BMRB Entry 34140

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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_anomalous, AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR34140
MolProbity Validation Chart

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Title:
Solution structure of the RNA binding domain of Nrd1
Deposition date:
2017-05-19
Original release date:
2017-07-27
Authors:
Martinez-Lumbreras, S.; Perez-Canadillas, J.
Citation:

Citation: Franco-Echevarria, E.; Gonzalez-Polo, N.; Zorrilla, S.; Martinez-Lumbreras, S.; Santiveri, C.; Campos-Olivas, R.; Sanchez, M.; Calvo, O.; Gonzalez, B.; Perez-Canadillas, J.. "The structure of transcription termination factor Nrd1 reveals an original mode for GUAA recognition."  Nucleic Acids Res. 45, 10293-10305 (2017).
PubMed: 28973465

Assembly members:

Assembly members:
entity_1, polymer, 179 residues, 20051.533 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: Escherichia coli

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: SIGAPNTTFGTNNHHLYPDE LNVSNNPHYRPKPVSYDSTL PPDHIKVYSRTLFIGGVPLN MKEWDLANVLKPFAEVQSVI LNNSRKHAFVKVYSRHEAEN VLQNFNKDGALPLRTRWGVG FGPRDCCDYQHGYSIIPMHR LTDADKKWSVSAQWGGTSGQ PLVTGIVFEEPDIIVGEGV

Data sets:
Data typeCount
13C chemical shifts453
15N chemical shifts182
1H chemical shifts1203

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1entity_11

Entities:

Entity 1, entity_1 179 residues - 20051.533 Da.

1   SERILEGLYALAPROASNTHRTHRPHEGLY
2   THRASNASNHISHISLEUTYRPROASPGLU
3   LEUASNVALSERASNASNPROHISTYRARG
4   PROLYSPROVALSERTYRASPSERTHRLEU
5   PROPROASPHISILELYSVALTYRSERARG
6   THRLEUPHEILEGLYGLYVALPROLEUASN
7   METLYSGLUTRPASPLEUALAASNVALLEU
8   LYSPROPHEALAGLUVALGLNSERVALILE
9   LEUASNASNSERARGLYSHISALAPHEVAL
10   LYSVALTYRSERARGHISGLUALAGLUASN
11   VALLEUGLNASNPHEASNLYSASPGLYALA
12   LEUPROLEUARGTHRARGTRPGLYVALGLY
13   PHEGLYPROARGASPCYSCYSASPTYRGLN
14   HISGLYTYRSERILEILEPROMETHISARG
15   LEUTHRASPALAASPLYSLYSTRPSERVAL
16   SERALAGLNTRPGLYGLYTHRSERGLYGLN
17   PROLEUVALTHRGLYILEVALPHEGLUGLU
18   PROASPILEILEVALGLYGLUGLYVAL

Samples:

sample_1: DTT 1 mM; Nrd1, [U-100% 13C; U-100% 15N], 600 uM; potassium phosphate 25 mM; sodium chloride 25 mM

sample_2: DTT 1 mM; Nrd1 800 uM; potassium phosphate 25 mM; sodium chloride 25 mM

sample_3: DTT 1 mM; Nrd1, [U-100% 13C; U-100% 15N] expect for Phe and Leu residues, 400 uM; potassium phosphate 25 mM; sodium chloride 25 mM

sample_4: DTT 1 mM; Nrd1, [U-100% 13C; U-100% 15N] expect for Ile residues, 400 uM; potassium phosphate 25 mM; sodium chloride 25 mM

sample_5: DTT 1 mM; Nrd1, [U-100% 13C; U-100% 15N] expect for Arg residues, 400 uM; potassium phosphate 25 mM; sodium chloride 25 mM

sample_conditions_1: ionic strength: 59.1 mM; pH: 6.5; 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 HNCOsample_1isotropicsample_conditions_1
3D CBCA(CO)NHsample_1isotropicsample_conditions_1
3D HCCH-TOCSYsample_1isotropicsample_conditions_1
2D 1H-1H NOESYsample_2isotropicsample_conditions_1
3D 1H-15N NOESYsample_1isotropicsample_conditions_1
2D 1H-1H NOESY F1filteredsample_3isotropicsample_conditions_1
2D 1H-1H NOESY F1filteredsample_4isotropicsample_conditions_1
2D 1H-1H NOESY F1filteredsample_5isotropicsample_conditions_1

Software:

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

Analysis, CCPN - chemical shift assignment

CYANA, Guntert, Mumenthaler and Wuthrich - structure calculation

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

TOPSPIN, Bruker Biospin - collection

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