Biological Assembly 1  

 3D View: Structure | 1D-3D View | Validation Report

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 13.71 kDa 
• Atom Count: 885 
• Modelled Residue Count: 112 
• Deposited Residue Count: 124 
• Unique protein chains: 2

2KWV

Solution Structure of UBM1 of murine Polymerase iota in Complex with Ubiquitin

• PDB DOI: 10.2210/pdb2KWV/pdb
• BMRB: 16885

• Classification: PROTEIN BINDING/SIGNALING PROTEIN
• Organism(s): Mus musculus, Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2010-04-20 Released: 2010-10-06 
• Deposition Author(s): Burschowsky, D., Rudolf, F., Rabut, G., Herrmann, T., Peter, M., Wider, G.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 200 
• Conformers Submitted: 20 
• Selection Criteria: structures with the lowest energy 

Literature

Structural analysis of the conserved ubiquitin-binding motifs (UBMs) of the translesion polymerase iota in complex with ubiquitin.

Burschowsky, D., Rudolf, F., Rabut, G., Herrmann, T., Matthias, P., Wider, G.

(2011) J Biol Chem 286: 1364-1373

• PubMed: 20929865 
• DOI: 10.1074/jbc.M110.135038
• Primary Citation of Related Structures:  
  2KWU, 2KWV


• PubMed Abstract: 
  

Ubiquitin-binding domains (UBDs) provide specificity to the ubiquitin system, which is also involved in translesion synthesis (TLS) in eukaryotic cells. Upon DNA damage, the UBDs (UBM domains) of polymerase iota (Pol ι) interact with ubiquitinated proliferating cell nuclear antigen to regulate the interchange between processive DNA polymerases and TLS. We report a biophysical analysis and solution structures of the two conserved UBM domains located in the C-terminal tail of murine Pol ι in complex with ubiquitin. The 35-amino acid core folds into a helix-turn-helix motif, which belongs to a novel domain fold. Similar to other UBDs, UBMs bind to ubiquitin on the hydrophobic surface delineated by Leu-8, Ile-44, and Val-70, however, slightly shifted toward the C terminus. In addition, UBMs also use electrostatic interactions to stabilize binding. NMR and fluorescence spectroscopy measurements revealed that UBMs bind monoubiquitin, and Lys-63- but not Lys-48-linked chains. Importantly, these biophysical data are supported by functional studies. Indeed, yeast cells expressing ubiquitin mutants specifically defective for UBM binding are viable but sensitive to DNA damaging conditions that require TLS for repair.

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Organizational Affiliation: 

Institute of Molecular Biology and Biophysics, ETH Zurich, 8093 Zurich, Switzerland.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA polymerase iota	A	48	Mus musculus	Mutation(s): 1  Gene Names: Poli, Rad30b EC: 2.7.7.7
UniProt & NIH Common Fund Data Resources
Find proteins for Q6R3M4 (Mus musculus) Explore Q6R3M4  Go to UniProtKB:  Q6R3M4
IMPC:  MGI:1347081

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin	B	76	Homo sapiens	Mutation(s): 0  Gene Names: RPS27A, UBA80, UBCEP1, UBA52, UBCEP2, UBB, UBC
UniProt & NIH Common Fund Data Resources
Find proteins for P0CG47 (Homo sapiens) Explore P0CG47  Go to UniProtKB:  P0CG47
PHAROS:  P0CG47

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 200 
• Conformers Submitted: 20 
• Selection Criteria: structures with the lowest energy 
• OLDERADO: 2KWV Olderado

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2010-04-20 
• Released Date: 2010-10-06 
Deposition Author(s): Burschowsky, D., Rudolf, F., Rabut, G., Herrmann, T., Peter, M., Wider, G.

Revision History  

• Version 1.0: 2010-10-06
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2020-02-05
  Changes: Data collection, Database references, Other