5H67

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.07 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.192 

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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: 10.1016/j.str.2017.02.008
  • Primary Citation of 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 ...

    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.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Chromosome partition protein SmcA199Bacillus 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
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Chromosome partition protein SmcB188Bacillus 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
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Segregation and condensation protein AC80Bacillus 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
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

Download Ideal Coordinates CCD File 
D [auth A]ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.07 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.192 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 88.009α = 90
b = 47.124β = 112.594
c = 97.698γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
PHENIXrefinement

Structure Validation

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Ligand Structure Quality Assessment 



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2016-11-11 
  • Released Date: 2017-03-15 
  • Deposition Author(s): Kamada, K., Hirano, T.

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