Biological Assembly 1  

 3D View: Structure | Electron Density | 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)

Macromolecule Content

• Total Structure Weight: 18.39 kDa 
• Atom Count: 1301 
• Modelled Residue Count: 142 
• Deposited Residue Count: 154 
• Unique protein chains: 1

4EZF

The Crystal Structure of a Human MitoNEET mutant with an Ala inserted between Asp 67 and Lys 68

• DOI: 10.2210/pdb4EZF/pdb

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


• Deposited: 2012-05-02 Released: 2012-12-26 
• Deposition Author(s): Baxter, E.L., Zuris, J.A., Wang, C., Axelrod, H.L., Cohen, A.E., Paddock, M.L., Nechushtai, R., Onuchic, J.N., Jennings, P.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.19 Å
• R-Value Free: 0.167 
• R-Value Work: 0.165 
• R-Value Observed: 0.165 

Literature

Allosteric control in a metalloprotein dramatically alters function.

Baxter, E.L., Zuris, J.A., Wang, C., Vo, P.L., Axelrod, H.L., Cohen, A.E., Paddock, M.L., Nechushtai, R., Onuchic, J.N., Jennings, P.A.

(2013) Proc Natl Acad Sci U S A 110: 948-953

• PubMed: 23271805 
• DOI: 10.1073/pnas.1208286110
• Primary Citation of Related Structures:  
  4F28, 4F1E, 4F2C, 4EZF


• PubMed Abstract: 
  

Metalloproteins (MPs) comprise one-third of all known protein structures. This diverse set of proteins contain a plethora of unique inorganic moieties capable of performing chemistry that would otherwise be impossible using only the amino acids found in nature. Most of the well-studied MPs are generally viewed as being very rigid in structure, and it is widely thought that the properties of the metal centers are primarily determined by the small fraction of amino acids that make up the local environment. Here we examine both theoretically and experimentally whether distal regions can influence the metal center in the diabetes drug target mitoNEET. We demonstrate that a loop (L2) 20 Å away from the metal center exerts allosteric control over the cluster binding domain and regulates multiple properties of the metal center. Mutagenesis of L2 results in significant shifts in the redox potential of the [2Fe-2S] cluster and orders of magnitude effects on the rate of [2Fe-2S] cluster transfer to an apo-acceptor protein. These surprising effects occur in the absence of any structural changes. An examination of the native basin dynamics of the protein using all-atom simulations shows that twisting in L2 controls scissoring in the cluster binding domain and results in perturbations to one of the cluster-coordinating histidines. These allosteric effects are in agreement with previous folding simulations that predicted L2 could communicate with residues surrounding the metal center. Our findings suggest that long-range dynamical changes in the protein backbone can have a significant effect on the functional properties of MPs.

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Organizational Affiliation: 

Department of Chemistry and Biochemistry and Center for Theoretical Biological Physics, University of California at San Diego, La Jolla, CA 92093, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CDGSH iron-sulfur domain-containing protein 1	A, B	77	Homo sapiens	Mutation(s): 0  Gene Names: C10orf70, CISD1, MDS029, mitoNEET, ZCD1
Find proteins for Q9NZ45 (Homo sapiens) Explore Q9NZ45  Go to UniProtKB:  Q9NZ45
NIH Common Fund Data Resources
PHAROS:  Q9NZ45 GTEx:  ENSG00000122873

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FES	A, B	FE2/S2 (INORGANIC) CLUSTER Fe2 S2 NIXDOXVAJZFRNF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.19 Å
• R-Value Free: 0.167 
• R-Value Work: 0.165 
• R-Value Observed: 0.165 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.626	α = 90
b = 55.356	β = 90
c = 58.924	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2012-05-02 
• Released Date: 2012-12-26 
Deposition Author(s): Baxter, E.L., Zuris, J.A., Wang, C., Axelrod, H.L., Cohen, A.E., Paddock, M.L., Nechushtai, R., Onuchic, J.N., Jennings, P.A.

Revision History  

• Version 1.0: 2012-12-26
  Type: Initial release
  
• Version 1.1: 2013-01-30
  Changes: Database references