BMRB Entry 34140

Name: Solution structure of the RNA binding domain of Nrd1
Published: 2017-07-27

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PDB ID: 5o1t
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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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title: Solution structure of the RNA binding domain of Nrd1 PubMed: 28973465

Deposition date: 2017-05-19 Original release date: 2017-07-27

Authors: Martinez-Lumbreras, S.; Perez-Canadillas, J.

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).

Assembly members:
entity_1, polymer, 179 residues, 20051.533 Da.

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

Experimental source: Production method: recombinant technology Host organism: Escherichia coli

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

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
13C chemical shifts	453
15N chemical shifts	182
1H chemical shifts	1203

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	entity_1	1

Entities:

Entity 1, entity_1 179 residues - 20051.533 Da.

1

SER

ILE

GLY

ALA

PRO

ASN

THR

PHE

GLY

2

THR

ASN

HIS

LEU

TYR

PRO

ASP

GLU

3

LEU

ASN

VAL

SER

ASN

PRO

HIS

TYR

ARG

4

PRO

LYS

PRO

VAL

SER

TYR

ASP

SER

THR

LEU

5

PRO

ASP

HIS

ILE

LYS

VAL

TYR

SER

ARG

6

THR

LEU

PHE

ILE

GLY

VAL

PRO

LEU

ASN

7

MET

LYS

GLU

TRP

ASP

LEU

ALA

ASN

VAL

LEU

8

LYS

PRO

PHE

ALA

GLU

VAL

GLN

SER

VAL

ILE

9

LEU

ASN

SER

ARG

LYS

HIS

ALA

PHE

VAL

10

LYS

VAL

TYR

SER

ARG

HIS

GLU

ALA

GLU

ASN

11

VAL

LEU

GLN

ASN

PHE

ASN

LYS

ASP

GLY

ALA

12

LEU

PRO

LEU

ARG

THR

ARG

TRP

GLY

VAL

GLY

13

PHE

GLY

PRO

ARG

ASP

CYS

ASP

TYR

GLN

14

HIS

GLY

TYR

SER

ILE

PRO

MET

HIS

ARG

15

LEU

THR

ASP

ALA

ASP

LYS

TRP

SER

VAL

16

SER

ALA

GLN

TRP

GLY

THR

SER

GLY

GLN

17

PRO

LEU

VAL

THR

GLY

ILE

VAL

PHE

GLU

18

PRO

ASP

ILE

VAL

GLY

GLU

GLY

VAL

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:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_1	isotropic	sample_conditions_1
3D HNCA	sample_1	isotropic	sample_conditions_1
3D HNCO	sample_1	isotropic	sample_conditions_1
3D CBCA(CO)NH	sample_1	isotropic	sample_conditions_1
3D HCCH-TOCSY	sample_1	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_2	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_1	isotropic	sample_conditions_1
2D 1H-1H NOESY F1filtered	sample_3	isotropic	sample_conditions_1
2D 1H-1H NOESY F1filtered	sample_4	isotropic	sample_conditions_1
2D 1H-1H NOESY F1filtered	sample_5	isotropic	sample_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 simulated HSQC data in one of the following formats:
CSV: Backbone or all simulated shifts
SPARKY: Backbone or all simulated shifts