8UY3 | pdb_00008uy3

Fem1B with FNIP1 and Tom20 fragment


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 
    0.264 (Depositor), 0.264 (DCC) 
  • R-Value Work: 
    0.239 (Depositor), 0.239 (DCC) 
  • R-Value Observed: 
    0.240 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Reactive oxygen species control protein degradation at the mitochondrial import gate.

McMinimy, R.Manford, A.G.Gee, C.L.Chandrasekhar, S.Mousa, G.A.Chuang, J.Phu, L.Shih, K.Y.Rose, C.M.Kuriyan, J.Bingol, B.Rape, M.

(2024) Mol Cell 84: 4612-4628.e13

  • DOI: https://doi.org/10.1016/j.molcel.2024.11.004
  • Primary Citation of Related Structures:  
    8UY3

  • PubMed Abstract: 

    While reactive oxygen species (ROS) have long been known to drive aging and neurodegeneration, their persistent depletion below basal levels also disrupts organismal function. Cells counteract loss of basal ROS via the reductive stress response, but the identity and biochemical activity of ROS sensed by this pathway remain unknown. Here, we show that the central enzyme of the reductive stress response, the E3 ligase Cullin 2-FEM1 homolog B (CUL2 FEM1B ), specifically acts at mitochondrial TOM complexes, where it senses ROS produced by complex III of the electron transport chain (ETC). ROS depletion during times of low ETC activity triggers the localized degradation of CUL2 FEM1B substrates, which sustains mitochondrial import and ensures the biogenesis of the rate-limiting ETC complex IV. As complex III yields most ROS when the ETC outpaces metabolic demands or oxygen availability, basal ROS are sentinels of mitochondrial activity that help cells adjust their ETC to changing environments, as required for cell differentiation and survival.


  • Organizational Affiliation

    Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA 94720, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protein fem-1 homolog BA,
B [auth C],
C [auth B],
D
381Mus musculusMutation(s): 0 
Gene Names: Fem1bF1aaKiaa0396
UniProt
Find proteins for Q9Z2G0 (Mus musculus)
Explore Q9Z2G0 
Go to UniProtKB:  Q9Z2G0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9Z2G0
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Folliculin-interacting protein 1E,
F,
I [auth H],
J [auth I]
31Mus musculusMutation(s): 0 
Gene Names: Fnip1Kiaa1961
UniProt & NIH Common Fund Data Resources
Find proteins for Q68FD7 (Mus musculus)
Explore Q68FD7 
Go to UniProtKB:  Q68FD7
IMPC:  MGI:2444668
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ68FD7
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial import receptor subunit TOM20 homologG [auth J],
H [auth K],
K [auth M]
66Homo sapiensMutation(s): 0 
Gene Names: TOMM20KIAA0016
UniProt & NIH Common Fund Data Resources
Find proteins for Q15388 (Homo sapiens)
Explore Q15388 
Go to UniProtKB:  Q15388
PHAROS:  Q15388
GTEx:  ENSG00000173726 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ15388
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
EPE
Query on EPE

Download Ideal Coordinates CCD File 
M [auth A]4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
P [auth C],
R [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
PO4
Query on PO4

Download Ideal Coordinates CCD File 
N [auth A]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
ZN (Subject of Investigation/LOI)
Query on ZN

Download Ideal Coordinates CCD File 
L [auth A]
O [auth C]
Q [auth B]
S [auth D]
T [auth E]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free:  0.264 (Depositor), 0.264 (DCC) 
  • R-Value Work:  0.239 (Depositor), 0.239 (DCC) 
  • R-Value Observed: 0.240 (Depositor) 
Space Group: P 21 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 183.715α = 90
b = 183.715β = 90
c = 183.715γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Howard Hughes Medical Institute (HHMI)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2025-03-19
    Type: Initial release