5VNY | pdb_00005vny

Crystal structure of DM14-3 domain of Lgd

• PDB DOI: https://doi.org/10.2210/pdb5VNY/pdb

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


• Deposited: 2017-05-01 Released: 2017-06-14 
• Deposition Author(s): McMillan, B.J., Blacklow, S.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.10 Å
• R-Value Free: 
  0.178 (Depositor), 0.179 (DCC) 
• R-Value Work: 
  0.170 (Depositor), 0.171 (DCC) 
• R-Value Observed: 
  0.170 (Depositor) 

Literature

Structural Basis for Regulation of ESCRT-III Complexes by Lgd.

McMillan, B.J., Tibbe, C., Drabek, A.A., Seegar, T.C.M., Blacklow, S.C., Klein, T.

(2017) Cell Rep 19: 1750-1757

• PubMed: 28564595 
• DOI: https://doi.org/10.1016/j.celrep.2017.05.026
• Primary Citation Related Structures: 
  5VNY, 5VO5


• PubMed Abstract: 
  

  The ESCRT-III complex induces outward membrane budding and fission through homotypic polymerization of its core component Shrub/CHMP4B. Shrub activity is regulated by its direct interaction with a protein called Lgd in flies, or CC2D1A or B in humans. Here, we report the structural basis for this interaction and propose a mechanism for regulation of polymer assembly. The isolated third DM14 repeat of Lgd binds Shrub, and an Lgd fragment containing only this DM14 repeat and its C-terminal C2 domain is sufficient for in vivo function. The DM14 domain forms a helical hairpin with a conserved, positively charged tip, that, in the structure of a DM14 domain-Shrub complex, occupies a negatively charged surface of Shrub that is otherwise used for homopolymerization. Lgd mutations at this interface disrupt its function in flies, confirming functional importance. Together, these data argue that Lgd regulates ESCRT activity by controlling access to the Shrub self-assembly surface.

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Organizational Affiliation: 
• Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA.
Institute of Genetics, Heinrich-Heine-University, Dusseldorf 40225, Germany.
Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Dana Farber Cancer Institute, Department of Cancer Biology, Boston, MA 02215, USA. Electronic address: [e-mail].
Institute of Genetics, Heinrich-Heine-University, Dusseldorf 40225, Germany. Electronic address: [e-mail].

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 7.43 kDa 
• Atom Count: 632 
• Modeled Residue Count: 65 
• Deposited Residue Count: 66 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lethal (2) giant discs 1, isoform B	A	66	Drosophila melanogaster	Mutation(s): 0  Gene Names: l(2)gd1, CG4713, Dmel_CG4713
UniProt
Find proteins for Q9VKJ9 (Drosophila melanogaster) Explore Q9VKJ9  Go to UniProtKB:  Q9VKJ9

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.10 Å
• R-Value Free:  0.178 (Depositor), 0.179 (DCC) 
• R-Value Work:  0.170 (Depositor), 0.171 (DCC) 
• R-Value Observed: 0.170 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 29.67	α = 90
b = 29.67	β = 90
c = 139.11	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-06-14 
Deposition Author(s): McMillan, B.J., Blacklow, S.C.

Revision History  

• Version 1.0: 2017-06-14
  Type: Initial release
  
• Version 1.1: 2024-11-20
  Changes: Data collection, Database references, Structure summary