8PV0 | pdb_00008pv0

Crystal structure of tropomyosin (Cdc8) cables, Conformers 2 and 3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.43 Å
  • R-Value Free: 
    0.311 (Depositor), 0.310 (DCC) 
  • R-Value Work: 
    0.251 (Depositor), 0.250 (DCC) 
  • R-Value Observed: 
    0.255 (Depositor) 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Crystal structures of cables formed by the acetylated and unacetylated forms of the Schizosaccharomyces pombe tropomyosin ortholog Tpm Cdc8.

Reinke, P.Y.A.Heiringhoff, R.S.Reindl, T.Baker, K.Taft, M.H.Meents, A.Mulvihill, D.P.Davies, O.R.Fedorov, R.Zahn, M.Manstein, D.J.

(2024) J Biological Chem 300: 107925-107925

  • DOI: https://doi.org/10.1016/j.jbc.2024.107925
  • Primary Citation of Related Structures:  
    8PUZ, 8PV0, 9FF9

  • PubMed Abstract: 

    Cables formed by head-to-tail polymerization of tropomyosin, localized along the length of sarcomeric and cytoskeletal actin filaments, play a key role in regulating a wide range of motile and contractile processes. The stability of tropomyosin cables, their interaction with actin filaments and the functional properties of the resulting co-filaments are thought to be affected by N-terminal acetylation of tropomyosin. Here, we present high-resolution structures of cables formed by acetylated and unacetylated Schizosaccharomyces pombe tropomyosin orthologue Tpm Cdc8 . The crystal structures represent different types of cables, each consisting of Tpm Cdc8 homodimers in a different conformation. The structures show how the interactions of the residues in the overlap junction contribute to cable formation and how local structural perturbations affect the conformational dynamics of the protein and its ability to transmit allosteric signals. In particular, N-terminal acetylation increases the helicity of the adjacent region, which leads to a local reduction in conformational dynamics and consequently to less fraying of the N-terminal region. This creates a more consistent complementary surface facilitating the formation of specific interactions across the overlap junction.


  • Organizational Affiliation
    • Institute for Biophysical Chemistry, Fritz-Hartmann-Centre for Medical Research, Hannover Medical School, 30625 Hannover, Germany,; Division for Structural Biochemistry, Hannover Medical School, 30625 Hannover, Germany,; FS-BMX, Deutsches Elektronen-Synchrotron DESY, Notkestraße 85, 22607 Hamburg, Germany.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Tropomyosin
A, B, C, D
161Schizosaccharomyces pombeMutation(s): 0 
Gene Names: cdc8SPAC27F1.02c
UniProt
Find proteins for Q02088 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Explore Q02088 
Go to UniProtKB:  Q02088
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ02088
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C, D
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.43 Å
  • R-Value Free:  0.311 (Depositor), 0.310 (DCC) 
  • R-Value Work:  0.251 (Depositor), 0.250 (DCC) 
  • R-Value Observed: 0.255 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.499α = 90
b = 77.667β = 94.2
c = 108.224γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PARROTphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)GermanyAB 1234/1-1

Revision History  (Full details and data files)

  • Version 1.0: 2024-07-24
    Type: Initial release
  • Version 1.1: 2024-10-16
    Changes: Structure summary
  • Version 1.2: 2024-11-06
    Changes: Database references, Derived calculations
  • Version 1.3: 2024-12-04
    Changes: Database references, Derived calculations
  • Version 1.4: 2025-04-02
    Changes: Derived calculations