4PQQ | pdb_00004pqq

The crystal structure of discoidin domain from muskelin

• PDB DOI: https://doi.org/10.2210/pdb4PQQ/pdb

• Classification: PROTEIN BINDING
• Organism(s): Mus musculus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2014-03-04 Released: 2014-11-12 
• Deposition Author(s): Kim, K.-H., Hong, S.K., Kim, E.E.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 
  0.176 (Depositor), 0.180 (DCC) 
• R-Value Work: 
  0.153 (Depositor), 0.160 (DCC) 
• R-Value Observed: 
  0.155 (Depositor) 

Literature

Structure of mouse muskelin discoidin domain and biochemical characterization of its self-association.

Kim, K.H., Hong, S.K., Hwang, K.Y., Kim, E.E.

(2014) Acta Crystallogr D Biol Crystallogr 70: 2863-2874

• PubMed: 25372678 
• DOI: https://doi.org/10.1107/S139900471401894X
• Primary Citation of Related Structures:  
  4PQQ


• PubMed Abstract: 
  

  Muskelin is an intracellular kelch-repeat protein comprised of discoidin, LisH, CTLH and kelch-repeat domains. It is involved in cell adhesion and the regulation of cytoskeleton dynamics as well as being a component of a putative E3 ligase complex. Here, the first crystal structure of mouse muskelin discoidin domain (MK-DD) is reported at 1.55 Å resolution, which reveals a distorted eight-stranded β-barrel with two short α-helices at one end of the barrel. Interestingly, the N- and C-termini are not linked by the disulfide bonds found in other eukaryotic discoidin structures. A highly conserved MIND motif appears to be the determinant for MK-DD specific interaction together with the spike loops. Analysis of interdomain interaction shows that MK-DD binds the kelch-repeat domain directly and that this interaction depends on the presence of the LisH domain.

---

Organizational Affiliation: 
• Biomedical Research Institute, Korea Institute of Science and Technology, Hwarang-ro 14-gil 5, Seongbuk-gu, Seoul 136-791, Republic of Korea.
Division of Biotechnology, College of Life Sciences and Biotechnology, Korea University, 145 Anam-ro, Seoul 136-701, Republic of Korea.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 18.76 kDa 
• Atom Count: 1,520 
• Modeled Residue Count: 156 
• Deposited Residue Count: 156 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Muskelin	A	156	Mus musculus	Mutation(s): 0  Gene Names: Mkln1
UniProt
Find proteins for O89050 (Mus musculus) Explore O89050  Go to UniProtKB:  O89050

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PG4	C [auth A], D [auth A]	TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N
PO4	B [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free:  0.176 (Depositor), 0.180 (DCC) 
• R-Value Work:  0.153 (Depositor), 0.160 (DCC) 
• R-Value Observed: 0.155 (Depositor) 

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.303	α = 90
b = 98.303	β = 90
c = 57.317	γ = 120

Software Package:

Software Name	Purpose
ADSC	data collection
SOLVE	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-11-12 
Deposition Author(s): Kim, K.-H., Hong, S.K., Kim, E.E.

Revision History  

• Version 1.0: 2014-11-12
  Type: Initial release
  
• Version 1.1: 2014-11-19
  Changes: Database references
• Version 1.2: 2024-02-28
  Changes: Data collection, Database references, Derived calculations