1D4X

Crystal Structure of Caenorhabditis Elegans Mg-ATP Actin Complexed with Human Gelsolin Segment 1 at 1.75 A resolution.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.231 

wwPDB Validation   3D Report Full Report


This is version 1.3 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, 1YAG, 1NMD, 1NLV, 1NM1

  • 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: 
    • Structure of gelsolin segment 1-actin complex and mechanosm 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)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
C. ELEGANS ACTIN 1/3A375Caenorhabditis elegansMutation(s): 0 
Gene Names: act-1T04C12.6
UniProt
Find proteins for P0DM41 (Caenorhabditis elegans)
Explore P0DM41 
Go to UniProtKB:  P0DM41
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
GELSOLINB [auth G]126Homo 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
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ATP (Subject of Investigation/LOI)
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
SO2
Query on SO2

Download Ideal Coordinates CCD File 
F [auth A]SULFUR DIOXIDE
O2 S
RAHZWNYVWXNFOC-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download Ideal Coordinates CCD File 
GCALCIUM 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: 1.75 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.231 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 177.82α = 90
b = 68.989β = 104.15
c = 56.593γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building
X-PLORrefinement
X-PLORphasing

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2001-05-02
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2021-07-07
    Changes: Derived calculations, Refinement description