BMRB Entry 34061

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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR34061
MolProbity Validation Chart

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Title:
Second zinc-binding domain from yeast Pcf11
Deposition date:
2016-11-02
Original release date:
2017-07-26
Authors:
Mackereth, C.
Citation:

Citation: Guegueniat, Julia; Dupin, Adrien; Stojko, Johan; Beaurepaire, Lionel; Cianferani, Sarah; Mackereth, Cameron; Minvielle-Sebastia, Lionel; Fribourg, Sebastien. "Distinct roles of Pcf11 zinc-binding domains in pre-mRNA 3'-end processing."  Nucleic Acids Res. 45, 10115-10131 (2017).
PubMed: 28973460

Assembly members:

Assembly members:
Protein PCF11, polymer, 97 residues, 10838.987 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 BL21   Vector: pET-His1a

Entity Sequences (FASTA):

Entity Sequences (FASTA):
Protein PCF11: GSVDNTLGSDRSNELEIRGK YVVVPETSQDMAFKCPICKE TVTGVYDEESGEWVWKNTIE VNGKYFHSTCYHETSQNSSK SNSGKVGLDDLKKLVTK

Data typeCount
13C chemical shifts228
15N chemical shifts52
1H chemical shifts352

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
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Assembly:

Entity Assembly IDEntity NameEntity ID
1entity_11
2ZINC ION2

Entities:

Entity 1, entity_1 97 residues - 10838.987 Da.

1   GLYSERVALASPASNTHRLEUGLYSERASP
2   ARGSERASNGLULEUGLUILEARGGLYLYS
3   TYRVALVALVALPROGLUTHRSERGLNASP
4   METALAPHELYSCYSPROILECYSLYSGLU
5   THRVALTHRGLYVALTYRASPGLUGLUSER
6   GLYGLUTRPVALTRPLYSASNTHRILEGLU
7   VALASNGLYLYSTYRPHEHISSERTHRCYS
8   TYRHISGLUTHRSERGLNASNSERSERLYS
9   SERASNSERGLYLYSVALGLYLEUASPASP
10   LEULYSLYSLEUVALTHRLYS

Entity 2, ZINC ION - 65.409 Da.

1   ZN

Samples:

sample_2: Pcf11, [U-99% 15N], 250 uM; TRIS 50 mM; sodium chloride 150 mM; zinc acetate 50 uM; H2O 90%; D2O 10%

sample_3: Pcf11, [U-99% 13C; U-99% 15N], 230 uM; TRIS 50 mM; sodium chloride 150 mM; zinc acetate 50 uM; H2O 90%; D2O 10%

sample_4: Pcf11, [U-99% 13C; U-99% 15N], 230 uM; TRIS 50 mM; sodium chloride 150 mM; zinc acetate 50 uM; D2O 100%

sample_5: Pcf11, [U-10% 13C; U-99% 15N], 100 uM; TRIS 50 mM; sodium chloride 150 mM; zinc acetate 50 uM; H2O 90%; D2O 10%

sample_1: Pcf11 360 uM; TRIS 50 mM; sodium chloride 150 mM; zinc acetate 50 uM; H2O 90%; D2O 10%

sample_conditions_1: ionic strength: 200 mM; pH: 7.5; pressure: 1 atm; temperature: 298 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_2isotropicsample_conditions_1
3D HNCOsample_3isotropicsample_conditions_1
3D HNCACOsample_3isotropicsample_conditions_1
3D HNCAsample_3isotropicsample_conditions_1
3D CBCA(CO)NHsample_3isotropicsample_conditions_1
3D HNCACBsample_3isotropicsample_conditions_1
3D HNHAsample_2isotropicsample_conditions_1
2D 1H-13C HSQCsample_4isotropicsample_conditions_1
3D H(CCO)NHsample_3isotropicsample_conditions_1
3D H(C)CH-TOCSYsample_4isotropicsample_conditions_1
3D (H)CCH-TOCSYsample_4isotropicsample_conditions_1
2D 1H-13C HSQC CTsample_5isotropicsample_conditions_1
3D 1H-15N NOESYsample_2isotropicsample_conditions_1
2D 1H-15N HMBCsample_2isotropicsample_conditions_1
3D 1H-13C NOESYsample_4isotropicsample_conditions_1
2D 1H-1H NOESYsample_1isotropicsample_conditions_1

Software:

ARIA, Linge, O'Donoghue and Nilges - structure calculation

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

SPARKY, Goddard - chemical shift assignment, peak picking

TOPSPIN, Bruker Biospin - collection

NMR spectrometers:

  • Bruker AvanceIII 800 MHz
  • Bruker Avanc 700 MHz

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