF4G like / Nuclear cap-binding protein subunit 2 ...Phosphorylated adapter RNA export protein / Phosphorylated adapter RNA export protein, RNA-binding domain / Phosphorylated adapter RNA export protein, RNA-binding domain superfamily / Phosphorylated adapter RNA export protein, RNA-binding domain / MIF4G-like, type 1 / MIF4G-like, type 2 / Nuclear cap-binding protein subunit 1 / MIF4G like / MIF4G like / Nuclear cap-binding protein subunit 2 / NCBP2, RNA recognition motif / Exportin-1, repeat 3 / Chromosome region maintenance repeat / Exportin-1, repeat 2 / Chromosome region maintenance or exportin repeat / CRM1 / Exportin repeat 2 / CRM1 / Exportin repeat 3 / CRM1 C terminal / Exportin-1, C-terminal / CRM1 C terminal / Exportin-1/5 / Exportin-1/Importin-beta-like / Exportin 1-like protein / MIF4G domain / Middle domain of eukaryotic initiation factor 4G (eIF4G) / MIF4G-like, type 3 / Ran GTPase / Small GTPase Ran-type domain profile. / Importin-beta N-terminal domain / Importin-beta N-terminal domain / Importin-beta N-terminal domain profile. / Importin-beta, N-terminal domain / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Rab subfamily of small GTPases / Armadillo-like helical / Small GTP-binding protein domain / Armadillo-type fold / Nucleotide-binding alpha-beta plait domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Chem-GTA / GUANOSINE-5'-TRIPHOSPHATE / RNA / RNA (> 10) / Exportin-1 / Nuclear cap-binding protein subunit 2 / GTP-binding nuclear protein Ran / Nuclear cap-binding protein subunit 1 / Phosphorylated adapter RNA export protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.62 Å
AuthorsDubiez, E. / Cusack, S. / Kadlec, J.
Funding support France, 1items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR) France
CitationJournal: Nat Struct Mol Biol / Year: 2025
Title: Structural basis for the synergistic assembly of the snRNA export complex.
Authors: Etienne Dubiez / William Garland / Maja Finderup Brask / Elisabetta Boeri Erba / Torben Heick Jensen / Jan Kadlec / Stephen Cusack /
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. ...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.
History
DepositionNov 18, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 16, 2025Provider: repository / Type: Initial release
Revision 1.1Aug 27, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _em_admin.last_update

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Exportin-1
B: GTP-binding nuclear protein Ran
C: Nuclear cap-binding protein subunit 1
D: Nuclear cap-binding protein subunit 2
N: Phosphorylated adapter RNA export protein
P: Phosphorylated adapter RNA export protein
R: RNA (5'-D(*(ADM))-R(P*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)352,66010
Polymers351,3257
Non-polymers1,3353
Water57632
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

-
Components

-
Protein , 3 types, 4 molecules ABNP

#1: Protein Exportin-1 / Exp1 / Chromosome region maintenance 1 protein homolog


Mass: 123518.359 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Human Exportin 1 CRM1 / Source: (gene. exp.) Homo sapiens (human) / Gene: XPO1, CRM1 / Production host: Escherichia coli (E. coli) / References: UniProt: O14980
#2: Protein GTP-binding nuclear protein Ran / Androgen receptor-associated protein 24 / GTPase Ran / Ras-like protein TC4 / Ras-related nuclear protein


Mass: 24441.135 Da / Num. of mol.: 1 / Mutation: Q69L
Source method: isolated from a genetically manipulated source
Details: RanGTP Q69L catalytic mutant / Source: (gene. exp.) Homo sapiens (human) / Gene: RAN, ARA24, OK/SW-cl.81 / Production host: Escherichia coli (E. coli)
References: UniProt: P62826, Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement
#5: Protein Phosphorylated adapter RNA export protein / RNA U small nuclear RNA export adapter protein


Mass: 44468.574 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PHAX, RNUXA / Production host: Escherichia coli (E. coli) / References: UniProt: Q9H814

-
Nuclear cap-binding protein subunit ... , 2 types, 2 molecules CD

#3: Protein Nuclear cap-binding protein subunit 1 / 80 kDa nuclear cap-binding protein / NCBP 80 kDa subunit


Mass: 91960.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Human NCBP1 CBP80 / Source: (gene. exp.) Homo sapiens (human) / Gene: NCBP1, CBP80, NCBP / Production host: Baculovirus expression vector pFastBac1-HM / References: UniProt: Q09161
#4: Protein Nuclear cap-binding protein subunit 2 / 20 kDa nuclear cap-binding protein / Cell proliferation-inducing gene 55 protein / NCBP 20 kDa ...20 kDa nuclear cap-binding protein / Cell proliferation-inducing gene 55 protein / NCBP 20 kDa subunit / CBP20 / NCBP-interacting protein 1 / NIP1


Mass: 18028.131 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Human NCBP2 CBP20 / Source: (gene. exp.) Homo sapiens (human) / Gene: NCBP2, CBP20, PIG55 / Production host: Escherichia coli (E. coli) / References: UniProt: P52298

-
RNA chain , 1 types, 1 molecules R

#6: RNA chain RNA (5'-D(*(ADM))-R(P*A)-3')


Mass: 4439.715 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

-
Non-polymers , 4 types, 35 molecules

#7: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: GTP, energy-carrying molecule*YM
#8: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#9: Chemical ChemComp-GTA / P1-7-METHYLGUANOSINE-P3-ADENOSINE-5',5'-TRIPHOSPHATE / 7-METHYL-GPPPA


Mass: 787.441 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H30N10O17P3 / Feature type: SUBJECT OF INVESTIGATION
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 32 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: Human snRNA export complex comprising CBC-PHAX-CRM1-RanGTP and capped-RNA
Type: COMPLEX / Entity ID: #1-#6 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2200 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 40.5 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

-
Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: NONE
3D reconstructionResolution: 2.62 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 202738 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00218191
ELECTRON MICROSCOPYf_angle_d0.42124647
ELECTRON MICROSCOPYf_dihedral_angle_d7.5572465
ELECTRON MICROSCOPYf_chiral_restr0.0352755
ELECTRON MICROSCOPYf_plane_restr0.0033129

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more