5WKP

Crystal Structure of the Human mitochondrial Cysteine Desulfurase in complex with ISD11 and Iron-Sulfur Cluster Scaffold Protein ISCU1, and E. coli ACP1 protein at 3.15A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.15 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.190 

wwPDB Validation 3D Report Full Report



Literature

Structure and functional dynamics of the mitochondrial Fe/S cluster synthesis complex.

Boniecki, M.T.Freibert, S.A.Muhlenhoff, U.Lill, R.Cygler, M.

(2017) Nat Commun 8: 1287-1287

  • DOI: 10.1038/s41467-017-01497-1
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Iron-sulfur (Fe/S) clusters are essential protein cofactors crucial for many cellular functions including DNA maintenance, protein translation, and energy conversion. De novo Fe/S cluster synthesis occurs on the mitochondrial scaffold protein ISCU an ...

    Iron-sulfur (Fe/S) clusters are essential protein cofactors crucial for many cellular functions including DNA maintenance, protein translation, and energy conversion. De novo Fe/S cluster synthesis occurs on the mitochondrial scaffold protein ISCU and requires cysteine desulfurase NFS1, ferredoxin, frataxin, and the small factors ISD11 and ACP (acyl carrier protein). Both the mechanism of Fe/S cluster synthesis and function of ISD11-ACP are poorly understood. Here, we present crystal structures of three different NFS1-ISD11-ACP complexes with and without ISCU, and we use SAXS analyses to define the 3D architecture of the complete mitochondrial Fe/S cluster biosynthetic complex. Our structural and biochemical studies provide mechanistic insights into Fe/S cluster synthesis at the catalytic center defined by the active-site Cys of NFS1 and conserved Cys, Asp, and His residues of ISCU. We assign specific regulatory rather than catalytic roles to ISD11-ACP that link Fe/S cluster synthesis with mitochondrial lipid synthesis and cellular energy status.


    Organizational Affiliation

    Department of Biochemistry, McGill University, 3649 Promenade Sir William Osler, Montreal, QC, Canada, H3G 0B1. Miroslaw.cygler@usask.ca.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cysteine desulfurase, mitochondrial
A, E
406Homo sapiensMutation(s): 0 
Gene Names: NFS1NIFSHUSSY-08
EC: 2.8.1.7
Find proteins for Q9Y697 (Homo sapiens)
Go to UniProtKB:  Q9Y697
NIH Common Fund Data Resources
PHAROS  Q9Y697
Protein Feature View
  • Reference Sequence

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
LYR motif-containing protein 4
B, F
91Homo sapiensMutation(s): 1 
Gene Names: LYRM4C6orf149ISD11CGI-203
Find proteins for Q9HD34 (Homo sapiens)
Go to UniProtKB:  Q9HD34
NIH Common Fund Data Resources
PHAROS  Q9HD34
Protein Feature View
  • Reference Sequence

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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Iron-sulfur cluster assembly enzyme ISCU, mitochondrial
D, H
150Homo sapiensMutation(s): 1 
Gene Names: ISCUNIFUN
Find proteins for Q9H1K1 (Homo sapiens)
Go to UniProtKB:  Q9H1K1
NIH Common Fund Data Resources
PHAROS  Q9H1K1
Protein Feature View
  • Reference Sequence

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Acyl carrier protein
C, G
77Escherichia coliMutation(s): 0 
Gene Names: acpPECS88_1108
Find proteins for P0A6A8 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A6A8
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
8Q1
Query on 8Q1

Download CCD File 
C, 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
 Ligand Interaction
PLP
Query on PLP

Download CCD File 
A, E
PYRIDOXAL-5'-PHOSPHATE
C8 H10 N O6 P
NGVDGCNFYWLIFO-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.15 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.190 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 98.36α = 90
b = 123.29β = 90
c = 151.724γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-11-15
    Type: Initial release