BMRB

Biological Magnetic Resonance Data Bank


A Repository for Data from NMR Spectroscopy on Proteins, Peptides, Nucleic Acids, and other Biomolecules
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BMRB Entry 16880

Title: Solution Structure of UBM2 of murine Polymerase iota in Complex with Ubiquitin   PubMed: 20929865

Authors: Burschowsky, Daniel; Rudolf, Fabian; Rabut, Gwenael; Herrmann, Torsten; Peter, Matthias; Wider, Gerhard

Citation: Burschowsky, Daniel; Rudolf, Fabian; Rabut, Gwenael; Herrmann, Torsten; Matthias, Peter; Wider, Gerhard. "Structural Analysis of the Conserved Ubiquitin-binding Motifs (UBMs) of the Translesion Polymerase iota in Complex with Ubiquitin."  J. Biol. Chem. 286, 1364-1373 (2011).

Assembly members:
DNA_polymerase_iota_UBM2, polymer, 50 residues, 4205.713 Da.
Ubiquitin, polymer, 76 residues, 8576.914 Da.

Natural source:   Common Name: house mouse   Taxonomy ID: 10090   Superkingdom: Eukaryota   Kingdom: Metazoa   Genus/species: Mus musculus

Experimental source:   Production method: recombinant technology   Host organism: Escherichia coli

Entity Sequences (FASTA):
DNA_polymerase_iota_UBM2: GSPEFDSAEEKLPFPPDIDP QVFYELPEEVQKELMAEWER AGAARPSAHR
Ubiquitin: MQIFVKTLTGKTITLEVEPS DTIENVKAKIQDKEGIPPDQ QRLIFAGKQLEDGRTLSDYN IQKESTLHLVLRLRGG

Data sets:
Data typeCount
13C chemical shifts432
15N chemical shifts130
1H chemical shifts907

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
  • Hide all

Assembly:

Entity Assembly IDEntity NameEntity ID
1DNA polymerase iota UBM21
2Ubiquitin2

Entities:

Entity 1, DNA polymerase iota UBM2 50 residues - 4205.713 Da.

Residues 668-672 represent non-native cloning artifacts. Residues 673-674 and 711-717 represent flexible flanking regions that are not shown in the Structure.

1   GLYSERPROGLUPHEASPSERALAGLUGLU
2   LYSLEUPROPHEPROPROASPILEASPPRO
3   GLNVALPHETYRGLULEUPROGLUGLUVAL
4   GLNLYSGLULEUMETALAGLUTRPGLUARG
5   ALAGLYALAALAARGPROSERALAHISARG

Entity 2, Ubiquitin 76 residues - 8576.914 Da.

1   METGLNILEPHEVALLYSTHRLEUTHRGLY
2   LYSTHRILETHRLEUGLUVALGLUPROSER
3   ASPTHRILEGLUASNVALLYSALALYSILE
4   GLNASPLYSGLUGLYILEPROPROASPGLN
5   GLNARGLEUILEPHEALAGLYLYSGLNLEU
6   GLUASPGLYARGTHRLEUSERASPTYRASN
7   ILEGLNLYSGLUSERTHRLEUHISLEUVAL
8   LEUARGLEUARGGLYGLY

Samples:

15NUBM2+ub: DNA polymerase iota UBM2, [U-99% 15N], 1 – 2 mM; Ubiquitin4 – 8 mM; sodium phosphate 25 mM; sodium chloride 25 mM; potassium chloride 100 mM; CHAPS 2 mM; PMSF 0.15 mM; sodium azide 0.2 % w/v; H2O 95%; D2O 5%

13C15NUBM2+ub: DNA polymerase iota UBM2, [U-95% 13C; U-99% 15N], 1 – 2 mM; Ubiquitin4 – 8 mM; sodium phosphate 25 mM; sodium chloride 25 mM; potassium chloride 100 mM; CHAPS 2 mM; PMSF 0.15 mM; sodium azide 0.2 % w/v; H2O 95%; D2O 5%

15NUbi+ubm2: DNA polymerase iota UBM24 – 8 mM; Ubiquitin, [U-99% 15N], 1 – 2 mM; sodium phosphate 25 mM; sodium chloride 25 mM; potassium chloride 100 mM; CHAPS 2 mM; PMSF 0.15 mM; sodium azide 0.2 % w/v; H2O 95%; D2O 5%

13C15NUbi+ubm2: DNA polymerase iota UBM24 – 8 mM; Ubiquitin, [U-95% 13C; U-99% 15N], 1 – 2 mM; sodium phosphate 25 mM; sodium chloride 25 mM; potassium chloride 100 mM; CHAPS 2 mM; PMSF 0.15 mM; sodium azide 0.2 % w/v; H2O 95%; D2O 5%

labUbi-overUBM2: DNA polymerase iota UBM21 – 2 mM; Ubiquitin, [U-95% 13C; U-99% 15N], 4 – 8 mM; sodium phosphate 25 mM; sodium chloride 25 mM; potassium chloride 100 mM; CHAPS 2 mM; PMSF 0.15 mM; sodium azide 0.2 % w/v; H2O 95%; D2O 5%

Sample_conditions: ionic strength: 0.189 M; pH: 6.0; pressure: 1 atm; temperature: 288 K

Experiments:

NameSampleSample stateSample conditions
3D HNCACB13C15NUBM2+ubisotropicSample_conditions
3D 1H-15N NOESY15NUBM2+ubisotropicSample_conditions
3D 1H-15N TOCSY15NUBM2+ubisotropicSample_conditions
3D 1H-13C NOESY13C15NUBM2+ubisotropicSample_conditions
3D HCCH-COSY13C15NUBM2+ubisotropicSample_conditions
2D 1H-15N HSQC15NUBM2+ubisotropicSample_conditions
2D 1H-13C HSQC13C15NUBM2+ubisotropicSample_conditions
3D HNCACB13C15NUbi+ubm2isotropicSample_conditions
3D 1H-15N NOESY15NUbi+ubm2isotropicSample_conditions
3D 1H-15N TOCSY15NUbi+ubm2isotropicSample_conditions
3D 1H-13C NOESY13C15NUbi+ubm2isotropicSample_conditions
3D HCCH-COSY13C15NUbi+ubm2isotropicSample_conditions
2D 1H-15N HSQC15NUbi+ubm2isotropicSample_conditions
2D 1H-13C HSQC13C15NUbi+ubm2isotropicSample_conditions
3D 1H-13C-filtered-13C-edited NOESY13C15NUBM2+ubisotropicSample_conditions
3D 1H-13C-filtered-13C-edited NOESY13C15NUbi+ubm2isotropicSample_conditions
3D 1H-13C-filtered-13C-edited NOESYlabUbi-overUBM2isotropicSample_conditions

Software:

AMBER v9, Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollm - refinement

TOPSPIN v2.1, Bruker Biospin - collection, processing

Molmol v2k.2, Koradi, Billeter and Wuthrich - geometry optimization

UNIO v1.0.4, T. Herrmann - chemical shift assignment, peak picking, structure solution

DYANA, Guntert, Braun and Wuthrich - structure solution

CARA v1.8.4, R. Keller - chemical shift assignment, data analysis

NMR spectrometers:

  • Bruker Avance 600 MHz
  • Bruker Avance 750 MHz
  • Bruker Avance 900 MHz

Related Database Links:

PDB
BMRB 11505 11547 15047 15410 15689 15866 15907 16228 16582 16626 16763 16885 16895 17059 17181 17239 17333 17439 17769 17919 18582 18583 18584 18610 18611 18737 19394 19399 19406 19412 19447 25070 25230 4245 4375 4983 5101 5387 6457 6466 6470 6488 68 7111
DBJ BAA03983 BAA09860 BAA11842 BAA11843 BAA23486
EMBL CAA25706 CAA26488 CAA28495 CAA30183 CAA30815
GB AAA02769 AAA28154 AAA28997 AAA28998 AAA28999
PIR I50437 I51568 I65237 JN0790 S13928
PRF 0412265A 1101405A 1212243A 1212243B 1212243C
REF NP_001005123 NP_001006688 NP_001009117 NP_001009202 NP_001009286
SP P0C273 P0C275 P0C276 P0CG47 P0CG48
TPD FAA00319
TPG DAA18802 DAA20663 DAA20672 DAA24675 DAA28295