4C0K | pdb_00004c0k

Crystal structure of Drosophila Miro EF hand and cGTPase domains bound to one calcium ion (Ca-MiroS)

• PDB DOI: https://doi.org/10.2210/pdb4C0K/pdb

• Classification: HYDROLASE
• Organism(s): Drosophila melanogaster
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2013-08-05 Released: 2013-10-09 
• Deposition Author(s): Klosowiak, J.L., Focia, P.J., Wawrzak, Z., Chakravarthy, S., Landahl, E.C., Freymann, D.M., Rice, S.E.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 
  0.242 (Depositor), 0.244 (DCC) 
• R-Value Work: 
  0.207 (Depositor), 0.211 (DCC) 
• R-Value Observed: 
  0.211 (Depositor) 

Starting Model: experimental

Literature

Structural Coupling of the EF Hand and C-Terminal Gtpase Domains in the Mitochondrial Protein Miro.

Klosowiak, J.L., Focia, P.J., Chakravarthy, S., Landahl, E.C., Freymann, D.M., Rice, S.E.

(2013) EMBO Rep 14: 968

• PubMed: 24071720 
• DOI: https://doi.org/10.1038/embor.2013.151
• Primary Citation Related Structures: 
  4C0J, 4C0K, 4C0L


• PubMed Abstract: 
  

  Miro is a highly conserved calcium-binding GTPase at the regulatory nexus of mitochondrial transport and autophagy. Here we present crystal structures comprising the tandem EF hand and carboxy terminal GTPase (cGTPase) domains of Drosophila Miro. The structures reveal two previously unidentified 'hidden' EF hands, each paired with a canonical EF hand. Each EF hand pair is bound to a helix that structurally mimics an EF hand ligand. A key nucleotide-sensing element and a Pink1 phosphorylation site both lie within an extensive EF hand-cGTPase interface. Our results indicate structural mechanisms for calcium, nucleotide and phosphorylation-dependent regulation of mitochondrial function by Miro.

---

Organizational Affiliation: 
• Department of Cell and Molecular Biology, Feinberg School of Medicine, Northwestern University, 303 East Chicago Avenue, Chicago, Illinois 60611, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 49.68 kDa 
• Atom Count: 3,325 
• Modeled Residue Count: 404 
• Deposited Residue Count: 423 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MITOCHONDRIAL RHO GTPASE	A	423	Drosophila melanogaster	Mutation(s): 0  EC: 3.6.5
UniProt
Find proteins for Q8IMX7 (Drosophila melanogaster) Explore Q8IMX7  Go to UniProtKB:  Q8IMX7

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HSE	B [auth A]	L-HOMOSERINE C4 H9 N O3 UKAUYVFTDYCKQA-VKHMYHEASA-N
SO4	D [auth A], E [auth A], F [auth A], G [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
CA	I [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
NA	H [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N
UNX	C [auth A]	UNKNOWN ATOM OR ION X

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free:  0.242 (Depositor), 0.244 (DCC) 
• R-Value Work:  0.207 (Depositor), 0.211 (DCC) 
• R-Value Observed: 0.211 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.24	α = 90
b = 82.24	β = 90
c = 156.441	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
MOSFLM	data reduction
Aimless	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-10-09 
Deposition Author(s): Klosowiak, J.L., Focia, P.J., Wawrzak, Z., Chakravarthy, S., Landahl, E.C., Freymann, D.M., Rice, S.E.

Revision History  

• Version 1.0: 2013-10-09
  Type: Initial release
  
• Version 1.1: 2013-11-13
  Changes: Database references
• Version 2.0: 2023-11-15
  Changes: Atomic model, Data collection, Database references, Derived calculations, Other
• Version 2.1: 2024-05-01
  Changes: Refinement description