1YAG

STRUCTURE OF THE YEAST ACTIN-HUMAN GELSOLIN SEGMENT 1 COMPLEX

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.193 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

The structure of nonvertebrate actin: Implications for the ATP hydrolytic mechanism

Vorobiev, S., Strokopytov, B., Drubin, D.G., Frieden, C., Ono, S., Condeelis, J., Rubenstein, P.A., Almo, S.C.

(2003) Proc Natl Acad Sci U S A 100: 5760-5765

  • DOI: 10.1073/pnas.0832273100
  • Primary Citation of Related Structures:  
    1D4X, 1NLV, 1NM1, 1NMD, 1YAG

  • PubMed Abstract: 

    • The structures of Saccharomyces cerevisiae, Dictyostelium, and Caenorhabditis elegans actin bound to gelsolin segment-1 have been solved and refined at resolutions between 1.9 and 1.75 A. These structures reveal several features relevant to the ATP hydrolytic mechanism, including identification of the nucleophilic water and the roles of Gln-137 and His-161 in positioning and activating the catalytic water, respectively ...

    The structures of Saccharomyces cerevisiae, Dictyostelium, and Caenorhabditis elegans actin bound to gelsolin segment-1 have been solved and refined at resolutions between 1.9 and 1.75 A. These structures reveal several features relevant to the ATP hydrolytic mechanism, including identification of the nucleophilic water and the roles of Gln-137 and His-161 in positioning and activating the catalytic water, respectively. The involvement of these residues in the catalytic mechanism is consistent with yeast genetics studies. This work highlights both structural and mechanistic similarities with the small and trimeric G proteins and restricts the types of mechanisms responsible for the considerable enhancement of ATP hydrolysis associated with actin polymerization. The conservation of functionalities involved in nucleotide binding and catalysis also provide insights into the mechanistic features of members of the family of actin-related proteins.

    Related Citations: 
    • The Structure of an Open State of Beta-Actin at 2.65 A Resolution
      Chik, J.K., Lindberg, U., Schutt, C.E.
      (1996) J Mol Biol 263: 607
    • Structure of Gelsolin Segment 1-Actin Complex and the Mechanism of Filament Severing
      Mclaughlin, P.J., Gooch, J.T., Mannherz, H.G., Weeds, A.G.
      (1993) Nature 364: 685
    • Atomic Structure of the Actin:DNase I Complex
      Kabsch, W., Mannherz, H.G., Suck, D., Pai, E.F., Holmes, K.C.
      (1990) Nature 347: 37
    Organizational Affiliation: 

    Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEIN (ACTIN)A375Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P60010 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P60010 
Go to UniProtKB:  P60010
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP60010
Protein Feature View
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  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEIN (GELSOLIN)B [auth G]125Homo sapiensMutation(s): 0 
Gene Names: GSN
UniProt & NIH Common Fund Data Resources
Find proteins for P06396 (Homo sapiens)
Explore P06396 
Go to UniProtKB:  P06396
PHAROS:  P06396
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP06396
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP
Download Ideal Coordinates CCD File 
E [auth A]ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N		 Ligand Interaction
SO4
Query on SO4
Download Ideal Coordinates CCD File 
D [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L		 Ligand Interaction
CA
Query on CA
Download Ideal Coordinates CCD File 
F [auth G]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N		 Ligand Interaction
MG
Query on MG
Download Ideal Coordinates CCD File 
C [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.193 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 176.662α = 90
b = 68.099β = 102.55
c = 54.598γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
X-PLORrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1999-10-09
    Type: Initial release
  • Version 1.1: 2007-10-16
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance