9L93 | pdb_00009l93

Crystal structure of NCOA4 in complex with HERC2

  • Classification: LIGASE
  • Organism(s): Homo sapiens
  • Expression System: Escherichia coli
  • Mutation(s): No 

  • Deposited: 2024-12-29 Released: 2025-11-05 
  • Deposition Author(s): Liu, H.B., Pan, L.F.
  • Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.73 Å
  • R-Value Free: 
    0.207 (Depositor), 0.208 (DCC) 
  • R-Value Work: 
    0.166 (Depositor), 0.167 (DCC) 
  • R-Value Observed: 
    0.168 (Depositor) 

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

Validation slider image for 9L93

This is version 1.0 of the entry. See complete history

Literature

Mechanistic insights into the iron-sulfur cluster-dependent interaction of the autophagy receptor NCOA4 with the E3 ligase HERC2.

Liu, H.Shen, L.Gong, X.Zhou, X.Huang, Y.Zhou, Y.Guo, Z.Guo, H.Wang, S.Pan, L.

(2025) Proc Natl Acad Sci U S A 122: e2510269122-e2510269122

  • DOI: https://doi.org/10.1073/pnas.2510269122
  • Primary Citation Related Structures: 
    9L8Y, 9L93

  • PubMed Abstract: 

    NCOA4, a dedicated autophagy receptor for mediating selective autophagy of ferritin (ferritinophagy), plays a vital role in maintaining cellular iron homeostasis. The cellular abundance of NCOA4 is regulated by the E3 ligase HERC2 that can specifically target NCOA4 for proteasomal degradation under iron-replete conditions. However, the detailed molecular mechanism governing the iron-dependent recognition of NCOA4 by HERC2 remains elusive. Here, using multidisciplinary approaches, we systematically characterize the HERC2-binding domain (HBD) of NCOA4 and its interaction with HERC2. We uncover that NCOA4 HBD harbors a [2Fe-2S] cluster and can exist in two different states, the apo -form state and the [2Fe-2S] cluster-bound state. Moreover, we unravel that HERC2 can effectively recognize the [2Fe-2S] cluster-bound NCOA4 HBD through its Cullin-7-PARC-HERC2 (CPH) domain and iron-sulfur cluster-dependent NCOA4-binding domain (INBD) with a synergistic binding mode. The determined crystal structures of HERC2(2540-2700) and its complex with the [2Fe-2S] cluster-bound NCOA4 HBD together with relevant biochemical and cellular results not only elucidate how NCOA4 HBD specifically senses cellular iron level by binding a [2Fe-2S] cluster but also reveal the molecular basis underlying the specific interaction of HERC2 with the [2Fe-2S] cluster-bound NCOA4 HBD. In summary, our findings provide mechanistic insights into the iron-dependent turnover of NCOA4 by HERC2 and expand our understanding of the regulatory mechanism of NCOA4-mediated ferritinophagy.


  • Organizational Affiliation
    • State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200032, China.

Macromolecule Content 

  • Total Structure Weight: 48.62 kDa 
  • Atom Count: 3,663 
  • Modeled Residue Count: 396 
  • Deposited Residue Count: 430 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
E3 ubiquitin-protein ligase HERC2
A, B
164Homo sapiensMutation(s): 0 
Gene Names: HERC2
EC: 2.3.2.26
UniProt & NIH Common Fund Data Resources
Find proteins for O95714 (Homo sapiens)
Explore O95714 
Go to UniProtKB:  O95714
PHAROS:  O95714
GTEx:  ENSG00000128731 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO95714
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Nuclear receptor coactivator 4
C, D
51Homo sapiensMutation(s): 0 
Gene Names: NCOA4ARA70ELE1RFG
UniProt & NIH Common Fund Data Resources
Find proteins for Q13772 (Homo sapiens)
Explore Q13772 
Go to UniProtKB:  Q13772
PHAROS:  Q13772
GTEx:  ENSG00000266412 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ13772
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.73 Å
  • R-Value Free:  0.207 (Depositor), 0.208 (DCC) 
  • R-Value Work:  0.166 (Depositor), 0.167 (DCC) 
  • R-Value Observed: 0.168 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.456α = 90
b = 41.886β = 95.93
c = 86.258γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
autoPROCdata reduction
autoPROCdata scaling
PHENIXphasing

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China21822705

Revision History  (Full details and data files)

  • Version 1.0: 2025-11-05
    Type: Initial release