5H66 | pdb_00005h66

Crystal structure of the Bacillus subtilis SMC head domain complexed with the cognate ScpA C-terminal domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.82 Å
  • R-Value Free: 
    0.228 (Depositor), 0.228 (DCC) 
  • R-Value Work: 
    0.211 (Depositor), 0.213 (DCC) 
  • R-Value Observed: 
    0.212 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.3 of the entry. See complete history

Literature

Overall Shapes of the SMC-ScpAB Complex Are Determined by Balance between Constraint and Relaxation of Its Structural Parts

Kamada, K.Su'etsugu, M.Takada, H.Miyata, M.Hirano, T.

(2017) Structure 25: 603-616.e4

  • DOI: https://doi.org/10.1016/j.str.2017.02.008
  • Primary Citation Related Structures: 
    5H66, 5H67, 5H68, 5H69

  • PubMed Abstract: 

    The SMC-ScpAB complex plays a crucial role in chromosome organization and segregation in many bacteria. It is composed of a V-shaped SMC dimer and an ScpAB subcomplex that bridges the two Structural Maintenance of Chromosomes (SMC) head domains. Despite its functional significance, the mechanistic details of SMC-ScpAB remain obscure. Here we provide evidence that ATP-dependent head-head engagement induces a lever movement of the SMC neck region, which might help to separate juxtaposed coiled-coil arms. Binding of the ScpA N-terminal domain (NTD) to the SMC neck region is negatively regulated by the ScpB C-terminal domain. Mutations in the ScpA NTD compromise this regulation and profoundly affect the overall shape of the complex. The SMC hinge domain is structurally relaxed when free from coiled-coil juxtaposition. Taken together, we propose that the structural parts of SMC-ScpAB are subjected to the balance between constraint and relaxation, cooperating to modulate dynamic conformational changes of the whole complex.


  • Organizational Affiliation
    • Chromosome Dynamics Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan. Electronic address: kamadak@riken.jp.

Macromolecule Content 

  • Total Structure Weight: 53.27 kDa 
  • Atom Count: 3,636 
  • Modeled Residue Count: 435 
  • Deposited Residue Count: 467 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Chromosome partition protein Smc199Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: smcylqABSU15940
UniProt
Find proteins for P51834 (Bacillus subtilis (strain 168))
Explore P51834 
Go to UniProtKB:  P51834
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP51834
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Chromosome partition protein Smc188Bacillus subtilis subsp. subtilis str. 168Mutation(s): 1 
Gene Names: smcylqABSU15940
UniProt
Find proteins for P51834 (Bacillus subtilis (strain 168))
Explore P51834 
Go to UniProtKB:  P51834
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP51834
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Segregation and condensation protein A80Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: scpAypuGBSU23220
UniProt
Find proteins for P35154 (Bacillus subtilis (strain 168))
Explore P35154 
Go to UniProtKB:  P35154
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP35154
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.82 Å
  • R-Value Free:  0.228 (Depositor), 0.228 (DCC) 
  • R-Value Work:  0.211 (Depositor), 0.213 (DCC) 
  • R-Value Observed: 0.212 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 88.151α = 90
b = 46.905β = 112.65
c = 97.194γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
SCALEPACKdata scaling
PHASERphasing
PHENIXrefinement
HKL-2000data reduction

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Grants-in-Aid for Science ResearchJapan--

Revision History  (Full details and data files)

  • Version 1.0: 2017-03-15
    Type: Initial release
  • Version 1.1: 2017-04-19
    Changes: Database references
  • Version 1.2: 2020-02-26
    Changes: Data collection
  • Version 1.3: 2023-11-08
    Changes: Data collection, Database references, Refinement description