BMRB

Biological Magnetic Resonance Data Bank


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BMRB Entry 34058

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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/BMR34058
MolProbity Validation Chart

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Title: Solution structure of Rtt103 CTD-interacting domain bound to a Ser2Ser7 phosphorylated CTD peptide   PubMed: 29073019

Deposition date: 2016-11-01 Original release date: 2017-10-09

Authors: Jasnovidova, O.; Kubicek, K.; Stefl, R.

Citation: Jasnovidova, O.; Klumpler, T.; Kubicek, K.; Kalynych, S.; Plevka, P.; Stefl, R.. "Structure and dynamics of the RNAPII CTDsome with Rtt103"  Proc. Natl. Acad. Sci. U. S. A. 114, 11133-11138 (2017).

Assembly members:
entity_1, polymer, 142 residues, 16569.100 Da.
entity_2, polymer, 16 residues, 1965.594 Da.

Natural source:   Common Name: baker's yeast   Taxonomy ID: 559292   Superkingdom: Eukaryota   Kingdom: Fungi   Genus/species: Saccharomyces cerevisiae

Experimental source:   Production method: recombinant technology   Host organism: Escherichia coli

Entity Sequences (FASTA):
entity_1: MAFSSEQFTTKLNTLEDSQE SISSASKWLLLQYRDAPKVA EMWKEYMLRPSVNTRRKLLG LYLMNHVVQQAKGQKIIQFQ DSFGKVAAEVLGRINQEFPR DLKKKLSRVVNILKERNIFS KQVVNDIERSLAAALEHHHH HH
entity_2: TSPXYXPTSPXYXPTS

Data sets:
Data typeCount
13C chemical shifts487
15N chemical shifts147
1H chemical shifts1013

Additional metadata:

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

Entity Assembly IDEntity NameEntity ID
1entity_11
2entity_22

Entities:

Entity 1, entity_1 142 residues - 16569.100 Da.

1   METALAPHESERSERGLUGLNPHETHRTHR
2   LYSLEUASNTHRLEUGLUASPSERGLNGLU
3   SERILESERSERALASERLYSTRPLEULEU
4   LEUGLNTYRARGASPALAPROLYSVALALA
5   GLUMETTRPLYSGLUTYRMETLEUARGPRO
6   SERVALASNTHRARGARGLYSLEULEUGLY
7   LEUTYRLEUMETASNHISVALVALGLNGLN
8   ALALYSGLYGLNLYSILEILEGLNPHEGLN
9   ASPSERPHEGLYLYSVALALAALAGLUVAL
10   LEUGLYARGILEASNGLNGLUPHEPROARG
11   ASPLEULYSLYSLYSLEUSERARGVALVAL
12   ASNILELEULYSGLUARGASNILEPHESER
13   LYSGLNVALVALASNASPILEGLUARGSER
14   LEUALAALAALALEUGLUHISHISHISHIS
15   HISHIS

Entity 2, entity_2 16 residues - 1965.594 Da.

1   THRSERPROSEPTYRSEPPROTHRSERPRO
2   SEPTYRSEPPROTHRSER

Samples:

sample_1: CTD-interacting domain of Rtt103p, [U-13C; U-15N], 1 ± 0.2 mM; THR-SER-PRO-SEP-TYR-SEP-PRO-THR-SER-PRO-SEP-TYR-SEP-PRO-THR-SER 1.5 ± 0.2 mM; KH2PO4 35 mM; KCl 100 mM

sample_conditions_1: ionic strength: 100 mM; pH: 6.8; pressure: 760 mmHg; temperature: 298 K

Experiments:

NameSampleSample stateSample conditions
3D 1H-15N NOESYsample_1anisotropicsample_conditions_1
3D 1H-13C NOESY aliphaticsample_1anisotropicsample_conditions_1
3D 1H-13C NOESY aromaticsample_1anisotropicsample_conditions_1
3D CBCA(CO)NHsample_1anisotropicsample_conditions_1
3D HCCH-TOCSYsample_1anisotropicsample_conditions_1
F1-13C/15N-filtered NOESY-[13C,1H]-HSQCsample_1anisotropicsample_conditions_1

Software:

AMBER v16, Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman - refinement

CYANA v3.97, Guntert, Mumenthaler and Wuthrich - structure calculation

SPARKY, Goddard - chemical shift assignment, peak picking

TOPSPIN v3.2, Bruker Biospin - collection

NMR spectrometers:

  • Bruker AvanceIII 700 MHz
  • Bruker AvanceIII 850 MHz
  • Bruker AvanceIII 950 MHz

Download simulated HSQC data in one of the following formats:
CSV: Backbone or all simulated shifts
SPARKY: Backbone or all simulated shifts