BMRB Entry 26691

Name: Chemical shift assignment of yeast Bcd1 protein zinc finger
Published: 2016-05-23

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PDB ID: 2n94
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR26691
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:

Chemical shift assignment of yeast Bcd1 protein zinc finger

Deposition date:

2015-10-22

Original release date:

2016-05-23

Authors:

Bragantini, Benoit; Quinternet, Marc; Manival, Xavier

Citation:

Citation: Bragantini, Benoit; Quinternet, Marc; Manival, Xavier; Charpentier, Bruno; Tiotiu, Decebal; Rothe, Benjamin; Saliou, Jean-Michel; Cianferani, Sarah. "Functional and structural insights into the zinc-finger HIT protein family involved in box C/D snoRNP biogenesis" J. Mol. Biol. 428, 2488-2506 (2016).
PubMed: 27139642

Assembly members:

Assembly members:
ZnF-Bcd1, polymer, 48 residues, 5341.2 Da.
entity_ZN, non-polymer, 65.409 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: pnEA-3cH

Entity Sequences (FASTA):

Entity Sequences (FASTA):
ZnF-Bcd1: GPHMAVLCGVCGIKEFKYKC PRCLVQTCSLECSKKHKTRD NCSGQTHD

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1
- assigned_chem_shift_list_2

Data type	Count
13C chemical shifts	369
15N chemical shifts	84
1H chemical shifts	583

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	ZnF-Bcd1	1
2	zinc ion, 1	2
3	zinc ion, 2	2

Entities:

Entity 1, ZnF-Bcd1 48 residues - 5341.2 Da.

Residues 1-3 represent non-native residues from affinity tag

1

GLY

PRO

HIS

MET

ALA

VAL

LEU

CYS

GLY

VAL

2

CYS

GLY

ILE

LYS

GLU

PHE

LYS

TYR

LYS

CYS

3

PRO

ARG

CYS

LEU

VAL

GLN

THR

CYS

SER

LEU

4

GLU

CYS

SER

LYS

HIS

LYS

THR

ARG

ASP

5

ASN

CYS

SER

GLY

GLN

THR

HIS

ASP

Entity 2, zinc ion, 1 - Zn - 65.409 Da.

1

ZN

Samples:

sample_1: ZnF-Bcd1, [U-100% 13C; U-100% 15N], 0.8 mM; sodium phosphate 10 mM; sodium chloride 150 mM; TCEP 0.5 mM; DTT, [U-2H], 3 mM

sample_conditions_1: ionic strength: 160 mM; pH: 6.4; pressure: 1 atm; temperature: 313 K

sample_conditions_2: ionic strength: 160 mM; pH: 6.4; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-1H NOESY	sample_1	isotropic	sample_conditions_1
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC aliphatic	sample_1	isotropic	sample_conditions_1
3D CBCA(CO)NH	sample_1	isotropic	sample_conditions_1
3D HNCO	sample_1	isotropic	sample_conditions_1
3D HNHA	sample_1	isotropic	sample_conditions_1
3D HNCACB	sample_1	isotropic	sample_conditions_1
3D HCCH-TOCSY	sample_1	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY aliphatic	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY aromatic	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC aromatic	sample_1	isotropic	sample_conditions_1
2D 1H-15N HSQC long range	sample_1	isotropic	sample_conditions_1
2D 1H-1H TOCSY	sample_1	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_1	isotropic	sample_conditions_1

Software:

CNS, Brunger, Adams, Clore, Gros, Nilges and Read - refinement, structure solution

NMR spectrometers:

Bruker Avance 600 MHz

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