BMRB Entry 34260

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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/BMR34260
MolProbity Validation Chart

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Title:
Structure of Nrd1 CID - Sen1 NIM complex
Deposition date:
2018-04-17
Original release date:
2020-01-31
Authors:
Jasnovidova, O.; Kubicek, K.; Stefl, R.
Citation:

Citation: Jasnovidova, O.; Kubicek, K.; Stefl, R.. "Structure of Nrd1 CID - Sen1 NIM complex"  .

Assembly members:

Assembly members:
entity_1, polymer, 161 residues, 18315.674 Da.
entity_2, polymer, 12 residues, 1371.274 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

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: MQQDDDFQNFVATLESFKDL KSGISGSRIKKLTTYALDHI DIESKIISLIIDYSRLCPDS HKLGSLYIIDSIGRAYLDET RSNSNSSSNKPGTCAHAINT LGEVIQELLSDAIAKSNQDH KEKIRMLLDIWDRSGLFQKS YLNAIRSKCFAMDLEHHHHH H
entity_2: DDDEDDYTPSIS

Data sets:
Data typeCount
13C chemical shifts470
15N chemical shifts150
1H chemical shifts972

Additional metadata:

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

Entity Assembly IDEntity NameEntity ID
1entity_11
2entity_22

Entities:

Entity 1, entity_1 161 residues - 18315.674 Da.

1   METGLNGLNASPASPASPPHEGLNASNPHE
2   VALALATHRLEUGLUSERPHELYSASPLEU
3   LYSSERGLYILESERGLYSERARGILELYS
4   LYSLEUTHRTHRTYRALALEUASPHISILE
5   ASPILEGLUSERLYSILEILESERLEUILE
6   ILEASPTYRSERARGLEUCYSPROASPSER
7   HISLYSLEUGLYSERLEUTYRILEILEASP
8   SERILEGLYARGALATYRLEUASPGLUTHR
9   ARGSERASNSERASNSERSERSERASNLYS
10   PROGLYTHRCYSALAHISALAILEASNTHR
11   LEUGLYGLUVALILEGLNGLULEULEUSER
12   ASPALAILEALALYSSERASNGLNASPHIS
13   LYSGLULYSILEARGMETLEULEUASPILE
14   TRPASPARGSERGLYLEUPHEGLNLYSSER
15   TYRLEUASNALAILEARGSERLYSCYSPHE
16   ALAMETASPLEUGLUHISHISHISHISHIS
17   HIS

Entity 2, entity_2 12 residues - 1371.274 Da.

1   ASPASPASPGLUASPASPTYRTHRPROSER
2   ILESER

Samples:

sample_1: CTD-interacting domain of Nrd1, [U-99% 13C; U-99% 15N], 1.0 ± 0.1 mM; ASP-ASP-ASP-GLU-ASP-ASP-TYR-THR-PRO-SER-ILE-SER 1.5 ± 0.1 mM

sample_conditions_1: ionic strength: 100 mM; pH: 8.0; pressure: 1 atm; temperature: 293 K

Experiments:

NameSampleSample stateSample conditions
3D HNCACBsample_1isotropicsample_conditions_1
HCCCONHsample_1isotropicsample_conditions_1
3D 1H-15N NOESYsample_1isotropicsample_conditions_1
3D 1H-13C NOESY aliphaticsample_1isotropicsample_conditions_1
3D 1H-13C NOESY aromaticsample_1isotropicsample_conditions_1
3D HNCAsample_1isotropicsample_conditions_1
3D HBHA(CO)NHsample_1isotropicsample_conditions_1
4D HCCH TOCSYsample_1isotropicsample_conditions_1
F1-13C/15N-filtered NOESY-[13C,1H]-HSQCsample_1isotropicsample_conditions_1

Software:

AMBER v16, Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman - refinement

CYANA v3.97, Guntert, Mumenthaler and Wuthrich - structure calculation

SPARKY, Goddard - chemical shift assignment, peak picking

TOPSPIN, Bruker Biospin - processing

NMR spectrometers:

  • Bruker AvanceIII 950 MHz
  • Bruker AvanceIII 850 MHz
  • Bruker AvanceIII 700 MHz

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