6XJ1 | pdb_00006xj1

Crystal Structure of CDC15 F-BAR Domain from Schizosaccharomyces pombe


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.52 Å
  • R-Value Free: 
    0.310 (Depositor), 0.307 (DCC) 
  • R-Value Work: 
    0.267 (Depositor), 0.269 (DCC) 
  • R-Value Observed: 
    0.269 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.2 of the entry. See complete history

Literature

Opposite Surfaces of the Cdc15 F-BAR Domain Create a Membrane Platform That Coordinates Cytoskeletal and Signaling Components for Cytokinesis.

Snider, C.E.Chandra, M.McDonald, N.A.Willet, A.H.Collier, S.E.Ohi, M.D.Jackson, L.P.Gould, K.L.

(2020) Cell Rep 33: 108526-108526

  • DOI: https://doi.org/10.1016/j.celrep.2020.108526
  • Primary Citation Related Structures: 
    6XJ1

  • PubMed Abstract: 

    Many eukaryotes assemble an actin- and myosin-based cytokinetic ring (CR) on the plasma membrane (PM) for cell division, but how it is anchored there remains unclear. In Schizosaccharomyces pombe, the F-BAR protein Cdc15 links the PM via its F-BAR domain to proteins in the CR's interior via its SH3 domain. However, Cdc15's F-BAR domain also directly binds formin Cdc12, suggesting that Cdc15 may polymerize a protein network directly adjacent to the membrane. Here, we determine that the F-BAR domain binds Cdc12 using residues on the face opposite its membrane-binding surface. These residues also bind paxillin-like Pxl1, promoting its recruitment with calcineurin to the CR. Mutation of these F-BAR domain residues results in a shallower CR, with components localizing ∼35% closer to the PM than in wild type, and aberrant CR constriction. Thus, F-BAR domains serve as oligomeric membrane-bound platforms that can modulate the architecture of an entire actin structure.


  • Organizational Affiliation
    • Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN 37232, USA.

Macromolecule Content 

  • Total Structure Weight: 68.07 kDa 
  • Atom Count: 4,458 
  • Modeled Residue Count: 543 
  • Deposited Residue Count: 588 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Cell division control protein 15
A, B
294Schizosaccharomyces pombe 972h-Mutation(s): 2 
Gene Names: cdc15SPAC20G8.05c
UniProt
Find proteins for Q09822 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Explore Q09822 
Go to UniProtKB:  Q09822
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ09822
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.52 Å
  • R-Value Free:  0.310 (Depositor), 0.307 (DCC) 
  • R-Value Work:  0.267 (Depositor), 0.269 (DCC) 
  • R-Value Observed: 0.269 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.777α = 90
b = 75.171β = 95.33
c = 93.239γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
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 StatesNIH R35GM119525

Revision History  (Full details and data files)

  • Version 1.0: 2020-12-16
    Type: Initial release
  • Version 1.1: 2021-06-30
    Changes: Database references
  • Version 1.2: 2023-10-18
    Changes: Data collection, Database references, Refinement description