1ATN

Atomic structure of the actin:DNASE I complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Work: 0.210 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Atomic structure of the actin:DNase I complex.

Kabsch, W.Mannherz, H.G.Suck, D.Pai, E.F.Holmes, K.C.

(1990) Nature 347: 37-44

  • DOI: 10.1038/347037a0

  • PubMed Abstract: 
  • The atomic models of the complex between rabbit skeletal muscle actin and bovine pancreatic deoxyribonuclease I both in the ATP and ADP forms have been determined by X-ray analysis at an effective resolution of 2.8 A and 3A, respectively. The two str ...

    The atomic models of the complex between rabbit skeletal muscle actin and bovine pancreatic deoxyribonuclease I both in the ATP and ADP forms have been determined by X-ray analysis at an effective resolution of 2.8 A and 3A, respectively. The two structures are very similar. The actin molecule consists of two domains which can be further subdivided into two subdomains. ADP or ATP is located in the cleft between the domains with a calcium ion bound to the beta- or beta- and gamma-phosphates, respectively. The motif of a five-stranded beta sheet consisting of a beta meander and a right handed beta alpha beta unit appears in each domain suggesting that gene duplication might have occurred. These sheets have the same topology as that found in hexokinase.


    Related Citations: 
    • Crystallographic Refinement and Structure of DNase I at 2 Angstroms Resolution
      Oefner, C.,Suck, D.
      (1986) J.Mol.Biol. 192: 605
    • Structure and Function of Actin
      Kabsch, W.,Vandekerckhove, J.
      (1992) Annu.Rev.Biophys.Biophys.Chem. 21: 49
    • Three-Dimensional Structure of the Complex of Actin and DNase I at 4.5 Angstroms Resolution
      Kabsch, W.,Mannherz, H.G.,Suck, D.
      (1985) Embo J. 4: 2113
    • Similarity of the Three-Dimensional Structures of Actin and the ATPase Fragment of a 70-kDa Heat Shock Cognate Protein
      Flaherty, K.M.,Mckay, D.B.,Kabsch, W.,Holmes, K.C.
      (1991) Proc.Natl.Acad.Sci.USA 88: 5041
    • Three-Dimensional Structure of the Complex of Skeletal Muscle Actin and Bovine Pancreatic DNase I at 6-Angstroms Resolution
      Suck, D.,Kabsch, W.,Mannherz, H.G.
      (1981) Proc.Natl.Acad.Sci.USA 78: 4319
    • Three-Dimensional Structure of Bovine Pancreatic DNase I at 2.5 Angstroms Resolution
      Suck, D.,Oefner, C.,Kabsch, W.
      (1984) Embo J. 3: 2423
    • Muscle Proteins: Actin
      Holmes, K.C.,Kabsch, W.
      (1991) Curr.Opin.Struct.Biol. 1: 270
    • Atomic Model of the Actin Filament
      Holmes, K.C.,Popp, D.,Gebhard, W.,Kabsch, W.
      (1990) Nature 347: 44


    Organizational Affiliation

    Max-Planck-Institut für medizinische Forschung, Abteilung Biophysik, Heidelberg, FRG.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ACTIN
A
373Oryctolagus cuniculusGene Names: ACTA1 (ACTA)
Find proteins for P68135 (Oryctolagus cuniculus)
Go to Gene View: ACTA1
Go to UniProtKB:  P68135
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
DEOXYRIBONUCLEASE I
D
260Bos taurusGene Names: DNASE1 (DNL1)
EC: 3.1.21.1
Find proteins for P00639 (Bos taurus)
Go to Gene View: DNASE1
Go to UniProtKB:  P00639
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

Download SDF File 
Download CCD File 
A
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
 Ligand Interaction
CA
Query on CA

Download SDF File 
Download CCD File 
A, D
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
BMA
Query on BMA

Download SDF File 
Download CCD File 
D
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
NDG
Query on NDG

Download SDF File 
Download CCD File 
D
2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
C8 H15 N O6
OVRNDRQMDRJTHS-PVFLNQBWSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
D
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
HIC
Query on HIC
A
L-PEPTIDE LINKINGC7 H11 N3 O2HIS
ACE
Query on ACE
A
NON-POLYMERC2 H4 O

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Work: 0.210 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 132.900α = 90.00
b = 56.300β = 90.00
c = 109.700γ = 90.00
Software Package:
Software NamePurpose
X-PLORrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1992-07-15
    Type: Initial release
  • Version 1.1: 2008-03-03
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance
  • Version 1.3: 2017-11-29
    Type: Derived calculations, Other