BMRB Entry 17315

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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/BMR17315
MolProbity Validation Chart

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Title:
Structure of C-terminal dsRBD of the Fission Yeast DICER (Dcr1)
Deposition date:
2010-11-23
Original release date:
2011-10-25
Authors:
Barraud, Pierre; Allain, Frederic
Citation:

Citation: Barraud, Pierre; Emmerth, Stephan; Shimada, Yukiko; Hotz, Hans-Rudolf; Allain, Frederic; Buhler, Marc. "An extended dsRBD with a novel zinc-binding motif mediates nuclear retention of fission yeast Dicer"  EMBO J. 30, 4223-4235 (2011).
PubMed: 21847092

Assembly members:

Assembly members:
dsRBD, polymer, 121 residues, 11806.978 Da.
ZN, non-polymer, 65.409 Da.

Natural source:

Natural source:   Common Name: fission yeast   Taxonomy ID: 4896   Superkingdom: Eukaryota   Kingdom: Fungi   Genus/species: Schizosaccharomyces pombe

Experimental source:

Experimental source:   Production method: recombinant technology   Host organism: Escherichia coli   Vector: pET28a+

Entity Sequences (FASTA):

Entity Sequences (FASTA):
dsRBD: MGSSHHHHHHSSGLVPRGSH MKGDIEHKVYQLLKDQGCED FGTKCVIEEVKSSHKTLLNT ELHLTKYYGFSFFRHGNIVA YGKSRKVANAKYIMKQRLLK LLEDKSNLLLYSCNCKFSKK K

Data sets:
Data typeCount
13C chemical shifts316
15N chemical shifts100
1H chemical shifts677

Additional metadata:

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

Entity Assembly IDEntity NameEntity ID
1dsRBD1
2ZINC ION2

Entities:

Entity 1, dsRBD 121 residues - 11806.978 Da.

1   METGLYSERSERHISHISHISHISHISHIS
2   SERSERGLYLEUVALPROARGGLYSERHIS
3   METLYSGLYASPILEGLUHISLYSVALTYR
4   GLNLEULEULYSASPGLNGLYCYSGLUASP
5   PHEGLYTHRLYSCYSVALILEGLUGLUVAL
6   LYSSERSERHISLYSTHRLEULEUASNTHR
7   GLULEUHISLEUTHRLYSTYRTYRGLYPHE
8   SERPHEPHEARGHISGLYASNILEVALALA
9   TYRGLYLYSSERARGLYSVALALAASNALA
10   LYSTYRILEMETLYSGLNARGLEULEULYS
11   LEULEUGLUASPLYSSERASNLEULEULEU
12   TYRSERCYSASNCYSLYSPHESERLYSLYS
13   LYS

Entity 2, ZINC ION - Zn - 65.409 Da.

1   ZN

Samples:

13C15N: dsRBD, [U-100% 13C; U-100% 15N], 0.5 mM; sodium phosphate 25 mM; potassium chloride 75 mM; DTT 2 mM; ZINC ION 0.01 mM; H2O 90%; D2O 10%

1H: dsRBD 0.5 mM; sodium phosphate 25 mM; potassium chloride 75 mM; DTT 2 mM; ZINC ION 0.01 mM; D2O 100%

15N: dsRBD, [U-100% 15N], 0.5 mM; sodium phosphate 25 mM; potassium chloride 75 mM; DTT 2 mM; ZINC ION 0.01 mM; H2O 90%; D2O 10%

sample_conditions_1: ionic strength: 100 mM; pH: 7.0; pressure: 1 atm; temperature: 298.0 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQC15Nisotropicsample_conditions_1
2D 1H-13C HSQC13C15Nisotropicsample_conditions_1
3D HNCA13C15Nisotropicsample_conditions_1
3D HNCACB13C15Nisotropicsample_conditions_1
3D CBCA(CO)NH13C15Nisotropicsample_conditions_1
3D 1H-15N TOCSY15Nisotropicsample_conditions_1
3D HCCH-TOCSY13C15Nisotropicsample_conditions_1
3D 1H-15N NOESY15Nisotropicsample_conditions_1
3D 1H-13C NOESY13C15Nisotropicsample_conditions_1
2D 1H-1H TOCSY1Hisotropicsample_conditions_1
2D 1H-1H NOESY1Hisotropicsample_conditions_1

Software:

CYANA, Guntert, Mumenthaler and Wuthrich - automatic noe assignment, structure calculation

SPARKY, Goddard - chemical shift assignment, data analysis

ATHNOS-CANDID, Herrmann, Guntert and Wuthrich - peak picking

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

NMR spectrometers:

  • Bruker Avance 500 MHz
  • Bruker Avance 700 MHz
  • Bruker Avance 900 MHz

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