2CXC | pdb_00002cxc

Crystal structure of archaeal transcription termination factor NusA

• PDB DOI: https://doi.org/10.2210/pdb2CXC/pdb

• Classification: TRANSCRIPTION
• Organism(s): Aeropyrum pernix K1
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2005-06-28 Released: 2005-12-28 
• Deposition Author(s): Shibata, R., Bessho, Y., Shirouzu, M., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.211 (Depositor), 0.211 (DCC) 
• R-Value Work: 
  0.184 (Depositor), 0.184 (DCC) 

Literature

Crystal structure and RNA-binding analysis of the archaeal transcription factor NusA

Shibata, R., Bessho, Y., Shinkai, A., Nishimoto, M., Fusatomi, E., Terada, T., Shirouzu, M., Yokoyama, S.

(2007) Biochem Biophys Res Commun 355: 122-128

• PubMed: 17288993 
• DOI: https://doi.org/10.1016/j.bbrc.2007.01.119
• Primary Citation Related Structures: 
  2CXC


• PubMed Abstract: 
  

  The transcription factor NusA functions in transcriptional regulation involving termination in bacteria. A NusA homolog consisting of only the two KH domains is widely conserved in archaea, but its function remains unknown. We have found that Aeropyrum pernix NusA strongly binds to a certain CU-rich sequence near a termination signal. Our crystal structure of A. pernix NusA revealed that its spatial arrangement is quite similar to that of the KH domains of bacterial NusA. Thus, we consider archaeal NusA to have retained some functions of bacterial NusA, including the ssRNA-binding ability. Remarkable structural differences between archaeal and bacterial NusA exist at the interface with RNAP, in connection with the different NusA-binding sites around the termination signals. Transcriptional termination in archaea could differ from all of the known bacterial and eukaryal mechanisms, in terms of the combination of a bacterial factor and a eukaryal-type RNAP.

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Organizational Affiliation: 
• RIKEN Genomic Sciences Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 16.07 kDa 
• Atom Count: 1,134 
• Modeled Residue Count: 138 
• Deposited Residue Count: 144 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NusA	A	144	Aeropyrum pernix K1	Mutation(s): 0
UniProt
Find proteins for Q9YAU4 (Aeropyrum pernix (strain ATCC 700893 / DSM 11879 / JCM 9820 / NBRC 100138 / K1)) Explore Q9YAU4  Go to UniProtKB:  Q9YAU4

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.211 (Depositor), 0.211 (DCC) 
• R-Value Work:  0.184 (Depositor), 0.184 (DCC) 

Space Group: I 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 100.348	α = 90
b = 100.348	β = 90
c = 45.77	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
SOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-12-28 
Deposition Author(s): Shibata, R., Bessho, Y., Shirouzu, M., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History  

• Version 1.0: 2005-12-28
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.3: 2024-03-13
  Changes: Data collection, Database references