6I1D

Structure of the Ysh1-Mpe1 nuclease complex from S.cerevisiae


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.28 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.173 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Activation of the Endonuclease that Defines mRNA 3' Ends Requires Incorporation into an 8-Subunit Core Cleavage and Polyadenylation Factor Complex.

Hill, C.H.Boreikaite, V.Kumar, A.Casanal, A.Kubik, P.Degliesposti, G.Maslen, S.Mariani, A.von Loeffelholz, O.Girbig, M.Skehel, M.Passmore, L.A.

(2019) Mol.Cell 73: 1217-1231.e11


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Endoribonuclease YSH1
A
474Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: YSH1 (BRR5)
EC: 3.1.27.-
Find proteins for Q06224 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q06224
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Protein MPE1
B
160Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: MPE1
Find proteins for P35728 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P35728
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.28 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.173 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 43.380α = 90.00
b = 124.270β = 103.21
c = 63.450γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
Cootmodel building
PHENIXrefinement
PHENIXmodel building
XDSdata reduction
Aimlessdata scaling
xia2data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research CouncilUnited Kingdom261151
European Research CouncilUnited Kingdom725685
Medical Research Council (United Kingdom)United KingdomMC_U105192715

Revision History 

  • Version 1.0: 2019-02-13
    Type: Initial release
  • Version 1.1: 2019-02-20
    Type: Data collection, Database references
  • Version 1.2: 2019-04-03
    Type: Data collection, Database references