8DYE

Crystal structure of human SDHA-SDHAF4 assembly intermediate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.44 Å
  • R-Value Free: 0.173 
  • R-Value Work: 0.155 
  • R-Value Observed: 0.156 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Disordered-to-ordered transitions in assembly factors allow the complex II catalytic subunit to switch binding partners.

Sharma, P.Maklashina, E.Voehler, M.Balintova, S.Dvorakova, S.Kraus, M.Vanova, K.H.Nahacka, Z.Zobalova, R.Boukalova, S.Cunatova, K.Mracek, T.Ghayee, H.K.Pacak, K.Rohlena, J.Neuzil, J.Cecchini, G.Iverson, T.M.

(2024) Nat Commun 15: 473-473

  • DOI: https://doi.org/10.1038/s41467-023-44563-7
  • Primary Citation of Related Structures:  
    8DYD, 8DYE

  • PubMed Abstract: 

    Complex II (CII) activity controls phenomena that require crosstalk between metabolism and signaling, including neurodegeneration, cancer metabolism, immune activation, and ischemia-reperfusion injury. CII activity can be regulated at the level of assembly, a process that leverages metastable assembly intermediates. The nature of these intermediates and how CII subunits transfer between metastable complexes remains unclear. In this work, we identify metastable species containing the SDHA subunit and its assembly factors, and we assign a preferred temporal sequence of appearance of these species during CII assembly. Structures of two species show that the assembly factors undergo disordered-to-ordered transitions without the appearance of significant secondary structure. The findings identify that intrinsically disordered regions are critical in regulating CII assembly, an observation that has implications for the control of assembly in other biomolecular complexes.


  • Organizational Affiliation

    Department of Pharmacology, Vanderbilt University, Nashville, TN, 37232, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial611Homo sapiensMutation(s): 0 
Gene Names: SDHASDH2SDHF
EC: 1.3.5.1
UniProt & NIH Common Fund Data Resources
Find proteins for P31040 (Homo sapiens)
Explore P31040 
Go to UniProtKB:  P31040
PHAROS:  P31040
GTEx:  ENSG00000073578 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP31040
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Succinate dehydrogenase assembly factor 4, mitochondrial98Homo sapiensMutation(s): 0 
Gene Names: SDHAF4C6orf57
UniProt & NIH Common Fund Data Resources
Find proteins for Q5VUM1 (Homo sapiens)
Explore Q5VUM1 
Go to UniProtKB:  Q5VUM1
PHAROS:  Q5VUM1
GTEx:  ENSG00000154079 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5VUM1
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FAD (Subject of Investigation/LOI)
Query on FAD

Download Ideal Coordinates CCD File 
C [auth A]FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
MLI (Subject of Investigation/LOI)
Query on MLI

Download Ideal Coordinates CCD File 
D [auth A]MALONATE ION
C3 H2 O4
OFOBLEOULBTSOW-UHFFFAOYSA-L
GOL
Query on GOL

Download Ideal Coordinates CCD File 
I [auth A],
M [auth A],
R [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
G [auth A]
H [auth A]
J [auth A]
E [auth A],
F [auth A],
G [auth A],
H [auth A],
J [auth A],
K [auth A],
L [auth A],
N [auth A],
O [auth A],
P [auth A],
Q [auth A],
S [auth A],
T [auth A],
U [auth A],
V [auth A],
W [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
NA
Query on NA

Download Ideal Coordinates CCD File 
X [auth A],
Y [auth A]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 139.049α = 90
b = 69.299β = 90
c = 72.657γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM61606
American Heart AssociationUnited States19POST34450093

Revision History  (Full details and data files)

  • Version 1.0: 2024-01-10
    Type: Initial release
  • Version 1.1: 2024-02-07
    Changes: Database references