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: 2.10 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.200 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


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:  
    4OAU, 4OAV

  • 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 complexes with synthetic and natural ligands and a fragment of an RNA substrate ...

    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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEIN (RNase L)A [auth B],
C [auth D]
699Homo sapiensMutation(s): 1 
Gene Names: RNASELRNS4
EC: 3.1.26
UniProt & NIH Common Fund Data Resources
Find proteins for Q05823 (Homo sapiens)
Explore Q05823 
Go to UniProtKB:  Q05823
PHAROS:  Q05823
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ05823
Protein Feature View
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  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChainsLengthOrganismImage
RNA (5'-R(P*(PO4)P*(PO4)P*AP*AP*AP*AP*(PO4))-2')B [auth A],
D [auth C]
7N/A
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PUP
Query on PUP

Download Ideal Coordinates CCD File 
K [auth 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 Ideal Coordinates CCD File 
E [auth B],
H [auth D]
PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER
C11 H18 N5 O12 P3
UFZTZBNSLXELAL-IOSLPCCCSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
F [auth B],
G [auth B],
I [auth D],
J [auth D]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.200 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.61α = 90
b = 160.7β = 90
c = 230.8γ = 90
Software Package:
Software NamePurpose
CBASSdata collection
PHENIXmodel building
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

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