BMRB Entry 36176

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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR36176
MolProbity Validation Chart

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Title:
Solution Structure of the N-terminal Domain of the Yeast Rpn5
Deposition date:
2018-04-05
Original release date:
2018-09-24
Authors:
Zhang, W.; Zhao, C.; Li, H.; Hu, Y.; Jin, C.
Citation:

Citation: Zhang, W.; Zhao, C.; Hu, Y.; Jin, C.. "Solution structure of the N-terminal domain of proteasome lid subunit Rpn5"  Biochem. Biophys. Res. Commun. 504, 225-230 (2018).
PubMed: 30177392

Assembly members:

Assembly members:
26S proteasome regulatory subunit RPN5, polymer, 136 residues, 15618.022 Da.

Natural source:

Natural source:   Common Name: Baker's yeast   Taxonomy ID: 559292   Superkingdom: Eukaryota   Kingdom: Fungi   Genus/species: Saccharomyces cerevisiae

Experimental source:

Experimental source:   Production method: recombinant technology   Host organism: Escherichia coli BL21(DE3)   Vector: pET28a

Entity Sequences (FASTA):

Entity Sequences (FASTA):
26S proteasome regulatory subunit RPN5: MSRDAPIKADKDYSQILKEE FPKIDSLAQNDCNSALDQLL VLEKKTRQASDLASSKEVLA KIVDLLASRNKWDDLNEQLT LLSKKHGQLKLSIQYMIQKV MEYLKSSKSLDLNTRISVIE TIRVVTENKIFVEVER

Data sets:
Data typeCount
13C chemical shifts557
15N chemical shifts144
1H chemical shifts866

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
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Assembly:

Entity Assembly IDEntity NameEntity ID
1entity_11

Entities:

Entity 1, entity_1 136 residues - 15618.022 Da.

1   METSERARGASPALAPROILELYSALAASP
2   LYSASPTYRSERGLNILELEULYSGLUGLU
3   PHEPROLYSILEASPSERLEUALAGLNASN
4   ASPCYSASNSERALALEUASPGLNLEULEU
5   VALLEUGLULYSLYSTHRARGGLNALASER
6   ASPLEUALASERSERLYSGLUVALLEUALA
7   LYSILEVALASPLEULEUALASERARGASN
8   LYSTRPASPASPLEUASNGLUGLNLEUTHR
9   LEULEUSERLYSLYSHISGLYGLNLEULYS
10   LEUSERILEGLNTYRMETILEGLNLYSVAL
11   METGLUTYRLEULYSSERSERLYSSERLEU
12   ASPLEUASNTHRARGILESERVALILEGLU
13   THRILEARGVALVALTHRGLUASNLYSILE
14   PHEVALGLUVALGLUARG

Samples:

sample_1: 26S proteasome regulatory subunit Rpn5, [U-95% 13C; U-95% 15N], 0.3 mM; DSS 0.1 mg/mL; DTT 1 mM; sodium phosphate 50 mM; sodium sulfate 50 mM; sucrose 5 % w/v; trifluoroethanol 2 % v/v; H2O 90 % v/v; D2O, [U-99% 2H], 10 % v/v

sample_conditions_1: ionic strength: 50 mM; pH: 6.0; pressure: 1 atm; temperature: 298 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
2D 1H-13C HSQCsample_1isotropicsample_conditions_1
3D HNCAsample_1isotropicsample_conditions_1
3D HN(CO)CAsample_1isotropicsample_conditions_1
3D HNCOsample_1isotropicsample_conditions_1
3D HNCACBsample_1isotropicsample_conditions_1
3D HN(CA)COsample_1isotropicsample_conditions_1
3D CBCA(CO)NHsample_1isotropicsample_conditions_1
3D HCCH-COSYsample_1isotropicsample_conditions_1
3D HBHA(CO)NHsample_1isotropicsample_conditions_1
3D HCCH-COSYsample_1isotropicsample_conditions_1
3D 15N-edited TOCSY-HSQCsample_1isotropicsample_conditions_1
3D 1H-15N NOESYsample_1isotropicsample_conditions_1
3D 1H-15C NOESYsample_1isotropicsample_conditions_1

Software:

AMBER v14, Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman - refinement

CYANA, Guntert, Mumenthaler and Wuthrich - structure calculation

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

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

NMR spectrometers:

  • Bruker AvanceIII 500 MHz
  • Bruker AvanceIII 950 MHz

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