Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 76.25 kDa 
• Atom Count: 5443 
• Modelled Residue Count: 657 
• Deposited Residue Count: 680 
• Unique protein chains: 1

5H68

Crystal structure of an engaged dimer of the Geobacillus stearothermophilus SMC head domain

• PDB DOI: 10.2210/pdb5H68/pdb

• Classification: DNA BINDING PROTEIN, CELL CYCLE
• Organism(s): Geobacillus stearothermophilus 10
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2016-11-11 Released: 2017-03-15 
• Deposition Author(s): Kamada, K., Hirano, T.
• Funding Organization(s): Grants-in-Aid for Science Research

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.98 Å
• R-Value Free: 0.232 
• R-Value Work: 0.189 
• R-Value Observed: 0.191 

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

• PubMed: 28286005 
• 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. 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.

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Organizational Affiliation: 

Chromosome Dynamics Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Chromosome partition protein Smc	A, B	340	Geobacillus stearothermophilus 10	Mutation(s): 1  Gene Names: smc, GT50_02560

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AGS	C [auth A], E [auth B]	PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER C10 H16 N5 O12 P3 S NLTUCYMLOPLUHL-KQYNXXCUSA-N
MG	D [auth A], F [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.98 Å
• R-Value Free: 0.232 
• R-Value Work: 0.189 
• R-Value Observed: 0.191 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.339	α = 90
b = 65.835	β = 108.11
c = 77.923	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
SCALEPACK	data scaling
PHASER	phasing
PHENIX	refinement
HKL-2000	data reduction

Structure Validation

Entry History & Funding Information

Deposition Data

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

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Funding Organization	Location	Grant Number
Grants-in-Aid for Science Research	Japan	--

Revision History  

• 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