BMRB Entry 25439

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PDB ID:
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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Title:
Solution structure and 1H, 13C, and 15N chemical shift assignments for Bud31p
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:

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).
PubMed: 25703931

Assembly members:

Assembly members:
Bud31p_polypeptide, polymer, 159 residues, 18554.609 Da.
ZINC ION, 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: pRK172

Entity Sequences (FASTA):

Entity Sequences (FASTA):
Bud31p_polypeptide: GGSPRIKTRRSKPAPDGFEK IKPTLTDFEIQLRDAQKDKS SKLAAKSNEQLWEIMQLHHQ RSRYIYTLYYKRKAISKDLY DWLIKEKYADKLLIAKWRKT GYEKLCCLRCIQKNETNNGS TCICRVPRAQLEEEARKKGT QVSFHQCVHCGCRGCASTD

Data sets:
Data typeCount
13C chemical shifts509
15N chemical shifts167
1H chemical shifts1022

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
  • Hide all

Assembly:

Entity Assembly IDEntity NameEntity ID
1Bud31p polypeptide1
2ZN12
3ZN22
4ZN32

Entities:

Entity 1, Bud31p polypeptide 159 residues - 18554.609 Da.

1   GLYGLYSERPROARGILELYSTHRARGARG
2   SERLYSPROALAPROASPGLYPHEGLULYS
3   ILELYSPROTHRLEUTHRASPPHEGLUILE
4   GLNLEUARGASPALAGLNLYSASPLYSSER
5   SERLYSLEUALAALALYSSERASNGLUGLN
6   LEUTRPGLUILEMETGLNLEUHISHISGLN
7   ARGSERARGTYRILETYRTHRLEUTYRTYR
8   LYSARGLYSALAILESERLYSASPLEUTYR
9   ASPTRPLEUILELYSGLULYSTYRALAASP
10   LYSLEULEUILEALALYSTRPARGLYSTHR
11   GLYTYRGLULYSLEUCYSCYSLEUARGCYS
12   ILEGLNLYSASNGLUTHRASNASNGLYSER
13   THRCYSILECYSARGVALPROARGALAGLN
14   LEUGLUGLUGLUALAARGLYSLYSGLYTHR
15   GLNVALSERPHEHISGLNCYSVALHISCYS
16   GLYCYSARGGLYCYSALASERTHRASP

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:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_3isotropicsample_conditions_1
2D 1H-13C HSQCsample_1isotropicsample_conditions_1
2D 1H-13C HSQC aliphatic (constant-time)sample_1isotropicsample_conditions_1
2D 1H-13C HSQC aromatic (constant-time)sample_1isotropicsample_conditions_1
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
2D 1H-1H NOESYsample_1isotropicsample_conditions_1
3D HNCACBsample_1isotropicsample_conditions_1
3D CBCA(CO)NHsample_1isotropicsample_conditions_1
3D HBHANHsample_1isotropicsample_conditions_1
3D HBHA(CO)NHsample_1isotropicsample_conditions_1
3D HC(C)H-COSYsample_1isotropicsample_conditions_1
3D HC(C)H-TOCSYsample_1isotropicsample_conditions_1
3D (H)CCH-TOCSYsample_1isotropicsample_conditions_1
3D HNHBsample_1isotropicsample_conditions_1
3D HACAHBsample_2isotropicsample_conditions_1
3D 1H-15N NOESY (50ms mixing)sample_1isotropicsample_conditions_1
3D 1H-13C NOESY aliphatic (50ms mixing)sample_1isotropicsample_conditions_1
3D 1H-13C NOESY aromatic (50ms mixing)sample_1isotropicsample_conditions_1
3D 1H-15N NOESY (150ms mixing)sample_1isotropicsample_conditions_1
3D 1H-13C NOESY aliphatic (150ms mixing)sample_1isotropicsample_conditions_1
3D 1H-13C NOESY aromatic (150ms mixing)sample_1isotropicsample_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 HSQC peak lists in one of the following formats:
CSV: Backbone or all simulated peaks
SPARKY: Backbone or all simulated peaks