4RS7 | pdb_00004rs7

Structure of pNOB8 ParB-C

• PDB DOI: https://doi.org/10.2210/pdb4RS7/pdb

• Classification: DNA BINDING PROTEIN
• Organism(s): Sulfolobus sp. NOB8H2
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2014-11-07 Released: 2015-09-16 
• Deposition Author(s): Schumacher, M.A., Lee, J., Chinnam, N.B., Barilla, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.224 (Depositor), 0.194 (DCC) 
• R-Value Work: 
  0.193 (Depositor), 0.191 (DCC) 
• R-Value Observed: 
  0.195 (Depositor) 

Literature

Structures of archaeal DNA segregation machinery reveal bacterial and eukaryotic linkages.

Schumacher, M.A., Tonthat, N.K., Lee, J., Rodriguez-Castaneda, F.A., Chinnam, N.B., Kalliomaa-Sanford, A.K., Ng, I.W., Barge, M.T., Shaw, P.L., Barilla, D.

(2015) Science 349: 1120-1124

• PubMed: 26339031 
• DOI: https://doi.org/10.1126/science.aaa9046
• Primary Citation of Related Structures:  
  4RS7, 4RS8, 5K5A, 5K5D, 5K5O, 5K5Q, 5K5R, 5K5Z


• PubMed Abstract: 
  

  Although recent studies have provided a wealth of information about archaeal biology, nothing is known about the molecular basis of DNA segregation in these organisms. Here, we unveil the machinery and assembly mechanism of the archaeal Sulfolobus pNOB8 partition system. This system uses three proteins: ParA; an atypical ParB adaptor; and a centromere-binding component, AspA. AspA utilizes a spreading mechanism to create a DNA superhelix onto which ParB assembles. This supercomplex links to the ParA motor, which contains a bacteria-like Walker motif. The C domain of ParB harbors structural similarity to CenpA, which dictates eukaryotic segregation. Thus, this archaeal system combines bacteria-like and eukarya-like components, which suggests the possible conservation of DNA segregation principles across the three domains of life.

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Organizational Affiliation: 
• Department of Biochemistry, Duke University School of Medicine, 243 Nanaline H. Duke, Box 3711, Durham, NC 27710, USA. [e-mail] [e-mail].
Department of Biochemistry, Duke University School of Medicine, 243 Nanaline H. Duke, Box 3711, Durham, NC 27710, USA.
Department of Biology, University of York, York YO10 5DD, UK.
Department of Biology, University of York, York YO10 5DD, UK. [e-mail] [e-mail].

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)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 46.9 kDa 
• Atom Count: 3,353 
• Modeled Residue Count: 349 
• Deposited Residue Count: 384 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ParB-C	A [auth R], B [auth D], C [auth A], D [auth B]	96	Sulfolobus sp. NOB8H2	Mutation(s): 0

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A [auth R], B [auth D], C [auth A], D [auth B]	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.224 (Depositor), 0.194 (DCC) 
• R-Value Work:  0.193 (Depositor), 0.191 (DCC) 
• R-Value Observed: 0.195 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.21	α = 90
b = 56.06	β = 94.4
c = 72.3	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
SOLVE	phasing
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-09-16 
Deposition Author(s): Schumacher, M.A., Lee, J., Chinnam, N.B., Barilla, D.

Revision History  

• Version 1.0: 2015-09-16
  Type: Initial release
  
• Version 1.1: 2024-10-16
  Changes: Data collection, Database references, Derived calculations, Structure summary