5I9E

Crystal structure of a nuclear actin ternary complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.232 
  • R-Value Observed: 0.234 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Crystal structure of a nuclear actin ternary complex.

Cao, T.Sun, L.Jiang, Y.Huang, S.Wang, J.Chen, Z.

(2016) Proc Natl Acad Sci U S A 113: 8985-8990

  • DOI: https://doi.org/10.1073/pnas.1602818113
  • Primary Citation of Related Structures:  
    5I9E

  • PubMed Abstract: 

    Actin polymerizes and forms filamentous structures (F-actin) in the cytoplasm of eukaryotic cells. It also exists in the nucleus and regulates various nucleic acid transactions, particularly through its incorporation into multiple chromatin-remodeling complexes. However, the specific structure of actin and the mechanisms that regulate its polymeric nature inside the nucleus remain unknown. Here, we report the crystal structure of nuclear actin (N-actin) complexed with actin-related protein 4 (Arp4) and the helicase-SANT-associated (HSA) domain of the chromatin remodeler Swr1. The inner face and barbed end of N-actin are sequestered by interactions with Arp4 and the HSA domain, respectively, which prevents N-actin from polymerization and binding to many actin regulators. The two major domains of N-actin are more twisted than those of globular actin (G-actin), and its nucleotide-binding pocket is occluded, freeing N-actin from binding to and regulation by ATP. These findings revealed the salient structural features of N-actin that distinguish it from its cytoplasmic counterpart and provide a rational basis for its functions and regulation inside the nucleus.


  • Organizational Affiliation

    Ministry of Education Key Laboratory of Protein Science, Tsinghua University, Beijing 100084, P.R. China; School of Life Science, Tsinghua University, Beijing 100084, P.R. China;


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Actin-related protein 4
A, C
490Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: ARP4ACT3YJL081CJ1012
UniProt
Find proteins for P80428 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P80428 
Go to UniProtKB:  P80428
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP80428
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Actin
B, D
375Saccharomyces bayanusMutation(s): 0 
Gene Names: ACT1
UniProt
Find proteins for P60011 (Saccharomyces bayanus)
Explore P60011 
Go to UniProtKB:  P60011
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP60011
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Helicase SWR1E [auth H],
F [auth E]
77Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SWR1YDR334WD9651.6
EC: 3.6.4.12
UniProt
Find proteins for Q05471 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q05471 
Go to UniProtKB:  Q05471
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ05471
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.232 
  • R-Value Observed: 0.234 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 110.26α = 90
b = 202.22β = 90
c = 87.01γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science FoundationChina31270762

Revision History  (Full details and data files)

  • Version 1.0: 2016-07-27
    Type: Initial release
  • Version 1.1: 2019-12-25
    Changes: Database references, Derived calculations, Structure summary
  • Version 1.2: 2023-11-08
    Changes: Data collection, Database references, Refinement description