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 18391

Title: Solution structure of the R3H domain from human Smubp-2 in complex with 2'-deoxyguanosine-5'-monophosphate   PubMed: 22999958

Deposition date: 2012-04-12 Original release date: 2012-10-22

Authors: Jaudzems, Kristaps; Zhulenkovs, Dmitry; Otting, Gottfried; Liepinsh, Edvards

Citation: Jaudzems, Kristaps; Jia, Xinying; Yagi, Hiromasa; Zhulenkovs, Dmitry; Graham, Bim; Otting, Gottfried; Liepinsh, Edvards. "Structural Basis for 5'-End-Specific Recognition of Single-Stranded DNA by the R3H Domain from Human Smubp-2"  J. Mol. Biol. 12, 760-767 (2012).

Assembly members:
Smubp2_R3H, polymer, 86 residues, 8359.341 Da.
2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE, non-polymer, 347.221 Da.

Natural source:   Common Name: Human   Taxonomy ID: 9606   Superkingdom: Eukaryota   Kingdom: Metazoa   Genus/species: Homo sapiens

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

Entity Sequences (FASTA):
Smubp2_R3H: MGSLNGGSPEGVESQDGVDH FRAMIVEFMASKKMQLEFPP SLNSHDRLRVHQIAEEHGLR HDSSGEGKRRFITVSKRAGS HHHHHH

Data typeCount
15N chemical shifts75
1H chemical shifts921

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1Smubp2_R3H1
22'-DEOXYGUANOSINE-5'-MONOPHOSPHATE2

Entities:

Entity 1, Smubp2_R3H 86 residues - 8359.341 Da.

1   METGLYSERLEUASNGLYGLYSERPROGLU
2   GLYVALGLUSERGLNASPGLYVALASPHIS
3   PHEARGALAMETILEVALGLUPHEMETALA
4   SERLYSLYSMETGLNLEUGLUPHEPROPRO
5   SERLEUASNSERHISASPARGLEUARGVAL
6   HISGLNILEALAGLUGLUHISGLYLEUARG
7   HISASPSERSERGLYGLUGLYLYSARGARG
8   PHEILETHRVALSERLYSARGALAGLYSER
9   HISHISHISHISHISHIS

Entity 2, 2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE - C10 H14 N5 O7 P - 347.221 Da.

1   DGP

Samples:

sample_1: Smubp2_R3H, [U-99% 15N], 0.9 ± 0.1 mM; 2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE 5.5 ± 0.1 mM; D2O, [U-100% 2H], 5 ± 0.1 %; sodium phosphate 10 ± 1 mM; sodium chloride 100 ± 5 mM; sodium azide 0.03 ± 0.005 %; H2O 95%

sample_conditions_1: ionic strength: 0.12 M; pH: 6.3; pressure: 1 atm; temperature: 298 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
2D 1H-1H TOCSYsample_1isotropicsample_conditions_1
2D 1H-1H NOESYsample_1isotropicsample_conditions_1
3D 1H-15N NOESYsample_1isotropicsample_conditions_1
3D HNHAsample_1isotropicsample_conditions_1

Software:

VNMRJ v2.1b, Varian - collection

NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

XEASY, Bartels et al. - chemical shift assignment, peak picking

CYANA v2.1, Guntert, Mumenthaler and Wuthrich - data analysis, structure solution

CNS, Brunger, Adams, Clore, Gros, Nilges and Read - refinement

NMR spectrometers:

  • Varian INOVA 600 MHz

Related Database Links:

PDB
DBJ BAD92039 BAG35460
GB AAA53082 AAA58611 AAA70430 AAH00290 AAH25299
REF NP_002171 XP_002821469 XP_003274011 XP_003828806 XP_004051731
SP P38935