Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 62.20 kDa 
• Atom Count: 4487 
• Modelled Residue Count: 515 
• Deposited Residue Count: 538 
• Unique protein chains: 1

1YQT

RNase-L Inhibitor

• DOI: 10.2210/pdb1YQT/pdb

• Classification: hydrolyase/translation
• Organism(s): Pyrococcus furiosus
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2005-02-02 Released: 2005-04-19 
• Deposition Author(s): Karcher, A., Buttner, K., Martens, B., Jansen, R.P., Hopfner, K.P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.225 
• R-Value Work: 0.199 
• R-Value Observed: 0.199 

Literature

X-ray structure of RLI, an essential twin cassette ABC ATPase involved in ribosome biogenesis and HIV capsid assembly.

Karcher, A., Buttner, K., Martens, B., Jansen, R.P., Hopfner, K.P.

(2005) Structure 13: 649-659

• PubMed: 15837203 
• DOI: 10.1016/j.str.2005.02.008
• Primary Citation of Related Structures:  
  1YQT


• PubMed Abstract: 
  

The ABC ATPase RNase-L inhibitor (RLI) emerges as a key enzyme in ribosome biogenesis, formation of translation preinitiation complexes, and assembly of HIV capsids. To help reveal the structural mechanism of RLI, we determined the Mg2+-ADP bound crystal structure of the twin cassette ATPase of P. furiosus RLI at 1.9 A resolution and analyzed functional motifs in yeast in vivo. RLI shows similarities but also differences to known ABC enzyme structures. Twin nucleotide binding domains (NBD1 and NBD2) are arranged to form two composite active sites in their interface cleft, indicating they undergo the ATP-driven clamp-like motion of the NBDs of ABC transporters. An unusual "hinge" domain along the NBD1:NBD2 interface provides a frame for association and possibly ATP-driven conformational changes of the NBDs. Our results establish a first structural basis for ABC domain heterodimers and suggest that RLI may act as mechanochemical enzyme in ribosome and HIV capsid biogenesis.

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Organizational Affiliation: 

Gene Center, Department of Chemistry and Biochemistry, University of Munich, Feodor-Lynen-Strasse 25, D-81377 Munich, Germany.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RNase l inhibitor	A	538	Pyrococcus furiosus	Mutation(s): 8
Find proteins for Q8U306 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)) Explore Q8U306  Go to UniProtKB:  Q8U306

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADP	D [auth A], E [auth A]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N
MG	B [auth A], C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	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: 0.225 
• R-Value Work: 0.199 
• R-Value Observed: 0.199 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.68	α = 90
b = 74.64	β = 90
c = 123.69	γ = 90

Software Package:

Software Name	Purpose
TRUNCATE	data reduction
SHARP	phasing
CNS	refinement
CCP4	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2005-02-02 
• Released Date: 2005-04-19 
Deposition Author(s): Karcher, A., Buttner, K., Martens, B., Jansen, R.P., Hopfner, K.P.

Revision History  

• Version 1.0: 2005-04-19
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-11
  Changes: Advisory, Refinement description