BMRB Entry 25439

Name: Solution structure and 1H, 13C, and 15N chemical shift assignments for Bud31p
Published: 2015-03-09

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PDB ID: 2my1
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_anomalous, AVS_full, LACS, SPARTA
BMRB Entry DOI: doi:10.13018/BMR25439
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 and 1H, 13C, and 15N chemical shift assignments for Bud31p PubMed: 25703931

Deposition date: 2015-01-19 Original release date: 2015-03-09

Authors: van Roon, Anne-Marie; Yang, Ji-Chun; Mathieu, Daniel; Bermel, Wolfgang; Nagai, Kiyoshi; Neuhaus, David

Citation: van Roon, Anne-Marie; Yang, Ji-Chun; Mathieu, Daniel; Bermel, Wolfgang; Nagai, Kiyoshi; Neuhaus, David. "113 Cd NMR Experiments Reveal an Unusual Metal Cluster in the Solution Structure of the Yeast Splicing Protein Bud31p" Angew. Chem. Int. Ed. Engl. 54, 4861-4864 (2015).

Assembly members:
Bud31p_polypeptide, polymer, 159 residues, 18554.609 Da.
ZINC ION, non-polymer, 65.409 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):
Bud31p_polypeptide: GGSPRIKTRRSKPAPDGFEK IKPTLTDFEIQLRDAQKDKS SKLAAKSNEQLWEIMQLHHQ RSRYIYTLYYKRKAISKDLY DWLIKEKYADKLLIAKWRKT GYEKLCCLRCIQKNETNNGS TCICRVPRAQLEEEARKKGT QVSFHQCVHCGCRGCASTD

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	509
15N chemical shifts	167
1H chemical shifts	1022

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	Bud31p polypeptide	1
2	ZN1	2
3	ZN2	2
4	ZN3	2

Entities:

Entity 1, Bud31p polypeptide 159 residues - 18554.609 Da.

1

GLY

SER

PRO

ARG

ILE

LYS

THR

ARG

2

SER

LYS

PRO

ALA

PRO

ASP

GLY

PHE

GLU

LYS

3

ILE

LYS

PRO

THR

LEU

THR

ASP

PHE

GLU

ILE

4

GLN

LEU

ARG

ASP

ALA

GLN

LYS

ASP

LYS

SER

5

SER

LYS

LEU

ALA

LYS

SER

ASN

GLU

GLN

6

LEU

TRP

GLU

ILE

MET

GLN

LEU

HIS

GLN

7

ARG

SER

ARG

TYR

ILE

TYR

THR

LEU

TYR

8

LYS

ARG

LYS

ALA

ILE

SER

LYS

ASP

LEU

TYR

9

ASP

TRP

LEU

ILE

LYS

GLU

LYS

TYR

ALA

ASP

10

LYS

LEU

ILE

ALA

LYS

TRP

ARG

LYS

THR

11

GLY

TYR

GLU

LYS

LEU

CYS

LEU

ARG

CYS

12

ILE

GLN

LYS

ASN

GLU

THR

ASN

GLY

SER

13

THR

CYS

ILE

CYS

ARG

VAL

PRO

ARG

ALA

GLN

14

LEU

GLU

ALA

ARG

LYS

GLY

THR

15

GLN

VAL

SER

PHE

HIS

GLN

CYS

VAL

HIS

CYS

16

GLY

CYS

ARG

GLY

CYS

ALA

SER

THR

ASP

Entity 2, ZN1 - Zn - 65.409 Da.

1

ZN

Samples:

sample_1: Bud31p (Zn)3, [U-98% 13C; U-98% 15N], 0.3 – 0.5 mM; sodium phosphate 20 mM; sodium chloride 150 mM; DTT, [U-2H], 1 mM; D2O 5%; H2O 95%

sample_2: Bud31p (Zn)3, [U-98% 13C; U-98% 15N], 0.3 – 0.5 mM; sodium phosphate 20 mM; sodium chloride 150 mM; DTT, [U-2H], 1 mM; D2O 100%

sample_3: Bud31p (Zn)3, [U-98% 15N], 0.3 – 0.5 mM; sodium phosphate 20 mM; sodium chloride 150 mM; DTT, [U-2H], 1 mM; D2O 5%; H2O 95%

sample_conditions_1: ionic strength: 0.27 M; pH: 6.5; pressure: 1 atm; temperature: 300 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_3	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC aliphatic (constant-time)	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC aromatic (constant-time)	sample_1	isotropic	sample_conditions_1
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_1	isotropic	sample_conditions_1
3D HNCACB	sample_1	isotropic	sample_conditions_1
3D CBCA(CO)NH	sample_1	isotropic	sample_conditions_1
3D HBHANH	sample_1	isotropic	sample_conditions_1
3D HBHA(CO)NH	sample_1	isotropic	sample_conditions_1
3D HC(C)H-COSY	sample_1	isotropic	sample_conditions_1
3D HC(C)H-TOCSY	sample_1	isotropic	sample_conditions_1
3D (H)CCH-TOCSY	sample_1	isotropic	sample_conditions_1
3D HNHB	sample_1	isotropic	sample_conditions_1
3D HACAHB	sample_2	isotropic	sample_conditions_1
3D 1H-15N NOESY (50ms mixing)	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY aliphatic (50ms mixing)	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY aromatic (50ms mixing)	sample_1	isotropic	sample_conditions_1
3D 1H-15N NOESY (150ms mixing)	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY aliphatic (150ms mixing)	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY aromatic (150ms mixing)	sample_1	isotropic	sample_conditions_1

Software:

TOPSPIN v3.1, Bruker Biospin - processing

SPARKY v3.115, Goddard - chemical shift assignment

X-PLOR_NIH v2.28, Schwieters, Kuszewski, Tjandra and Clore - structure solution

NMR spectrometers:

Bruker Avance AVI 800 MHz
Bruker DMX 600 MHz
Bruker DRX 500 MHz

Download simulated HSQC data in one of the following formats:
CSV: Backbone or all simulated shifts
SPARKY: Backbone or all simulated shifts