9D45 | pdb_00009d45

Cryo-EM structure of yeast Exportin Msn5 bound to cargo Pho4 and RanGTP

  • Classification: TRANSPORT PROTEIN
  • Organism(s): Saccharomyces cerevisiae
  • Expression System: Escherichia coli
  • Mutation(s): Yes 

  • Deposited: 2024-08-12 Released: 2025-03-19 
  • Deposition Author(s): Fung, H.Y.J., Chook, Y.M.
  • Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), Welch Foundation, Other private, Cancer Prevention and Research Institute of Texas (CPRIT)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Models: in silico, experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 9D45

This is version 1.1 of the entry. See complete history

Literature

Phosphate-dependent nuclear export via a non-classical NES class recognized by exportin Msn5.

Fung, H.Y.J.Mittal, S.R.Niesman, A.B.Jiou, J.Shakya, B.Yoshizawa, T.Cansizoglu, A.E.Rout, M.P.Chook, Y.M.

(2025) Nat Commun 16: 2580-2580

  • DOI: https://doi.org/10.1038/s41467-025-57752-3
  • Primary Citation Related Structures: 
    9D43, 9D45, 9DXM, 9DZ6

  • PubMed Abstract: 

    Gene expression in response to environmental stimuli is dependent on nuclear localization of key signaling components, which can be tightly regulated by phosphorylation. This is exemplified by the phosphate-sensing transcription factor Pho4, which requires phosphorylation for nuclear export by the yeast exportin Msn5. Here, we present a high resolution cryogenic-electron microscopy structure showing the phosphorylated 35-residue nuclear export signal of Pho4, which binds the concave surface of Msn5 through two Pho4 phospho-serines that align with two Msn5 basic patches. These findings characterize a mechanism of phosphate-specific recognition mediated by a non-classical signal distinct from that for Exportin-1. Furthermore, the discovery that unliganded Msn5 is autoinhibited explains the positive cooperativity of Pho4/Ran-binding and proposes a mechanism for Pho4's release in the cytoplasm. These findings advance our understanding of the diversity of signals that drive nuclear export and how cargo phosphorylation is crucial in regulating nuclear transport and controlling cellular signaling pathways.


  • Organizational Affiliation
    • Department of Pharmacology, UT Southwestern Medical Center, Dallas, TX, 75039, US.

Macromolecule Content 

  • Total Structure Weight: 187.4 kDa 
  • Atom Count: 11,123 
  • Modeled Residue Count: 1,354 
  • Deposited Residue Count: 1,618 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Protein MSN51,230Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: MSN5YDR335WD9651.5
UniProt
Find proteins for P52918 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P52918 
Go to UniProtKB:  P52918
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP52918
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
GTP-binding nuclear protein GSP1/CNR1186Saccharomyces cerevisiaeMutation(s): 1 
Gene Names: GSP1CNR1CST17YLR293CL8003.19
UniProt
Find proteins for P32835 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P32835 
Go to UniProtKB:  P32835
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP32835
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Phosphate system positive regulatory protein PHO4202Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: PHO4YFR034C
UniProt
Find proteins for P07270 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P07270 
Go to UniProtKB:  P07270
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP07270
Sequence Annotations
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Reference Sequence

Small Molecules

Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
SEP
Query on SEP
C
L-PEPTIDE LINKINGC3 H8 N O6 PSER

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC3
MODEL REFINEMENTPHENIX1.20.1_4487:
MODEL REFINEMENTCoot0.9
MODEL REFINEMENTISOLDE
MODEL REFINEMENTUCSF ChimeraX

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR35GM141461
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM069909
Welch FoundationUnited StatesI-1532
Other privateUTSW Gilman Special Opportunities Award
Cancer Prevention and Research Institute of Texas (CPRIT)United StatesRP220582

Revision History  (Full details and data files)

  • Version 1.0: 2025-03-19
    Type: Initial release
  • Version 1.1: 2025-04-02
    Changes: Data collection, Database references