4PL7

Structure of Komagataella pastoris actin-thymosin beta4 hybrid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.198 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Structural basis of thymosin-beta 4/profilin exchange leading to actin filament polymerization.

Xue, B.Leyrat, C.Grimes, J.M.Robinson, R.C.

(2014) Proc Natl Acad Sci U S A 111: E4596-E4605

  • DOI: 10.1073/pnas.1412271111
  • Primary Citation of Related Structures:  
    4PL7, 4PL8

  • PubMed Abstract: 
  • Thymosin-β4 (Tβ4) and profilin are the two major sequestering proteins that maintain the pool of monomeric actin (G-actin) within cells of higher eukaryotes. Tβ4 prevents G-actin from joining a filament, whereas profilin:actin only supports barbed-end elongation ...

    Thymosin-β4 (Tβ4) and profilin are the two major sequestering proteins that maintain the pool of monomeric actin (G-actin) within cells of higher eukaryotes. Tβ4 prevents G-actin from joining a filament, whereas profilin:actin only supports barbed-end elongation. Here, we report two Tβ4:actin structures. The first structure shows that Tβ4 has two helices that bind at the barbed and pointed faces of G-actin, preventing the incorporation of the bound G-actin into a filament. The second structure displays a more open nucleotide binding cleft on G-actin, which is typical of profilin:actin structures, with a concomitant disruption of the Tβ4 C-terminal helix interaction. These structures, combined with biochemical assays and molecular dynamics simulations, show that the exchange of bound actin between Tβ4 and profilin involves both steric and allosteric components. The sensitivity of profilin to the conformational state of actin indicates a similar allosteric mechanism for the dissociation of profilin during filament elongation.


    Organizational Affiliation

    Institute of Molecular and Cell Biology, A*STAR (Agency for Science, Technology and Research), Biopolis, Singapore 138673; Department of Biochemistry, National University of Singapore, Singapore 117597.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Actin,Thymosin beta-4A, B440Komagataella phaffii GS115Homo sapiens
This entity is chimeric
Mutation(s): 0 
Gene Names: ACT1PAS_chr3_1169TMSB4XTB4XTHYB4TMSB4
UniProt & NIH Common Fund Data Resources
Find proteins for Q9P4D1 (Komagataella phaffii (strain GS115 / ATCC 20864))
Explore Q9P4D1 
Go to UniProtKB:  Q9P4D1
Find proteins for P62328 (Homo sapiens)
Explore P62328 
Go to UniProtKB:  P62328
PHAROS:  P62328
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsQ9P4D1P62328
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

Download Ideal Coordinates CCD File 
C [auth A],
E [auth B]
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
 Ligand Interaction
CA
Query on CA

Download Ideal Coordinates CCD File 
D [auth A],
F [auth B]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.198 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.508α = 90
b = 139.495β = 116.21
c = 56.485γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
DENZOdata collection
SCALEPACKdata reduction
PHASERphasing
PDB_EXTRACTdata extraction
Cootmodel building
PHASERmodel building
PHENIXrefinement
DENZOdata reduction
SCALEPACKdata 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: 2014-10-22
    Type: Initial release
  • Version 1.1: 2014-11-12
    Changes: Database references