BMRB Entry 34668

Name: Solution structure of the chimeric Nrd1-Nab3 heterodimerization domains
Published: 2022-01-07

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PDB ID: 7prd
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR34668
MolProbity Validation Chart

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Nicholas Rego and David Koes
3Dmol.js: molecular visualization with WebGL
Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

Solution structure of the chimeric Nrd1-Nab3 heterodimerization domains

Deposition date:

2021-09-21

Original release date:

2022-01-07

Authors:

Chaves-Arquero, B.; Martinez-Lumbreras, S.; Perez-Canadillas, J.

Citation:

Citation: Chaves-Arquero, B.; Martinez-Lumbreras, S.; Camero, S.; Santiveri, C.; Mirassou, Y.; Campos-Olivas, R.; Jimenez, M.; Calvo, O.; Perez-Canadillas, J.. "Structural basis of Nrd1-Nab3 heterodimerization" Life Sci. Alliance 5, e202101252-e202101252 (2022).
PubMed: 35022249

Assembly members:

Assembly members:
entity_1, polymer, 125 residues, 13943.856 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 BL21(DE3)

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: TANTASQQLSLDPKQRSKQI LSNLKKSPPLNLNISLPTDL TSTDPAKQQAALFQVIAALQ KHFKTNMENVNYDLLQKQVK YIMDSNMLNLPQFQHLPQEE KMSAILAMLNSNSDTALSVP PHDST

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
13C chemical shifts	547
15N chemical shifts	140
1H chemical shifts	916

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	unit_1	1

Entities:

Entity 1, unit_1 125 residues - 13943.856 Da.

1

THR

ALA

ASN

THR

ALA

SER

GLN

LEU

SER

2

LEU

ASP

PRO

LYS

GLN

ARG

SER

LYS

GLN

ILE

3

LEU

SER

ASN

LEU

LYS

SER

PRO

LEU

4

ASN

LEU

ASN

ILE

SER

LEU

PRO

THR

ASP

LEU

5

THR

SER

THR

ASP

PRO

ALA

LYS

GLN

ALA

6

ALA

LEU

PHE

GLN

VAL

ILE

ALA

LEU

GLN

7

LYS

HIS

PHE

LYS

THR

ASN

MET

GLU

ASN

VAL

8

ASN

TYR

ASP

LEU

GLN

LYS

GLN

VAL

LYS

9

TYR

ILE

MET

ASP

SER

ASN

MET

LEU

ASN

LEU

10

PRO

GLN

PHE

GLN

HIS

LEU

PRO

GLN

GLU

11

LYS

MET

SER

ALA

ILE

LEU

ALA

MET

LEU

ASN

12

SER

ASN

SER

ASP

THR

ALA

LEU

SER

VAL

PRO

13

PRO

HIS

ASP

SER

THR

Samples:

sample_1: sodium acetate 10 mM; sodium chloride 25 mM; DTT 1 mM; Nrd1-Nab3 chimera, [U-100% 13C; U-100% 15N], 1000 uM

sample_2: sodium acetate 10 mM; sodium chloride 25 mM; DTT 1 mM; Nrd1-Nab3 chimera, [U-100% 13C; U-100% 15N], 1000 uM

sample_3: sodium acetate 10 mM; sodium chloride 25 mM; DTT 1 mM; Nrd1-Nab3 chimera, [13C - methyl (IVL)], 1000 uM

sample_4: sodium acetate 10 mM; sodium chloride 25 mM; DTT 1 mM; Nrd1-Nab3 chimera 1000 uM

sample_5: sodium acetate 10 mM; sodium chloride 25 mM; DTT 1 mM; Nrd1-Nab3 chimera 1000 uM

sample_conditions_1: ionic strength: 35 mM; pH: 5.1; 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_2	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 HNCACB	sample_1	isotropic	sample_conditions_1
3D HCCH-TOCSY	sample_2	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_4	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_5	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY	sample_3	isotropic	sample_conditions_1
3D 1H-13C HSQC NOESY 1H-13C HSQC	sample_3	isotropic	sample_conditions_1

Software:

TopSpin, Bruker Biospin - collection

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

CcpNmr Analysis, CCPN - chemical shift assignment

CYANA, Guntert, Mumenthaler and Wuthrich - structure calculation

NMR spectrometers:

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