8RMD

Structure of the FDX2-bound core ISC complex (distal conformation)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.52 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Models: experimental
View more details

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Two-stage binding of mitochondrial ferredoxin-2 to the core iron-sulfur cluster assembly complex.

Steinhilper, R.Boss, L.Freibert, S.A.Schulz, V.Krapoth, N.Kaltwasser, S.Lill, R.Murphy, B.J.

(2024) Nat Commun 15: 10559-10559

  • DOI: https://doi.org/10.1038/s41467-024-54585-4
  • Primary Citation of Related Structures:  
    8RMC, 8RMD, 8RME, 8RMF, 8RMG

  • PubMed Abstract: 

    Iron-sulfur (FeS) protein biogenesis in eukaryotes begins with the de novo assembly of [2Fe-2S] clusters by the mitochondrial core iron-sulfur cluster assembly (ISC) complex. This complex comprises the scaffold protein ISCU2, the cysteine desulfurase subcomplex NFS1-ISD11-ACP1, the allosteric activator frataxin (FXN) and the electron donor ferredoxin-2 (FDX2). The structural interaction of FDX2 with the complex remains unclear. Here, we present cryo-EM structures of the human FDX2-bound core ISC complex showing that FDX2 and FXN compete for overlapping binding sites. FDX2 binds in either a 'distal' conformation, where its helix F interacts electrostatically with an arginine patch of NFS1, or a 'proximal' conformation, where this interaction tightens and the FDX2-specific C terminus binds to NFS1, facilitating the movement of the [2Fe-2S] cluster of FDX2 closer to the ISCU2 FeS cluster assembly site for rapid electron transfer. Structure-based mutational studies verify the contact areas of FDX2 within the core ISC complex.


  • Organizational Affiliation

    Redox and Metalloprotein Research Group, Max Planck Institute of Biophysics, Max-von-Laue-Str. 3, 60438, Frankfurt am Main, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Isoform Mitochondrial of Cysteine desulfuraseA,
F [auth E]
404Homo sapiensMutation(s): 0 
Gene Names: NFS1NIFSHUSSY-08
EC: 2.8.1.7
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y697 (Homo sapiens)
Explore Q9Y697 
Go to UniProtKB:  Q9Y697
PHAROS:  Q9Y697
GTEx:  ENSG00000244005 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9Y697
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
LYR motif-containing protein 4B,
G [auth F]
115Homo sapiensMutation(s): 1 
Gene Names: LYRM4C6orf149ISD11CGI-203
UniProt & NIH Common Fund Data Resources
Find proteins for Q9HD34 (Homo sapiens)
Explore Q9HD34 
Go to UniProtKB:  Q9HD34
PHAROS:  Q9HD34
GTEx:  ENSG00000214113 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9HD34
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Acyl carrier proteinC,
H [auth G]
78Escherichia coli BL21(DE3)Mutation(s): 0 
UniProt
Find proteins for P0A6A8 (Escherichia coli (strain K12))
Explore P0A6A8 
Go to UniProtKB:  P0A6A8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A6A8
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Isoform 1 of Iron-sulfur cluster assembly enzyme ISCUD,
I [auth H]
143Homo sapiensMutation(s): 0 
Gene Names: ISCUNIFUN
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H1K1 (Homo sapiens)
Explore Q9H1K1 
Go to UniProtKB:  Q9H1K1
PHAROS:  Q9H1K1
GTEx:  ENSG00000136003 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9H1K1
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Ferredoxin-2, mitochondrialE [auth I]121Homo sapiensMutation(s): 0 
Gene Names: FDX2FDX1L
UniProt & NIH Common Fund Data Resources
Find proteins for Q6P4F2 (Homo sapiens)
Explore Q6P4F2 
Go to UniProtKB:  Q6P4F2
PHAROS:  Q6P4F2
GTEx:  ENSG00000267673 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6P4F2
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
8Q1 (Subject of Investigation/LOI)
Query on 8Q1

Download Ideal Coordinates CCD File 
J [auth C],
M [auth G]
S-[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] dodecanethioate
C23 H45 N2 O8 P S
MVHUOSAYFQKAMT-NRFANRHFSA-N
FES (Subject of Investigation/LOI)
Query on FES

Download Ideal Coordinates CCD File 
L [auth I]FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
FE2 (Subject of Investigation/LOI)
Query on FE2

Download Ideal Coordinates CCD File 
K [auth D],
N [auth H]
FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
LLP
Query on LLP
A,
F [auth E]
L-PEPTIDE LINKINGC14 H22 N3 O7 PLYS
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.52 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC4.1.2
MODEL REFINEMENTPHENIX1.20.1

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Max Planck SocietyGermany--

Revision History  (Full details and data files)

  • Version 1.0: 2024-12-18
    Type: Initial release
  • Version 1.1: 2024-12-25
    Changes: Data collection