BMRB Entry 18049

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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS, SPARTA
BMRB Entry DOI: doi:10.13018/BMR18049
MolProbity Validation Chart

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Title:
Low resolution structure of RNA-binding subunit of the TRAMP complex
Deposition date:
2011-11-10
Original release date:
2012-03-19
Authors:
Holub, Peter; Lalakova, Jana; Cerna, Hana; Sarazova, Marie; Pasulka, Josef; Hrazdilova, Kristyna; Arce, Maria; Stefl, Richard; Vanacova, Stepanka
Citation:

Citation: Holub, Peter; Lalakova, Jana; Cerna, Hana; Pasulka, Josef; Sarazova, Marie; Hrazdilova, Kristyna; Arce, Maria Sanudo; Hobor, Fruzsina; Stefl, Richard; Vanacova, Stepanka. "Air2p is critical for the assembly and RNA-binding of the TRAMP complex and the KOW domain of Mtr4p is crucial for exosome activation."  Nucleic Acids Res. 40, 5679-5693 (2012).
PubMed: 22402490

Assembly members:

Assembly members:
RNA-binding subunit of the TRAMP complex, polymer, 124 residues, 14263.607 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: Saccharomyces cerevisiae   Vector: pNOPPATA1L

Entity Sequences (FASTA):

Entity Sequences (FASTA):
RNA-binding subunit of the TRAMP complex: KEAAPKCNNCSQRGHLKKDC PHIICSYCGATDDHYSRHCP KAIQCSKCDEVGHYRSQCPH KWKKVQCTLCKSKKHSKERC PSIWRAYILVDDNEKAKPKV LPFHTIYCYNCGGKGHFGDD CKEK

Data sets:
Data typeCount
13C chemical shifts240
15N chemical shifts89
1H chemical shifts431

Additional metadata:

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

Entity Assembly IDEntity NameEntity ID
1RNA-binding subunit of the TRAMP complex1
2ZINC ION_12
3ZINC ION_22
4ZINC ION_32
5ZINC ION_42
6ZINC ION_52

Entities:

Entity 1, RNA-binding subunit of the TRAMP complex 124 residues - 14263.607 Da.

1   LYSGLUALAALAPROLYSCYSASNASNCYS
2   SERGLNARGGLYHISLEULYSLYSASPCYS
3   PROHISILEILECYSSERTYRCYSGLYALA
4   THRASPASPHISTYRSERARGHISCYSPRO
5   LYSALAILEGLNCYSSERLYSCYSASPGLU
6   VALGLYHISTYRARGSERGLNCYSPROHIS
7   LYSTRPLYSLYSVALGLNCYSTHRLEUCYS
8   LYSSERLYSLYSHISSERLYSGLUARGCYS
9   PROSERILETRPARGALATYRILELEUVAL
10   ASPASPASNGLULYSALALYSPROLYSVAL
11   LEUPROPHEHISTHRILETYRCYSTYRASN
12   CYSGLYGLYLYSGLYHISPHEGLYASPASP
13   CYSLYSGLULYS

Entity 2, ZINC ION_1 - Zn - 65.409 Da.

1   ZN

Samples:

sample_1: RNA-binding_sub, [U-99% 13C; U-99% 15N], 100 uM; H2O 90%; D2O 10%; sodium phosphate buffer 50 mM; sodium chloride 500 mM; beta-mercaptoethanol 10 mM

sample_conditions_1: ionic strength: 0.5 M; pH: 8; pressure: 1 atm; temperature: 293 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
3D 1H-15N NOESYsample_1isotropicsample_conditions_1
3D 1H-13C NOESY aliphaticsample_1isotropicsample_conditions_1
3D HNCACBsample_1isotropicsample_conditions_1
3D CBCA(CO)NHsample_1isotropicsample_conditions_1
3D HNHAsample_1isotropicsample_conditions_1
3D HNCAsample_1isotropicsample_conditions_1

Software:

CYANA v2.1, Guntert, Mumenthaler and Wuthrich - structure solution

NMR spectrometers:

  • Bruker Avance 600 MHz
  • Bruker Avance 900 MHz

Related Database Links:

PDB
DBJ GAA22076
EMBL CAA91570 CAA98749 CAY78334
GB AHY74840 AJP37581 AJU57693 AJU58396 AJU59085
REF NP_010106
SP Q12476
TPG DAA11687
AlphaFold Q12476

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