8UC6 | pdb_00008uc6

Calpain-7:IST1 Complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 
    0.285 (Depositor), 0.287 (DCC) 
  • R-Value Work: 
    0.211 (Depositor), 0.213 (DCC) 
  • R-Value Observed: 
    0.218 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.1 of the entry. See complete history

Literature

The Calpain-7 protease functions together with the ESCRT-III protein IST1 within the midbody to regulate the timing and completion of abscission.

Paine, E.L.Skalicky, J.J.Whitby, F.G.Mackay, D.R.Ullman, K.S.Hill, C.P.Sundquist, W.I.

(2023) Elife 12

  • DOI: https://doi.org/10.7554/eLife.84515
  • Primary Citation Related Structures: 
    8UC6

  • PubMed Abstract: 

    The Endosomal Sorting Complexes Required for Transport (ESCRT) machinery mediates the membrane fission step that completes cytokinetic abscission and separates dividing cells. Filaments composed of ESCRT-III subunits constrict membranes of the intercellular bridge midbody to the abscission point. These filaments also bind and recruit cofactors whose activities help execute abscission and/or delay abscission timing in response to mitotic errors via the NoCut/Abscission checkpoint. We previously showed that the ESCRT-III subunit IST1 binds the cysteine protease Calpain-7 (CAPN7) and that CAPN7 is required for both efficient abscission and NoCut checkpoint maintenance (Wenzel et al., 2022). Here, we report biochemical and crystallographic studies showing that the tandem microtubule-interacting and trafficking (MIT) domains of CAPN7 bind simultaneously to two distinct IST1 MIT interaction motifs. Structure-guided point mutations in either CAPN7 MIT domain disrupted IST1 binding in vitro and in cells, and depletion/rescue experiments showed that the CAPN7-IST1 interaction is required for (1) CAPN7 recruitment to midbodies, (2) efficient abscission, and (3) NoCut checkpoint arrest. CAPN7 proteolytic activity is also required for abscission and checkpoint maintenance. Hence, IST1 recruits CAPN7 to midbodies, where its proteolytic activity is required to regulate and complete abscission.


  • Organizational Affiliation
    • Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, United States.

Macromolecule Content 

  • Total Structure Weight: 47.01 kDa 
  • Atom Count: 2,821 
  • Modeled Residue Count: 345 
  • Deposited Residue Count: 420 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Calpain-7A [auth C],
C [auth B]
165Homo sapiensMutation(s): 0 
Gene Names: CAPN7
EC: 3.4.22
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y6W3 (Homo sapiens)
Explore Q9Y6W3 
Go to UniProtKB:  Q9Y6W3
PHAROS:  Q9Y6W3
GTEx:  ENSG00000131375 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9Y6W3
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
IST1 homologB [auth G],
D [auth E]
45Homo sapiensMutation(s): 0 
Gene Names: IST1
UniProt & NIH Common Fund Data Resources
Find proteins for P53990 (Homo sapiens)
Explore P53990 
Go to UniProtKB:  P53990
PHAROS:  P53990
GTEx:  ENSG00000182149 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP53990
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free:  0.285 (Depositor), 0.287 (DCC) 
  • R-Value Work:  0.211 (Depositor), 0.213 (DCC) 
  • R-Value Observed: 0.218 (Depositor) 
Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 87.841α = 90
b = 87.841β = 90
c = 183.894γ = 120
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
PHASERphasing

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States1F31GM139318
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States5R01GM112080
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesS10OD030326

Revision History  (Full details and data files)

  • Version 1.0: 2023-10-25
    Type: Initial release
  • Version 1.1: 2024-05-15
    Changes: Database references