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
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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: Bacikova, Veronika; Pasulka, Josef; Kubicek, Karel; Stefl, Richard. "Structure and semi-sequence-specific RNA binding of Nrd1" Not known ., .-..
Assembly members:
entity, polymer, 185 residues, 20597.416 Da.
Natural source: Common Name: baker Taxonomy ID: 4932 Superkingdom: not available Kingdom: not available Genus/species: Eukaryota Fungi
Experimental source: Production method: recombinant technology Host organism: Escherichia coli
Entity Sequences (FASTA):
entity: PDELNVSNNPHYRPKPVSYD
STLPPDHIKVYSRTLFIGGV
PLNMKEWDLANVLKPFAEVQ
SVILNNSRKHAFVKVYSRHE
AENVLQNFNKDGALPLRTRW
GVGFGPRDCCDYQHGYSIIP
MHRLTDADKKWSVSAQWGGT
SGQPLVTGIVFEEPDIIVGE
GVSSKAISQKMPTDSGRNGP
RSGKP
- assigned_chemical_shifts
| Data type | Count |
| 13C chemical shifts | 71 |
| 15N chemical shifts | 127 |
| 1H chemical shifts | 327 |
Additional metadata:
Assembly:
| Entity Assembly ID | Entity Name | Entity ID |
|---|---|---|
| 1 | two-domain RNA-binding fragment of Nrd1 | 1 |
Entities:
Entity 1, two-domain RNA-binding fragment of Nrd1 185 residues - 20597.416 Da.
| 1 | PRO | ASP | GLU | LEU | ASN | VAL | SER | ASN | ASN | PRO | ||||
| 2 | HIS | TYR | ARG | PRO | LYS | PRO | VAL | SER | TYR | ASP | ||||
| 3 | SER | THR | LEU | PRO | PRO | ASP | HIS | ILE | LYS | VAL | ||||
| 4 | TYR | SER | ARG | THR | LEU | PHE | ILE | GLY | GLY | VAL | ||||
| 5 | PRO | LEU | ASN | MET | LYS | GLU | TRP | ASP | LEU | ALA | ||||
| 6 | ASN | VAL | LEU | LYS | PRO | PHE | ALA | GLU | VAL | GLN | ||||
| 7 | SER | VAL | ILE | LEU | ASN | ASN | SER | ARG | LYS | HIS | ||||
| 8 | ALA | PHE | VAL | LYS | VAL | TYR | SER | ARG | HIS | GLU | ||||
| 9 | ALA | GLU | ASN | VAL | LEU | GLN | ASN | PHE | ASN | LYS | ||||
| 10 | ASP | GLY | ALA | LEU | PRO | LEU | ARG | THR | ARG | TRP | ||||
| 11 | GLY | VAL | GLY | PHE | GLY | PRO | ARG | ASP | CYS | CYS | ||||
| 12 | ASP | TYR | GLN | HIS | GLY | TYR | SER | ILE | ILE | PRO | ||||
| 13 | MET | HIS | ARG | LEU | THR | ASP | ALA | ASP | LYS | LYS | ||||
| 14 | TRP | SER | VAL | SER | ALA | GLN | TRP | GLY | GLY | THR | ||||
| 15 | SER | GLY | GLN | PRO | LEU | VAL | THR | GLY | ILE | VAL | ||||
| 16 | PHE | GLU | GLU | PRO | ASP | ILE | ILE | VAL | GLY | GLU | ||||
| 17 | GLY | VAL | SER | SER | LYS | ALA | ILE | SER | GLN | LYS | ||||
| 18 | MET | PRO | THR | ASP | SER | GLY | ARG | ASN | GLY | PRO | ||||
| 19 | ARG | SER | GLY | LYS | PRO |
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:
| Name | Sample | Sample state | Sample conditions |
|---|---|---|---|
| 2D 1H-15N HSQC | sample_1 | isotropic | sample_conditions_1 |
| 3D HNCA | sample_1 | isotropic | sample_conditions_1 |
| 3D HN(CO)CA | sample_1 | isotropic | sample_conditions_1 |
| 3D HNCACB | sample_1 | isotropic | sample_conditions_1 |
| 3D HN(COCA)CB | sample_1 | isotropic | sample_conditions_1 |
| 2D 1H-15N HSQC | sample_2 | isotropic | sample_conditions_2 |
| 3D HNCO | sample_2 | isotropic | sample_conditions_2 |
| 3D HCACO | sample_2 | isotropic | sample_conditions_2 |
| 4D HCCH methyl NOESY | sample_3 | isotropic | sample_conditions_3 |
| 3D HCCCONH | sample_3 | isotropic | sample_conditions_3 |
| 3D CCH TOCSY | sample_3 | isotropic | sample_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 |
Download simulated HSQC data in one of the following formats:
CSV: Backbone
or all simulated shifts
SPARKY: Backbone
or all simulated shifts