4ABK | pdb_00004abk

HUMAN PARP14 (ARTD8, BAL2) - MACRO DOMAIN 3 IN COMPLEX WITH ADENOSINE- 5-DIPHOSPHORIBOSE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 
    0.206 (Depositor), 0.212 (DCC) 
  • R-Value Work: 
    0.166 (Depositor), 0.178 (DCC) 
  • R-Value Observed: 
    0.168 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

Recognition of Mono-Adp-Ribosylated Artd10 Substrates by Artd8 Macrodomains

Forst, A.H.Karlberg, T.Herzog, N.Thorsell, A.G.Gross, A.Feijs, K.L.H.Verheugd, P.Kursula, P.Nijmeijer, B.Kremmer, E.Kleine, H.Ladurner, A.G.Schuler, H.Luscher, B.

(2013) Structure 21: 462

  • DOI: https://doi.org/10.1016/j.str.2012.12.019
  • Primary Citation Related Structures: 
    3Q6Z, 3Q71, 3V2B, 3VFQ, 4ABK, 4ABL, 4D86

  • PubMed Abstract: 

    ADP-ribosyltransferases (ARTs) catalyze the transfer of ADP-ribose from NAD(+) onto substrates. Some ARTs generate in an iterative process ADP-ribose polymers that serve as adaptors for distinct protein domains. Other ARTs, exemplified by ARTD10, function as mono-ADP-ribosyltransferases, but it has been unclear whether this modification occurs in cells and how it is read. We observed that ARTD10 colocalized with ARTD8 and defined its macrodomains 2 and 3 as readers of mono-ADP-ribosylation both in vitro and in cells. The crystal structures of these two ARTD8 macrodomains and isothermal titration calorimetry confirmed their interaction with ADP-ribose. These macrodomains recognized mono-ADP-ribosylated ARTD10, but not poly-ADP-ribosylated ARTD1. This distinguished them from the macrodomain of macroH2A1.1, which interacted with poly- but not mono-ADP-ribosylated substrates. Moreover, Ran, an ARTD10 substrate, was also read by ARTD8 macrodomains. This identifies readers of mono-ADP-ribosylated proteins, defines their structures, and demonstrates the presence of this modification in cells.


  • Organizational Affiliation
    • Institute of Biochemistry and Molecular Biology, Medical School, RWTH Aachen University, Aachen, Germany.

Macromolecule Content 

  • Total Structure Weight: 20.37 kDa 
  • Atom Count: 1,573 
  • Modeled Residue Count: 182 
  • Deposited Residue Count: 183 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
POLY [ADP-RIBOSE] POLYMERASE 14183Homo sapiensMutation(s): 0 
EC: 2.4.2.30 (PDB Primary Data), 2.4.2 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q460N5 (Homo sapiens)
Explore Q460N5 
Go to UniProtKB:  Q460N5
PHAROS:  Q460N5
GTEx:  ENSG00000173193 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ460N5
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
AR6

Query on AR6



Download:Ideal Coordinates CCD File
B [auth A][(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL[HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE
C15 H23 N5 O14 P2
SRNWOUGRCWSEMX-ZQSHOCFMSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free:  0.206 (Depositor), 0.212 (DCC) 
  • R-Value Work:  0.166 (Depositor), 0.178 (DCC) 
  • R-Value Observed: 0.168 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 32.949α = 90
b = 41.253β = 90
c = 108.538γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-12-19
    Type: Initial release
  • Version 1.1: 2013-03-13
    Changes: Database references
  • Version 1.2: 2013-03-20
    Changes: Database references
  • Version 1.3: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description, Structure summary