BMRB Entry 19232

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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, SPARTA
BMRB Entry DOI: doi:10.13018/BMR19232
MolProbity Validation Chart

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Title:
NMR structure of a two-domain RNA-binding fragment of Nrd1
Deposition date:
2013-05-08
Original release date:
2014-05-12
Authors:
Bacikova, Veronika; Pasulka, Josef; Kubicek, Karel; Stefl, Richard
Citation:

Citation: Bacikova, Veronika; Pasulka, Josef; Kubicek, Karel; Stefl, Richard. "Structure and semi-sequence-specific RNA binding of Nrd1"  .

Assembly members:

Assembly members:
entity, polymer, 185 residues, 20597.416 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   Vector: pET22b

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity: PDELNVSNNPHYRPKPVSYD STLPPDHIKVYSRTLFIGGV PLNMKEWDLANVLKPFAEVQ SVILNNSRKHAFVKVYSRHE AENVLQNFNKDGALPLRTRW GVGFGPRDCCDYQHGYSIIP MHRLTDADKKWSVSAQWGGT SGQPLVTGIVFEEPDIIVGE GVSSKAISQKMPTDSGRNGP RSGKP

Data sets:
Data typeCount
13C chemical shifts71
15N chemical shifts127
1H chemical shifts327

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1two-domain RNA-binding fragment of Nrd11

Entities:

Entity 1, two-domain RNA-binding fragment of Nrd1 185 residues - 20597.416 Da.

1   PROASPGLULEUASNVALSERASNASNPRO
2   HISTYRARGPROLYSPROVALSERTYRASP
3   SERTHRLEUPROPROASPHISILELYSVAL
4   TYRSERARGTHRLEUPHEILEGLYGLYVAL
5   PROLEUASNMETLYSGLUTRPASPLEUALA
6   ASNVALLEULYSPROPHEALAGLUVALGLN
7   SERVALILELEUASNASNSERARGLYSHIS
8   ALAPHEVALLYSVALTYRSERARGHISGLU
9   ALAGLUASNVALLEUGLNASNPHEASNLYS
10   ASPGLYALALEUPROLEUARGTHRARGTRP
11   GLYVALGLYPHEGLYPROARGASPCYSCYS
12   ASPTYRGLNHISGLYTYRSERILEILEPRO
13   METHISARGLEUTHRASPALAASPLYSLYS
14   TRPSERVALSERALAGLNTRPGLYGLYTHR
15   SERGLYGLNPROLEUVALTHRGLYILEVAL
16   PHEGLUGLUPROASPILEILEVALGLYGLU
17   GLYVALSERSERLYSALAILESERGLNLYS
18   METPROTHRASPSERGLYARGASNGLYPRO
19   ARGSERGLYLYSPRO

Samples:

sample_1: entity, [U-13C; U-15N], 0.4 mM; sodium phosphate 50 mM; sodium chloride 300 mM; beta-mercaptoethanol 10 mM

sample_2: entity, [U-100% 13C; U-100% 15N; U-80% 2H], 0.4 mM; sodium phosphate 50 mM; sodium chloride 300 mM; beta-mercaptoethanol 10 mM

sample_3: entity, [U-13C; U-15N; U-2H], 0.4 mM; sodium phosphate 50 mM; sodium chloride 300 mM; beta-mercaptoethanol 10 mM

sample_conditions_1: pH: 8; pressure: 1 atm; temperature: 273 K

sample_conditions_2: pH: 8; pressure: 1 atm; temperature: 273 K

sample_conditions_3: pH: 8; pressure: 1 atm; temperature: 273 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
3D HNCAsample_1isotropicsample_conditions_1
3D HN(CO)CAsample_1isotropicsample_conditions_1
3D HNCACBsample_1isotropicsample_conditions_1
3D HN(COCA)CBsample_1isotropicsample_conditions_1
2D 1H-15N HSQCsample_2isotropicsample_conditions_2
3D HNCOsample_2isotropicsample_conditions_2
3D HCACOsample_2isotropicsample_conditions_2
4D HCCH methyl NOESYsample_3isotropicsample_conditions_3
3D HCCCONHsample_3isotropicsample_conditions_3
3D CCH TOCSYsample_3isotropicsample_conditions_3

Software:

SPARKY, Goddard - NMR spectra analysis, peak picking

Procheck, Laskowski, MacArthur, Smith, Jones, Hutchinson, Morris, Moss and Thornton - quality validation

WhatIF, Vriend - quality validation

CYANA, Guntert, Mumenthaler and Wuthrich - structure solution

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

Molmol, Koradi, Billeter and Wuthrich - visualization

TOPSPIN, Bruker Biospin - processing

NMR spectrometers:

  • Bruker Avance 600 MHz
  • Bruker Avance 700 MHz
  • Bruker Avance 950 MHz
  • Bruker Avance 900 MHz

Related Database Links:

PDB
DBJ GAA25857
EMBL CAA65493 CAA96158 CAY82359
GB AAC49568 AHY76857 AJP41095 AJT01532 AJT01902
REF NP_014148
SP P53617
TPG DAA10308
AlphaFold P53617

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