4OAV

Complete human RNase L in complex with 2-5A (5'-ppp heptamer), AMPPCP and RNA substrate.

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.198 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history. 

Literature

Structure of human RNase L reveals the basis for regulated RNA decay in the IFN response.

Han, Y., Donovan, J., Rath, S., Whitney, G., Chitrakar, A., Korennykh, A.

(2014) Science 343: 1244-1248

  • DOI: 10.1126/science.1249845
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • One of the hallmark mechanisms activated by type I interferons (IFNs) in human tissues involves cleavage of intracellular RNA by the kinase homology endoribonuclease RNase L. We report 2.8 and 2.1 angstrom crystal structures of human RNase L in compl ...

    One of the hallmark mechanisms activated by type I interferons (IFNs) in human tissues involves cleavage of intracellular RNA by the kinase homology endoribonuclease RNase L. We report 2.8 and 2.1 angstrom crystal structures of human RNase L in complexes with synthetic and natural ligands and a fragment of an RNA substrate. RNase L forms a crossed homodimer stabilized by ankyrin (ANK) and kinase homology (KH) domains, which positions two kinase extension nuclease (KEN) domains for asymmetric RNA recognition. One KEN protomer recognizes an identity nucleotide (U), whereas the other protomer cleaves RNA between nucleotides +1 and +2. The coordinated action of the ANK, KH, and KEN domains thereby provides regulated, sequence-specific cleavage of viral and host RNA targets by RNase L.

    Organizational Affiliation: 

    Department of Molecular Biology, Princeton University, 216 Schultz Laboratory, Princeton, NJ 08540, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (RNase L)
B, D
699Homo sapiensMutation(s): 1 
Gene Names: RNASEL (RNS4)
EC: 3.1.26.-
Find proteins for Q05823 (Homo sapiens)
Go to Gene View: RNASEL
Go to UniProtKB:  Q05823
Entity ID: 2
MoleculeChainsLengthOrganism
RNA (5'-R(P*(PO4)P*(PO4)P*AP*AP*AP*AP*(PO4))-2')A,C7N/A
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG
Download SDF File 
Download CCD File 
B, D
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
PUP
Query on PUP
Download SDF File 
Download CCD File 
D
(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-4-hydroxy-2-({[(S)-hydroxy{[(2R,3S,4S)-4-hydroxy-2-(hydroxymethyl)tetrahydrofuran-3-yl]oxy}phosphoryl]oxy}methyl)tetrahydrofuran-3-yl dihydrogen phosphate
C14 H22 N2 O15 P2
CTEYAHSJKMGMOL-HHUJUQMJSA-N
 Ligand Interaction
ACP
Query on ACP
Download SDF File 
Download CCD File 
B, D
PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER
ADENOSINE-5'-[BETA, GAMMA-METHYLENE]TRIPHOSPHATE
C11 H18 N5 O12 P3
UFZTZBNSLXELAL-IOSLPCCCSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
PO4
Query on PO4
A, C
NON-POLYMERO4 P

--

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.198 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 58.610α = 90.00
b = 160.700β = 90.00
c = 230.800γ = 90.00
Software Package:
Software NamePurpose
PHENIXmodel building
XDSdata reduction
PHENIXrefinement
PHENIXphasing
CBASSdata collection
XDSdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-03-12
    Type: Initial release
  • Version 1.1: 2014-04-02
    Type: Database references