2A5X

Crystal Structure of a Cross-linked Actin Dimer


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.49 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.197 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

The crystal structure of a cross-linked actin dimer suggests a detailed molecular interface in F-actin

Kudryashov, D.S.Sawaya, M.R.Adisetiyo, H.Norcross, T.Hegyi, G.Reisler, E.Yeates, T.O.

(2005) Proc Natl Acad Sci U S A 102: 13105-13110

  • DOI: 10.1073/pnas.0506429102
  • Primary Citation of Related Structures:  
    2A5X

  • PubMed Abstract: 
  • The 2.5-A resolution crystal structure is reported for an actin dimer, composed of two protomers cross-linked along the longitudinal (or vertical) direction of the F-actin filament. The crystal structure provides an atomic resolution view of a molecular interface between actin protomers, which we argue represents a near-native interaction in the F-actin filament ...

    The 2.5-A resolution crystal structure is reported for an actin dimer, composed of two protomers cross-linked along the longitudinal (or vertical) direction of the F-actin filament. The crystal structure provides an atomic resolution view of a molecular interface between actin protomers, which we argue represents a near-native interaction in the F-actin filament. The interaction involves subdomains 3 and 4 from distinct protomers. The atomic positions in the interface visualized differ by 5-10 A from those suggested by previous models of F-actin. Such differences fall within the range of uncertainties allowed by the fiber diffraction and electron microscopy methods on which previous models have been based. In the crystal, the translational arrangement of protomers lacks the slow twist found in native filaments. A plausible model of F-actin can be constructed by reintroducing the known filament twist, without disturbing significantly the interface observed in the actin dimer crystal.


    Organizational Affiliation

    Department of Chemistry and Biochemistry and Molecular Biology Institute, University of California, Los Angeles, CA 90095, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Actin, alpha skeletal muscleA375Oryctolagus cuniculusMutation(s): 0 
Gene Names: ACTA1ACTA
Find proteins for P68135 (Oryctolagus cuniculus)
Explore P68135 
Go to UniProtKB:  P68135
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ANP
Query on ANP

Download Ideal Coordinates CCD File 
D [auth A]PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
C10 H17 N6 O12 P3
PVKSNHVPLWYQGJ-KQYNXXCUSA-N
 Ligand Interaction
LAR
Query on LAR

Download Ideal Coordinates CCD File 
E [auth A]LATRUNCULIN A
C22 H31 N O5 S
DDVBPZROPPMBLW-IZGXTMSKSA-N
 Ligand Interaction
NSB
Query on NSB

Download Ideal Coordinates CCD File 
F [auth A]N,N,N-TRIMETHYL-3-SULFOPROPAN-1-AMINIUM
C6 H16 N O3 S
WFJHXXPYPMNRPK-UHFFFAOYSA-O
 Ligand Interaction
MPD
Query on MPD

Download Ideal Coordinates CCD File 
G [auth A], H [auth A](4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
 Ligand Interaction
CA
Query on CA

Download Ideal Coordinates CCD File 
B [auth A], C [auth A]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
LARIC50:  70   nM  BindingDB
LARIC50:  40   nM  BindingDB
LARIC50:  110   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.49 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.197 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 207.377α = 90
b = 54.372β = 98.62
c = 36.2γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
Blu-Icedata collection
SCALEPACKdata scaling
EPMRphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-08-23
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.3: 2017-10-11
    Changes: Refinement description