Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 22149.92 
• Atom Count: 1393 
• Residue Count: 199 
• Unique protein chains: 1

3V2B

Human poly(adp-ribose) polymerase 15 (ARTD7, BAL3), macro domain 2 in complex with adenosine-5-diphosphoribose

• DOI: 10.2210/pdb3V2B/pdb
• Entry 3V2B supersedes 3KH6

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)


• Deposited: 2011-12-12 Released: 2011-12-21 
• Deposition Author(s): Karlberg, T., Moche, M., Arrowsmith, C.H., Berglund, H., Bountra, C., Collins, R., Edwards, A.M., Flodin, S., Flores, A., Graslund, S., Hammarstrom, M., Johansson, I., Kallas, A., Kotenyova, T., Kotzcsh, A., Kraulis, P., Nielsen, T.K., Nordlund, P., Nyman, T., Persson, C., Roos, A.K., Schutz, P., Siponen, M.I., Thorsell, A.G., Tresaugues, L., Van den berg, S., Weigelt, J., Welin, M., Wisniewska, M., Schuler, H., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.2 Å
• R-Value Free: 0.238 
• R-Value Work: 0.173 

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., Verheugd, P., Kursula, P., Nijmeijer, B., Kremmer, E., Kleine, H., Ladurner, A.G., Schuler, H., Luscher, B.

(2013) Structure 21: 462-475

• PubMed: 23473667 
• DOI: 10.1016/j.str.2012.12.019
• Primary Citation of Related Structures:  
  3Q71, 4D86, 4ABL, 4ABK, 3VFQ, 3Q6Z


• 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.

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Organizational Affiliation: 

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

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Poly [ADP-ribose] polymerase 15	A	199	Homo sapiens	Mutation(s): 0  Gene Names: PARP15 (BAL3) EC: 2.4.2.-
Find proteins for Q460N3 (Homo sapiens) Go to Gene View: PARP15 Go to UniProtKB:  Q460N3

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
AR6	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: 2.2 Å
• R-Value Free: 0.238 
• R-Value Work: 0.173 
• Space Group: C 2 2 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 68.102	α = 90.00
b = 91.187	β = 90.00
c = 62.851	γ = 90.00

Software Package:

Software Name	Purpose
REFMAC	refinement
MxCuBE	data collection
BALBES	phasing
XDS	data reduction
XSCALE	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2011-12-12 
• Released Date: 2011-12-21 
• Deposition Author(s): Karlberg, T., Moche, M., Arrowsmith, C.H., Berglund, H., Bountra, C., Collins, R., Edwards, A.M., Flodin, S., Flores, A., Graslund, S., Hammarstrom, M., Johansson, I., Kallas, A., Kotenyova, T., Kotzcsh, A., Kraulis, P., Nielsen, T.K., Nordlund, P., Nyman, T., Persson, C., Roos, A.K., Schutz, P., Siponen, M.I., Thorsell, A.G., Tresaugues, L., Van den berg, S., Weigelt, J., Welin, M., Wisniewska, M., Schuler, H., Structural Genomics Consortium (SGC)
• This entry supersedes: 3KH6

Revision History 

• Version 1.0: 2011-12-21
  Type: Initial release
• Version 1.1: 2013-03-20
  Type: Database references