3U4L | pdb_00003u4l

Cryocooled bovine profilin:actin crystal structure to 2.4 A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 
    0.331 (Depositor), 0.328 (DCC) 
  • R-Value Work: 
    0.244 (Depositor), 0.243 (DCC) 
  • R-Value Observed: 
    0.249 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Structural basis for profilin-mediated actin nucleotide exchange.

Porta, J.C.Borgstahl, G.E.

(2012) J Mol Biology 418: 103-116

  • DOI: https://doi.org/10.1016/j.jmb.2012.02.012
  • Primary Citation Related Structures: 
    3U4L, 3UB5

  • PubMed Abstract: 

    Actin is a ubiquitous eukaryotic protein that is responsible for cellular scaffolding, motility, and division. The ability of actin to form a helical filament is the driving force behind these cellular activities. Formation of a filament depends on the successful exchange of actin's ADP for ATP. Mammalian profilin is a small actin binding protein that catalyzes the exchange of nucleotide and facilitates the addition of an actin monomer to a growing filament. Here, crystal structures of profilin-actin have been determined to show an actively exchanging ATP. Structural analysis shows how the binding of profilin to the barbed end of actin causes a rotation of the small domain relative to the large domain. This conformational change is propagated to the ATP site and causes a shift in nucleotide loops, which in turn causes a repositioning of Ca(2+) to its canonical position as the cleft closes around ATP. Reversal of the solvent exposure of Trp356 is also involved in cleft closure. In addition, secondary calcium binding sites were identified.


  • Organizational Affiliation
    • Department of Biochemistry and Molecular Biology, 987696 Nebraska Medical Center, Omaha, NE 68198-7696, USA.

Macromolecule Content 

  • Total Structure Weight: 57.34 kDa 
  • Atom Count: 3,810 
  • Modeled Residue Count: 493 
  • Deposited Residue Count: 515 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Actin, cytoplasmic 1375Bos taurusMutation(s): 0 
EC: 3.6.4
UniProt
Find proteins for P60712 (Bos taurus)
Explore P60712 
Go to UniProtKB:  P60712
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP60712
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Profilin-1B [auth P]140Bos taurusMutation(s): 1 
UniProt
Find proteins for P02584 (Bos taurus)
Explore P02584 
Go to UniProtKB:  P02584
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02584
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free:  0.331 (Depositor), 0.328 (DCC) 
  • R-Value Work:  0.244 (Depositor), 0.243 (DCC) 
  • R-Value Observed: 0.249 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 38.3α = 90
b = 71.1β = 90
c = 171.5γ = 90
Software Package:
Software NamePurpose
CrystalCleardata collection
REFMACrefinement
EVAL15data reduction
SADABSdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-04-25
    Type: Initial release
  • Version 1.1: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.2: 2024-10-16
    Changes: Structure summary