3WEE

Structure of the full-length yeast Arp7-Arp9 Heterodimer

• PDB DOI: https://doi.org/10.2210/pdb3WEE/pdb

• Classification: TRANSCRIPTION REGULATOR
• Organism(s): Saccharomyces cerevisiae S288C
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2013-07-06 Released: 2014-02-26 
• Deposition Author(s): Lobsiger, J., Richmond, T.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free: 0.220 
• R-Value Work: 0.199 
• R-Value Observed: 0.201 

Literature

Structure of the full-length yeast Arp7-Arp9 heterodimer.

Lobsiger, J., Hunziker, Y., Richmond, T.J.

(2014) Acta Crystallogr D Biol Crystallogr 70: 310-316

• PubMed: 24531465 
• DOI: https://doi.org/10.1107/S1399004713027417
• Primary Citation of Related Structures:  
  3WEE


• PubMed Abstract: 
  

  The nuclear actin-related proteins Arp7 and Arp9 are components of the yeast SWI/SNF and RSC chromatin-remodelling complexes. The 3.1 Å resolution crystal structure reported here shows that the full-length Arp7 and Arp9 proteins exist as a dimer without a requirement for additional polypeptides. Of the 11 actin-related proteins, Arp7 and Arp9 are the only two directly demonstrated to form a dimer within this family. The Arp7-Arp9 heterodimer is unlikely to form an actin-like filament based on modelling using the structure. The Arp7-Arp9 structure reveals that its dimerization interface is not altered when bound in a complex with the SWI/SNF Snf2 HSA domain and the regulatory protein Rtt102.

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Organizational Affiliation: 

Institute of Molecular Biology and Biophysics, Department of Biology, ETH Zürich, Schafmattstrasse 20, ETH-Hönggerberg, CH-8093 Zürich, Switzerland.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 111.01 kDa 
• Atom Count: 6,763 
• Modelled Residue Count: 840 
• Deposited Residue Count: 961 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Actin-like protein ARP9	A	476	Saccharomyces cerevisiae S288C	Mutation(s): 1  Gene Names: ARP9, SWP59, YM9973.07, YMR033W
UniProt
Find proteins for Q05123 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q05123  Go to UniProtKB:  Q05123

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Actin-related protein 7	B	485	Saccharomyces cerevisiae S288C	Mutation(s): 0  Gene Names: ARP7, SWP61, YP9367.14, YPR034W
UniProt
Find proteins for Q12406 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q12406  Go to UniProtKB:  Q12406

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CXS	D [auth B]	3-CYCLOHEXYL-1-PROPYLSULFONIC ACID C9 H19 N O3 S PJWWRFATQTVXHA-UHFFFAOYSA-N
SO4	C [auth A], E [auth B], F [auth B], G [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CMH	A	L-PEPTIDE LINKING	C4 H9 Hg N O2 S		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free: 0.220 
• R-Value Work: 0.199 
• R-Value Observed: 0.201 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 103.774	α = 90
b = 103.774	β = 90
c = 184.451	γ = 120

Software Package:

Software Name	Purpose
XDS	data scaling
PHENIX	model building
PHENIX	refinement
XDS	data reduction
SCALA	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-02-26 
Deposition Author(s): Lobsiger, J., Richmond, T.J.

Revision History  

• Version 1.0: 2014-02-26
  Type: Initial release
  
• Version 1.1: 2017-11-22
  Changes: Refinement description
• Version 1.2: 2019-12-18
  Changes: Database references, Derived calculations
• Version 1.3: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Structure summary