4E61 | pdb_00004e61

Crystal structure of the EB1-like motif of Bim1p

• PDB DOI: https://doi.org/10.2210/pdb4E61/pdb

• Classification: CELL CYCLE
• Organism(s): Saccharomyces cerevisiae
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-03-15 Released: 2012-04-11 
• Deposition Author(s): Huels, D., Storchova, Z., Niessing, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.45 Å
• R-Value Free: 
  0.241 (Depositor), 0.271 (DCC) 
• R-Value Work: 
  0.211 (Depositor), 0.226 (DCC) 

Starting Model: experimental

Literature

Post-translational Modifications Regulate Assembly of Early Spindle Orientation Complex in Yeast.

Huls, D., Storchova, Z., Niessing, D.

(2012) J Biological Chem 287: 16238-16245

• PubMed: 22461628 
• DOI: https://doi.org/10.1074/jbc.M112.347872
• Primary Citation Related Structures: 
  4E61


• PubMed Abstract: 
  

  Mitosis begins with the tethering of chromosomes to the mitotic spindle and their orientation perpendicular to the axis of cell division. In budding yeast, mitotic spindle orientation and the subsequent chromosome segregation are two independent processes. Early spindle orientation is driven by the actin-bound myosin Myo2p, which interacts with the adapter Kar9p. The latter also binds to microtubule-associated Bim1p, thereby connecting both types of cytoskeleton. This study focuses on the interaction between Kar9p and Bim1p and its regulation. We solved the crystal structure of the previously reported Kar9p-binding motif of Bim1p and identified a second, novel Kar9p interaction domain. We further show that two independent post-translational modification events regulate their interaction. Whereas Kar9p sumoylation is required for efficient complex formation with Bim1p, Aurora B/Ipl1p-dependent phosphorylation of Bim1p down-regulates their interaction. The observed effects of these modifications allow us to propose a novel regulatory framework for the assembly and disassembly of the early spindle orientation complex.

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Organizational Affiliation: 
• Institute of Structural Biology, Helmholtz Zentrum München-German Research Center for Environmental Health, 85764 Neuherberg, Germany.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 23.62 kDa 
• Atom Count: 1,363 
• Modeled Residue Count: 175 
• Deposited Residue Count: 212 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein BIM1	A, B	106	Saccharomyces cerevisiae	Mutation(s): 0  Gene Names: BIM1, YER016W
UniProt
Find proteins for P40013 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P40013  Go to UniProtKB:  P40013

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.45 Å
• R-Value Free:  0.241 (Depositor), 0.271 (DCC) 
• R-Value Work:  0.211 (Depositor), 0.226 (DCC) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 28	α = 90
b = 42.5	β = 90.3
c = 100.5	γ = 90

Software Package:

Software Name	Purpose
XCUBE	data collection
SHELX	model building
SHELXD	phasing
SHELXE	model building
BUSTER-TNT	refinement
XDS	data reduction
XSCALE	data scaling
SHELX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-04-11 
Deposition Author(s): Huels, D., Storchova, Z., Niessing, D.

Revision History  

• Version 1.0: 2012-04-11
  Type: Initial release
  
• Version 1.1: 2012-06-13
  Changes: Database references
• Version 1.2: 2017-11-15
  Changes: Refinement description
• Version 1.3: 2024-02-28
  Changes: Data collection, Database references
• Version 1.4: 2024-04-03
  Changes: Refinement description