Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 9.69 kDa 
• Atom Count: 689 
• Modelled Residue Count: 75 
• Deposited Residue Count: 78 
• Unique protein chains: 1

6DE9

mitoNEET bound to furosemide

• PDB DOI: 10.2210/pdb6DE9/pdb

• Classification: METAL BINDING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2018-05-11 Released: 2019-05-15 
• Deposition Author(s): Robart, A.R., Geldenhuys, W.J.
• Funding Organization(s): National Institutes of Health/National Center for Advancing Translational Sciences (NIH/NCATS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.221 
• R-Value Work: 0.200 
• R-Value Observed: 0.202 

Literature

Crystal structure of the mitochondrial protein mitoNEET bound to a benze-sulfonide ligand.

Geldenhuys, W.J., Long, T.E., Saralkar, P., Iwasaki, T., Nunez, R.A.A., Nair, R.R., Konkle, M.E., Menze, M.A., Pinti, M.V., Hollander, J.M., Hazlehurst, L.A., Robart, A.R.

(2019) Commun Chem 2

• PubMed: 32382661 
• DOI: 10.1038/s42004-019-0172-x
• Primary Citation of Related Structures:  
  6DE9


• PubMed Abstract: 
  

MitoNEET (gene cisd1 ) is a mitochondrial outer membrane [2Fe-2S] protein and is a potential drug target in several metabolic diseases. Previous studies have demonstrated that mitoNEET functions as a redox-active and pH-sensing protein that regulates mitochondrial metabolism, although the structural basis of the potential drug binding site(s) remains elusive. Here we report the crystal structure of the soluble domain of human mitoNEET with a sulfonamide ligand, furosemide. Exploration of the high-resolution crystal structure is used to design mitoNEET binding molecules in a pilot study of molecular probes for use in future development of mitochondrial targeted therapies for a wide variety of metabolic diseases, including obesity, diabetes and neurodegenerative diseases such as Alzheimer's and Parkinson's disease.

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Organizational Affiliation: 

Department of Biochemistry, School of Medicine West Virginia University, Morgantown, WV 26506, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CDGSH iron-sulfur domain-containing protein 1	A	78	Homo sapiens	Mutation(s): 0  Gene Names: CISD1, C10orf70, ZCD1, MDS029
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NZ45 (Homo sapiens) Explore Q9NZ45  Go to UniProtKB:  Q9NZ45
PHAROS:  Q9NZ45 GTEx:  ENSG00000122873

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FUN (Subject of Investigation/LOI)	C [auth A]	5-(AMINOSULFONYL)-4-CHLORO-2-[(2-FURYLMETHYL)AMINO]BENZOIC ACID C12 H11 Cl N2 O5 S ZZUFCTLCJUWOSV-UHFFFAOYSA-N
FES	B [auth A]	FE2/S2 (INORGANIC) CLUSTER Fe2 S2 NIXDOXVAJZFRNF-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
FUN	BindingDB:  6DE9	Ki: 2285 (nM) from 1 assay(s)
		IC50: 5.35e+4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.221 
• R-Value Work: 0.200 
• R-Value Observed: 0.202 
• Space Group: I 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.83	α = 90
b = 58.83	β = 90
c = 176.75	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
MOSFLM	data reduction
Aimless	data scaling
PDB_EXTRACT	data extraction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2018-05-11 
• Released Date: 2019-05-15 
Deposition Author(s): Robart, A.R., Geldenhuys, W.J.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Center for Advancing Translational Sciences (NIH/NCATS)	United States	--

Revision History  

• Version 1.0: 2019-05-15
  Type: Initial release
  
• Version 1.1: 2019-12-04
  Changes: Author supporting evidence
• Version 1.2: 2022-03-23
  Changes: Database references