BMRB Entry 36787

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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR36787
MolProbity Validation Chart

NMR-STAR file interactive viewer.
NMR-STAR v3 text file.
All files associated with the entry

Title:
Solution structure of the complex between the UBA-like domain of mouse HBS1L and ubiquitin
Deposition date:
2025-09-09
Original release date:
2026-05-07
Authors:
He, F.; Takahashi, M.; Tsuda, K.; Nagata, T.; Tanaka, A.; Kobayashi, N.; Kigawa, T.; Guntert, P.; Shirouzu, M.; Nameki, N.; Yokoyama, S.; Kuwasako, K.; Muto, Y.; RIKEN Structural Genomics/Proteomics Initiative (RSGI), RIKEN
Citation:

Citation: He, F.; Nameki, N.; Tsuda, K.; Takahashi, M.; Nagata, T.; Kobayashi, N.; Shirouzu, M.; Kigawa, T.; Guntert, P.; Yokoyama, S.; Muto, Y.; Kuwasako, K.. "Solution structure of mouse HBS1L/SKI7-specific UBA domain in complex with ubiquitin: Implications for stalled ribosome recognition."  Plos One ., .-. (2026).

Assembly members:

Assembly members:
HBS1-like protein, polymer, 83 residues, 8975.762 Da.
Ubiquitin-ribosomal protein eS31 fusion protein, polymer, 83 residues, 9096.297 Da.

Natural source:

Natural source:   Common Name: house mouse   Taxonomy ID: 10090   Superkingdom: not available   Kingdom: Metazoa   Genus/species: Mus musculus

Experimental source:

Experimental source:   Production method: recombinant technology   Host organism: Cell-free gateway cloning vector N-term 8xHis pCellFree_G01

Entity Sequences (FASTA):

Entity Sequences (FASTA):
HBS1-like protein: GSSGSSGEYGYEDLRESSNS LLNHQLSEIDQARLYSCLDH MREVLGDAVPDDILTEAILK HKFDVQKALSVVLEQDGSGP SSG
Ubiquitin-ribosomal protein eS31 fusion protein: GSSGSSGMQIFVKTLTGKTI TLEVEPSDTIENVKAKIQDK EGIPPDQQRLIFAGKQLEDG RTLSDYNIQKESTLHLVLRL RGG

Data sets:
Data typeCount
13C chemical shifts681
15N chemical shifts155
1H chemical shifts1088

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1entity_11
2entity_22

Entities:

Entity 1, entity_1 83 residues - 8975.762 Da.

1   GLYSERSERGLYSERSERGLYGLUTYRGLY
2   TYRGLUASPLEUARGGLUSERSERASNSER
3   LEULEUASNHISGLNLEUSERGLUILEASP
4   GLNALAARGLEUTYRSERCYSLEUASPHIS
5   METARGGLUVALLEUGLYASPALAVALPRO
6   ASPASPILELEUTHRGLUALAILELEULYS
7   HISLYSPHEASPVALGLNLYSALALEUSER
8   VALVALLEUGLUGLNASPGLYSERGLYPRO
9   SERSERGLY

Entity 2, entity_2 83 residues - 9096.297 Da.

1   GLYSERSERGLYSERSERGLYMETGLNILE
2   PHEVALLYSTHRLEUTHRGLYLYSTHRILE
3   THRLEUGLUVALGLUPROSERASPTHRILE
4   GLUASNVALLYSALALYSILEGLNASPLYS
5   GLUGLYILEPROPROASPGLNGLNARGLEU
6   ILEPHEALAGLYLYSGLNLEUGLUASPGLY
7   ARGTHRLEUSERASPTYRASNILEGLNLYS
8   GLUSERTHRLEUHISLEUVALLEUARGLEU
9   ARGGLYGLY

Samples:

sample_1: mouse HBS1L N-terminal domain, [U-99% 13C; U-99% 15N], 1.0 mM; Ubiquitin, [U-99% 13C; U-99% 15N], 1.0 mM; NaN3 0.02%; NaCL 100 mM; sodium phosphate 20 mM; H2O 90%; D2O, [U-2H], 10%

sample_conditions_1: ionic strength: 120 mM; pH: 6.0; pressure: 1 atm; temperature: 298 K

Experiments:

NameSampleSample stateSample conditions
3D_13C,15N-SEPARATED_NOESYsample_1isotropicsample_conditions_1
3D CBCA(CO)NH,HNCACBsample_1isotropicsample_conditions_1
3D HCCH-COSY,TOCSYsample_1isotropicsample_conditions_1

Software:

Amber v24, Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman - refinement

CYANA v2.1, Guntert, Mumenthaler and Wuthrich - structure calculation

KUJIRA v0.863, N. Kobayashi, T. Kigawa, S. Yokoyama - chemical shift assignment

NMRView v5.0.4, Johnson, One Moon Scientific - peak picking

NMRPipe v2007, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

TALOS v2007, Cornilescu, Delaglio and Bax - geometry optimization

NMR spectrometers:

  • Bruker AVANCE 600 MHz
  • Bruker AVANCE 800 MHz

Download HSQC peak lists in one of the following formats:
CSV: Backbone or all simulated peaks
SPARKY: Backbone or all simulated peaks