6XG7 | pdb_00006xg7

1.3 A Resolution Structure of the of the NHL Repeat Region of D. melanogaster Thin

• PDB DOI: https://doi.org/10.2210/pdb6XG7/pdb

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


• Deposited: 2020-06-17 Released: 2020-12-16 
• Deposition Author(s): Kashipathy, M.M., Lovell, S., Battaile, K.P., Bawa, S., Geisbrecht, E.R.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free: 
  0.174 (Depositor), 0.184 (DCC) 
• R-Value Work: 
  0.138 (Depositor), 0.152 (DCC) 
• R-Value Observed: 
  0.140 (Depositor) 

Starting Model: experimental

Literature

Costameric integrin and sarcoglycan protein levels are altered in a Drosophila model for Limb-girdle muscular dystrophy type 2H.

Bawa, S., Gameros, S., Baumann, K., Brooks, D.S., Kollhoff, J.A., Zolkiewski, M., Re Cecconi, A.D., Panini, N., Russo, M., Piccirillo, R., Johnson, D.K., Kashipathy, M.M., Battaile, K.P., Lovell, S., Bouyain, S.E.A., Kawakami, J., Geisbrecht, E.R.

(2021) Mol Biol Cell 32: 260-273

• PubMed: 33296226 
• DOI: https://doi.org/10.1091/mbc.E20-07-0453
• Primary Citation Related Structures: 
  6XG7


• PubMed Abstract: 
  

  Mutations in two different domains of the ubiquitously expressed TRIM32 protein give rise to two clinically separate diseases, one of which is Limb-girdle muscular dystrophy type 2H (LGMD2H). Uncovering the muscle-specific role of TRIM32 in LGMD2H pathogenesis has proven difficult, as neurogenic phenotypes, independent of LGMD2H pathology, are present in TRIM32 KO mice. We previously established a platform to study LGMD2H pathogenesis using Drosophila melanogaster as a model. Here we show that LGMD2H disease-causing mutations in the NHL domain are molecularly and structurally conserved between fly and human TRIM32. Furthermore, transgenic expression of a subset of myopathic alleles (R394H, D487N, and 520fs) induce myofibril abnormalities, altered nuclear morphology, and reduced TRIM32 protein levels, mimicking phenotypes in patients afflicted with LGMD2H. Intriguingly, we also report for the first time that the protein levels of βPS integrin and sarcoglycan δ, both core components of costameres, are elevated in TRIM32 disease-causing alleles. Similarly, murine myoblasts overexpressing a catalytically inactive TRIM32 mutant aberrantly accumulate α- and β-dystroglycan and α-sarcoglycan. We speculate that the stoichiometric loss of costamere components disrupts costamere complexes to promote muscle degeneration.

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Organizational Affiliation: 
• Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, KS 66506.
School of Biological Sciences, University of Missouri-Kansas City, MO 64110.
Department of Neuroscience and.
Department of Oncology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, 20156 Milan, Italy.
Molecular Graphics and Modeling Laboratory, Computational Chemical Biology Core, University of Kansas, Lawrence, KS 66047.
Protein Structure Laboratory, University of Kansas, Lawrence, KS 66047.
NYX, New York Structural Biology Center, Upton, NY 11973.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 33.47 kDa 
• Atom Count: 2,540 
• Modeled Residue Count: 288 
• Deposited Residue Count: 307 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thin, isoform D	A	307	Drosophila melanogaster	Mutation(s): 0  Gene Names: tn, Abba, Dmel\CG15105, l(2)tn, CG15105, Dmel_CG15105
UniProt
Find proteins for B7YZK8 (Drosophila melanogaster) Explore B7YZK8  Go to UniProtKB:  B7YZK8

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PG4	C [auth A]	TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N
SO4	B [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSO	A	L-PEPTIDE LINKING	C3 H7 N O3 S		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free:  0.174 (Depositor), 0.184 (DCC) 
• R-Value Work:  0.138 (Depositor), 0.152 (DCC) 
• R-Value Observed: 0.140 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.633	α = 90
b = 51.917	β = 90
c = 105.119	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2020-12-16 
Deposition Author(s): Kashipathy, M.M., Lovell, S., Battaile, K.P., Bawa, S., Geisbrecht, E.R.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	P30 GM110761

Revision History  

• Version 1.0: 2020-12-16
  Type: Initial release
  
• Version 1.1: 2021-02-10
  Changes: Database references
• Version 1.2: 2023-10-18
  Changes: Data collection, Database references, Refinement description
• Version 1.3: 2023-11-15
  Changes: Data collection
• Version 1.4: 2024-10-16
  Changes: Structure summary