BMRB Entry 19954

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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_anomalous, AVS_full, LACS, SPARTA
BMRB Entry DOI: doi:10.13018/BMR19954
MolProbity Validation Chart

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Title:
Structure of Nrd1p CID - Trf4p NIM complex
Deposition date:
2014-05-06
Original release date:
2014-08-11
Authors:
Kabzinski, Tomek; Stefl, Richard; Kubicek, Karel
Citation:

Citation: Tudek, Agnieszka; Porrua, Odil; Kabzinski, Tomasz; Lidschreiber, Michael; Kubicek, Karel; Fortova, Andrea; Lacroute, Fran ois; Vanacova, Stepanka; Cramer, Patrick; Stefl, Richard; Libri, Domenico. "Molecular Basis for Coordinating Transcription Termination with Noncoding RNA Degradation"  Mol. Cell 55, 467-481 (2014).
PubMed: 25066235

Assembly members:

Assembly members:
entity_1, polymer, 161 residues, 18315.812 Da.
entity_2, polymer, 12 residues, 1416.371 Da.

Natural source:

Natural source:   Common Name: baker's yeast   Taxonomy ID: 4932   Superkingdom: Eukaryota   Kingdom: Fungi   Genus/species: Saccharomyces cerevisiae

Experimental source:

Experimental source:   Production method: recombinant technology   Host organism: Saccharomyces cerevisiae   Vector: pET22b

Entity Sequences (FASTA):

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

Data sets:
Data typeCount
1H chemical shifts949
15N chemical shifts152
13C chemical shifts374

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 - 18315.812 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 - 1416.371 Da.

1   ASPASPASPGLUASPGLYTYRASNPROTYR
2   THRLEU

Samples:

sample_1: entity_2 1.5 mM; entity_1, [U-99% 13C; U-99% 15N], 1 mM; sodium chloride 100 mM; sodium phosphate 50 mM

sample_conditions_1: temperature: 293.15 K; pH: 8.0; pressure: 1 atm; ionic strength: 0.1 M

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
3D HNCAsample_1isotropicsample_conditions_1
3D HN(CO)CAsample_1isotropicsample_conditions_1
3D HBHA(CO)NHsample_1isotropicsample_conditions_1
3D 1H-15N NOESYsample_1isotropicsample_conditions_1
3D 1H-13C NOESYsample_1isotropicsample_conditions_1
3D F1-13C/15N-filtered NOESY-[13C,1H]-HSQCsample_1isotropicsample_conditions_1
2D F1, F2-13C/15N-filtered [1H,1H]-NOESYsample_1isotropicsample_conditions_1

Software:

CYANA, Guntert, Mumenthaler and Wuthrich - refinement

NMR spectrometers:

  • Bruker Avance 950 MHz
  • Bruker Avance 700 MHz

Related Database Links:

BMRB 17173
PDB
DBJ GAA25857
EMBL CAA65493 CAA96158 CAY82359
GB AAC49568 AHY76857 AJP41095 AJT01532 AJT02278
REF NP_014148
SP P53617
TPG DAA10308
AlphaFold P53617 D6W1V2

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