BMRB Entry 25953

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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, SPARTA
BMRB Entry DOI: doi:10.13018/BMR25953
MolProbity Validation Chart

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Title:
Structure of CCHC zinc finger domain of Pcf11
Deposition date:
2016-01-12
Original release date:
2016-11-17
Authors:
Yang, Fan; Varani, Gabriele
Citation:

Citation: Yang, Fan; Hsu, Peter; Lee, Susan; Yang, Wen; Hoskinson, Derick; Xu, Weihao; Moore, Claire; Varani, Gabriele. "The C-terminus of Pcf11 forms a novel zinc-finger structure that plays an essential role in mRNA 3'- end processing"  RNA 23, 98-107 (2017).
PubMed: 27780845

Assembly members:

Assembly members:
entity_1, polymer, 76 residues, 8701.422 Da.
ZINC ION, non-polymer, 65.409 Da.

Natural source:

Natural source:   Common Name: bakers 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: pET-28a

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: GGSEFSDRSNELEIRGKYVV VPETSQDMAFKXPIXKETVT GVYDEESGEWVWKNTIEVNG KYFXSTXYXETSQNSS

Data sets:
Data typeCount
13C chemical shifts291
15N chemical shifts77
1H chemical shifts457

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 76 residues - 8701.422 Da.

1   GLYGLYSERGLUPHESERASPARGSERASN
2   GLULEUGLUILEARGGLYLYSTYRVALVAL
3   VALPROGLUTHRSERGLNASPMETALAPHE
4   LYSCY2PROILECY2LYSGLUTHRVALTHR
5   GLYVALTYRASPGLUGLUSERGLYGLUTRP
6   VALTRPLYSASNTHRILEGLUVALASNGLY
7   LYSTYRPHEHE1SERTHRCY2TYRHIEGLU
8   THRSERGLNASNSERSER

Entity 2, ZINC ION - 65.409 Da.

1   ZN

Samples:

sample_1: entity_1, [U-99% 13C; U-99% 15N], 1 mM; H2O 90%; D2O 10%

sample_2: entity_1, [U-99% 15N], 1 mM; H2O 90%; D2O 10%

sample_3: entity_1, [U-99% 13C; U-99% 15N], 1 mM; D2O 100%

sample_conditions_1: ionic strength: 120 mM; pH: 7.4; pressure: 1 atm; temperature: 298 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_2isotropicsample_conditions_1
2D 1H-13C HSQCsample_3isotropicsample_conditions_1
3D HNCOsample_1isotropicsample_conditions_1
3D HNCAsample_1isotropicsample_conditions_1
3D HNCACBsample_1isotropicsample_conditions_1
3D CBCA(CO)NHsample_1isotropicsample_conditions_1
3D HBHA(CO)NHsample_1isotropicsample_conditions_1
3D HCCH-TOCSYsample_3isotropicsample_conditions_1
3D 1H-15N NOESY-HSQCsample_2isotropicsample_conditions_1
3D 1H-13C NOESY-HSQCsample_3isotropicsample_conditions_1

Software:

AMBER, Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollman - refinement

TOPSPIN, Bruker Biospin - collection

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

CCPNMR, CCPN - chemical shift assignment

CYANA, Guntert, Mumenthaler and Wuthrich - structure solution

NMR spectrometers:

  • Bruker Avance 500 MHz
  • 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