3DAV | pdb_00003dav

Schizosaccharomyces Pombe Profilin crystallized from Sodium formate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 
    0.260 (Depositor), 0.228 (DCC) 
  • R-Value Work: 
    0.174 (Depositor), 0.191 (DCC) 
  • R-Value Observed: 
    0.176 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 3DAV

This is version 1.3 of the entry. See complete history

Literature

Incompatibility with Formin Cdc12p Prevents Human Profilin from Substituting for Fission Yeast Profilin: INSIGHTS FROM CRYSTAL STRUCTURES OF FISSION YEAST PROFILIN.

Ezezika, O.C.Younger, N.S.Lu, J.Kaiser, D.A.Corbin, Z.A.Nolen, B.J.Kovar, D.R.Pollard, T.D.

(2009) J Biological Chem 284: 2088-2097

  • DOI: https://doi.org/10.1074/jbc.M807073200
  • Primary Citation Related Structures: 
    3D9Y, 3DAV

  • PubMed Abstract: 

    Expression of human profilin-I does not complement the temperature-sensitive cdc3-124 mutation of the single profilin gene in fission yeast Schizosaccharomyces pombe, resulting in death from cytokinesis defects. Human profilin-I and S. pombe profilin have similar affinities for actin monomers, the FH1 domain of fission yeast formin Cdc12p and poly-L-proline (Lu, J., and Pollard, T. D. (2001) Mol. Biol. Cell 12, 1161-1175), but human profilin-I does not stimulate actin filament elongation by formin Cdc12p like S. pombe profilin. Two crystal structures of S. pombe profilin and homology models of S. pombe profilin bound to actin show how the two profilins bind to identical surfaces on animal and yeast actins even though 75% of the residues on the profilin side of the interaction differ in the two profilins. Overexpression of human profilin-I in fission yeast expressing native profilin also causes cytokinesis defects incompatible with viability. Human profilin-I with the R88E mutation has no detectable affinity for actin and does not have this dominant overexpression phenotype. The Y6D mutation reduces the affinity of human profilin-I for poly-l-proline by 1000-fold, but overexpression of Y6D profilin in fission yeast is lethal. The most likely hypotheses to explain the incompatibility of human profilin-I with Cdc12p are differences in interactions with the proline-rich sequences in the FH1 domain of Cdc12p and wider "wings" that interact with actin.


  • Organizational Affiliation
    • Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06520-8103, USA.

Macromolecule Content 

  • Total Structure Weight: 27.05 kDa 
  • Atom Count: 2,108 
  • Modeled Residue Count: 252 
  • Deposited Residue Count: 254 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Profilin
A, B
127Schizosaccharomyces pombeMutation(s): 0 
Gene Names: cdc3SPAC4A8.15c
UniProt
Find proteins for P39825 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Explore P39825 
Go to UniProtKB:  P39825
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP39825
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NA

Query on NA



Download:Ideal Coordinates CCD File
C [auth A]
D [auth A]
E [auth A]
F [auth B]
G [auth B]
C [auth A],
D [auth A],
E [auth A],
F [auth B],
G [auth B],
H [auth B],
I [auth B],
J [auth B],
K [auth B]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free:  0.260 (Depositor), 0.228 (DCC) 
  • R-Value Work:  0.174 (Depositor), 0.191 (DCC) 
  • R-Value Observed: 0.176 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 35.873α = 90
b = 82.426β = 92.59
c = 39.742γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-12-16
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-10-25
    Changes: Refinement description
  • Version 1.3: 2023-08-30
    Changes: Data collection, Database references, Derived calculations, Refinement description