7T92

Structure of the peroxisomal retro-translocon formed by a heterotrimeric ubiquitin ligase complex


Experimental Data Snapshot

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

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

A peroxisomal ubiquitin ligase complex forms a retrotranslocation channel.

Feng, P.Wu, X.Erramilli, S.K.Paulo, J.A.Knejski, P.Gygi, S.P.Kossiakoff, A.A.Rapoport, T.A.

(2022) Nature 607: 374-380

  • DOI: https://doi.org/10.1038/s41586-022-04903-x
  • Primary Citation of Related Structures:  
    7T92, 7T9X

  • PubMed Abstract: 

    Peroxisomes are ubiquitous organelles that house various metabolic reactions and are essential for human health 1-4 . Luminal peroxisomal proteins are imported from the cytosol by mobile receptors, which then recycle back to the cytosol by a poorly understood process 1-4 . Recycling requires receptor modification by a membrane-embedded ubiquitin ligase complex comprising three RING finger domain-containing proteins (Pex2, Pex10 and Pex12) 5,6 . Here we report a cryo-electron microscopy structure of the ligase complex, which together with biochemical and in vivo experiments reveals its function as a retrotranslocation channel for peroxisomal import receptors. Each subunit of the complex contributes five transmembrane segments that co-assemble into an open channel. The three ring finger domains form a cytosolic tower, with ring finger 2 (RF2) positioned above the channel pore. We propose that the N terminus of a recycling receptor is inserted from the peroxisomal lumen into the pore and monoubiquitylated by RF2 to enable extraction into the cytosol. If recycling is compromised, receptors are polyubiquitylated by the concerted action of RF10 and RF12 and degraded. This polyubiquitylation pathway also maintains the homeostasis of other peroxisomal import factors. Our results clarify a crucial step during peroxisomal protein import and reveal why mutations in the ligase complex cause human disease.


  • Organizational Affiliation

    Department of Cell Biology, Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA. peiqiang_feng@hms.harvard.edu.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Peroxin-12A [auth B]439Thermothelomyces thermophilus ATCC 42464Mutation(s): 0 
Gene Names: MYCTH_2053677
Membrane Entity: Yes 
UniProt
Find proteins for G2Q5N0 (Thermothelomyces thermophilus (strain ATCC 42464 / BCRC 31852 / DSM 1799))
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Go to UniProtKB:  G2Q5N0
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UniProt GroupG2Q5N0
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Peroxin-2B [auth A]347Thermothelomyces thermophilus ATCC 42464Mutation(s): 0 
Gene Names: MYCTH_2294472
Membrane Entity: Yes 
UniProt
Find proteins for G2Q1C9 (Thermothelomyces thermophilus (strain ATCC 42464 / BCRC 31852 / DSM 1799))
Explore G2Q1C9 
Go to UniProtKB:  G2Q1C9
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UniProt GroupG2Q1C9
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Peroxin-10454Thermothelomyces thermophilus ATCC 42464Mutation(s): 0 
Gene Names: MYCTH_2294231
Membrane Entity: Yes 
UniProt
Find proteins for G2Q0E2 (Thermothelomyces thermophilus (strain ATCC 42464 / BCRC 31852 / DSM 1799))
Explore G2Q0E2 
Go to UniProtKB:  G2Q0E2
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UniProt GroupG2Q0E2
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Fab heavy chainD [auth H]114synthetic constructMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Fab light chainE [auth L]105synthetic constructMutation(s): 0 
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Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
LBN
Query on LBN

Download Ideal Coordinates CCD File 
AA [auth C]
BA [auth C]
G [auth B]
H [auth B]
I [auth B]
AA [auth C],
BA [auth C],
G [auth B],
H [auth B],
I [auth B],
J [auth B],
K [auth B],
N [auth A],
Q [auth A],
R [auth A],
S [auth A],
T [auth A],
U [auth A],
Y [auth C],
Z [auth C]
1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine
C42 H82 N O8 P
WTJKGGKOPKCXLL-VYOBOKEXSA-N
CLR
Query on CLR

Download Ideal Coordinates CCD File 
CA [auth C],
DA [auth C],
O [auth A],
P [auth A],
X [auth C]
CHOLESTEROL
C27 H46 O
HVYWMOMLDIMFJA-DPAQBDIFSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
F [auth B],
L [auth A],
M [auth A],
V [auth C],
W [auth C]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 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 Institute (HHMI)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2022-07-06
    Type: Initial release
  • Version 1.1: 2022-07-13
    Changes: Database references
  • Version 1.2: 2022-07-27
    Changes: Database references
  • Version 1.3: 2024-02-28
    Changes: Data collection