6VCD | pdb_00006vcd

Cryo-EM structure of IRP2-FBXL5-SKP1 complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 6VCD

This is version 1.1 of the entry. See complete history

Literature

FBXL5 Regulates IRP2 Stability in Iron Homeostasis via an Oxygen-Responsive [2Fe2S] Cluster.

Wang, H.Shi, H.Rajan, M.Canarie, E.R.Hong, S.Simoneschi, D.Pagano, M.Bush, M.F.Stoll, S.Leibold, E.A.Zheng, N.

(2020) Mol Cell 78: 31-41.e5

  • DOI: https://doi.org/10.1016/j.molcel.2020.02.011
  • Primary Citation Related Structures: 
    6VCD

  • PubMed Abstract: 

    Cellular iron homeostasis is dominated by FBXL5-mediated degradation of iron regulatory protein 2 (IRP2), which is dependent on both iron and oxygen. However, how the physical interaction between FBXL5 and IRP2 is regulated remains elusive. Here, we show that the C-terminal substrate-binding domain of FBXL5 harbors a [2Fe2S] cluster in the oxidized state. A cryoelectron microscopy (cryo-EM) structure of the IRP2-FBXL5-SKP1 complex reveals that the cluster organizes the FBXL5 C-terminal loop responsible for recruiting IRP2. Interestingly, IRP2 binding to FBXL5 hinges on the oxidized state of the [2Fe2S] cluster maintained by ambient oxygen, which could explain hypoxia-induced IRP2 stabilization. Steric incompatibility also allows FBXL5 to physically dislodge IRP2 from iron-responsive element RNA to facilitate its turnover. Taken together, our studies have identified an iron-sulfur cluster within FBXL5, which promotes IRP2 polyubiquitination and degradation in response to both iron and oxygen concentrations.


  • Organizational Affiliation
    • Department of Pharmacology, University of Washington, Seattle, WA 98195, USA; Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA.

Macromolecule Content 

  • Total Structure Weight: 178.85 kDa 
  • Atom Count: 8,082 
  • Modeled Residue Count: 1,033 
  • Deposited Residue Count: 1,618 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Iron-responsive element binding protein 2, isoform CRA_a963Homo sapiensMutation(s): 0 
Gene Names: IREB2hCG_38938
UniProt & NIH Common Fund Data Resources
Find proteins for P48200 (Homo sapiens)
Explore P48200 
Go to UniProtKB:  P48200
PHAROS:  P48200
GTEx:  ENSG00000136381 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP48200
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
F-box/LRR-repeat protein 5492Homo sapiensMutation(s): 0 
Gene Names: FBXL5FBL4FBL5FLR1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UKA1 (Homo sapiens)
Explore Q9UKA1 
Go to UniProtKB:  Q9UKA1
PHAROS:  Q9UKA1
GTEx:  ENSG00000118564 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UKA1
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
S-phase kinase-associated protein 1163Homo sapiensMutation(s): 0 
Gene Names: SKP1EMC19OCP2SKP1ATCEB1L
UniProt & NIH Common Fund Data Resources
Find proteins for P63208 (Homo sapiens)
Explore P63208 
Go to UniProtKB:  P63208
PHAROS:  P63208
GTEx:  ENSG00000113558 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP63208
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FES
(Subject of Investigation/LOI)

Query on FES



Download:Ideal Coordinates CCD File
D [auth B]FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Howard Hughes Medical InstituteUnited States--

Revision History  (Full details and data files)

  • Version 1.0: 2020-08-05
    Type: Initial release
  • Version 1.1: 2024-03-06
    Changes: Data collection, Database references