6OZN | pdb_00006ozn

Crystal structure of Mus musculus (Mm) Endonuclease V in complex with a 23mer RNA oligo containing an inosine after a 15 min soak in 10 mM Mn2+

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 
    0.221 (Depositor), 0.222 (DCC) 
  • R-Value Work: 
    0.192 (Depositor), 0.193 (DCC) 
  • R-Value Observed: 
    0.193 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 6OZN

This is version 1.2 of the entry. See complete history. 

Literature

Evolution of Inosine-Specific Endonuclease V from Bacterial DNase to Eukaryotic RNase.

Wu, J., Samara, N.L., Kuraoka, I., Yang, W.

(2019) Mol Cell 76: 44

  • DOI: https://doi.org/10.1016/j.molcel.2019.06.046
  • Primary Citation Related Structures: 
    6OZE, 6OZF, 6OZG, 6OZH, 6OZI, 6OZJ, 6OZK, 6OZL, 6OZM, 6OZN, 6OZO, 6OZP, 6OZQ, 6OZR, 6OZS

  • PubMed Abstract: 

    Endonuclease V (EndoV) cleaves the second phosphodiester bond 3' to a deaminated adenosine (inosine). Although highly conserved, EndoV homologs change substrate preference from DNA in bacteria to RNA in eukaryotes. We have characterized EndoV from six different species and determined crystal structures of human EndoV and three EndoV homologs from bacteria to mouse in complex with inosine-containing DNA/RNA hybrid or double-stranded RNA (dsRNA). Inosine recognition is conserved, but changes in several connecting loops in eukaryotic EndoV confer recognition of 3 ribonucleotides upstream and 7 or 8 bp of dsRNA downstream of the cleavage site, and bacterial EndoV binds only 2 or 3 nt flanking the scissile phosphate. In addition to the two canonical metal ions in the active site, a third Mn 2+ that coordinates the nucleophilic water appears necessary for product formation. Comparison of EndoV with its homologs RNase H1 and Argonaute reveals the principles by which these enzymes recognize RNA versus DNA.

    • Organizational Affiliation: 
    • Laboratory of Molecular Biology, NIDDK, NIH, Bethesda, MD 20892, USA.

Macromolecule Content 

  • Total Structure Weight: 72.64 kDa 
  • Atom Count: 4,798 
  • Modeled Residue Count: 520 
  • Deposited Residue Count: 552 
  • Unique protein chains: 1
  • Unique hybrid chains: 1

Macromolecules


Find similar proteins by:
|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Endonuclease V
A, B
253Mus musculusMutation(s): 0 
Gene Names: Endov
EC: 3.1.26
UniProt & NIH Common Fund Data Resources
Find proteins for Q8C9A2 (Mus musculus)
Explore Q8C9A2 
Go to UniProtKB:  Q8C9A2
IMPC:  MGI:2444688
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8C9A2
Sequence Annotations
Expand
Reference Sequence
Find similar nucleic acids by:  Sequence
Entity ID: 2
MoleculeChains LengthOrganismImage
DNA/RNA (5'-R(P*CP*GP*GP*UP*AP*AP*CP*CP*C)-D(P*I)-R(P*AP*UP*AP*UP*GP*CP*AP*UP*GP*CP*AP*UP*U)-3')
C, D
23synthetic construct
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
P6G

Query on P6G


Download:Ideal Coordinates CCD File
N [auth A]HEXAETHYLENE GLYCOL
C12 H26 O7
IIRDTKBZINWQAW-UHFFFAOYSA-N
PG4

Query on PG4


Download:Ideal Coordinates CCD File
O [auth A],
P [auth A]		TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
PGE

Query on PGE


Download:Ideal Coordinates CCD File
I [auth A],
T [auth B]		TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
GOL

Query on GOL


Download:Ideal Coordinates CCD File
H [auth A],
V [auth C]		GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO

Query on EDO


Download:Ideal Coordinates CCD File
J [auth A],
K [auth A],
L [auth A],
M [auth A]		1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
MN
(Subject of Investigation/LOI)

Query on MN


Download:Ideal Coordinates CCD File
E [auth A]
F [auth A]
G [auth A]
Q [auth B]
R [auth B]
E [auth A],
F [auth A],
G [auth A],
Q [auth B],
R [auth B],
S [auth B],
U [auth C],
W [auth D],
X [auth D],
Y [auth D]
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free:  0.221 (Depositor), 0.222 (DCC) 
  • R-Value Work:  0.192 (Depositor), 0.193 (DCC) 
  • R-Value Observed: 0.193 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.402α = 90
b = 72.936β = 90
c = 155.354γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
Aimlessdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report



View more in-depth experimental data

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-09-04
    Type: Initial release
  • Version 1.1: 2019-10-16
    Changes: Data collection, Database references
  • Version 1.2: 2024-03-13
    Changes: Data collection, Database references, Derived calculations