BMRB

Biological Magnetic Resonance Data Bank


A Repository for Data from NMR Spectroscopy on Proteins, Peptides, Nucleic Acids, and other Biomolecules
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BMRB Entry 18439

Title: solution structures of BRD4 second bromodomain with NF-kB-K310ac peptide   PubMed: 22645123

Deposition date: 2012-05-03 Original release date: 2012-06-05

Authors: Zhang, Guangtao; Liu, Ruijie; Zhong, Yifei; Plotnikov, Alexander; Zhang, Weijia; Rusinova, Elena; Gerona-Nevarro, Guillermo; Moshkina, Natasha; Joshua, Jennifer; Chuang, Peter; Ohlmeyer, Michael; He, John Cijiang

Citation: Zhang, Guangtao; Liu, Ruijie; Zhong, Yifei; Plotnikov, Alexander; Zhang, Weijia; Zeng, Lei; Rusinova, Elena; Gerona-Nevarro, Guillermo; Moshkina, Natasha; Joshua, Jennifer; Chuang, Peter; Ohlmeyer, Michael; He, John Cijiang; Zhou, Ming-Ming. "Down-regulation of NF-B transcriptional activity in HIV-associated kidney disease by BRD4 inhibition."  J. Biol. Chem. 287, 28840-28851 (2012).

Assembly members:
entity_1, polymer, 13 residues, 1663.968 Da.
entity_2, polymer, 128 residues, 14842.159 Da.

Natural source:   Common Name: Human   Taxonomy ID: 9606   Superkingdom: Eukaryota   Kingdom: Metazoa   Genus/species: Homo sapiens

Experimental source:   Production method: chemical synthesis

Entity Sequences (FASTA):
entity_1: RTYETFXSIMKKS
entity_2: KDVPDSQQHPAPEKSSKVSE QLKCCSGILKEMFAKKHAAY AWPFYKPVDVEALGLHDYCD IIKHPMDMSTIKSKLEAREY RDAQEFGADVRLMFSNCYKY NPPDHEVVAMARKLQDVFEM RFAKMPDE

Data sets:
Data typeCount
13C chemical shifts444
15N chemical shifts117
1H chemical shifts874

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
  • Hide all

Assembly:

Entity Assembly IDEntity NameEntity ID
1NF-kB-K310ac peptide1
2BRD4 second bromodomain2

Entities:

Entity 1, NF-kB-K310ac peptide 13 residues - 1663.968 Da.

1   ARGTHRTYRGLUTHRPHEALYSERILEMET
2   LYSLYSSER

Entity 2, BRD4 second bromodomain 128 residues - 14842.159 Da.

1   LYSASPVALPROASPSERGLNGLNHISPRO
2   ALAPROGLULYSSERSERLYSVALSERGLU
3   GLNLEULYSCYSCYSSERGLYILELEULYS
4   GLUMETPHEALALYSLYSHISALAALATYR
5   ALATRPPROPHETYRLYSPROVALASPVAL
6   GLUALALEUGLYLEUHISASPTYRCYSASP
7   ILEILELYSHISPROMETASPMETSERTHR
8   ILELYSSERLYSLEUGLUALAARGGLUTYR
9   ARGASPALAGLNGLUPHEGLYALAASPVAL
10   ARGLEUMETPHESERASNCYSTYRLYSTYR
11   ASNPROPROASPHISGLUVALVALALAMET
12   ALAARGLYSLEUGLNASPVALPHEGLUMET
13   ARGPHEALALYSMETPROASPGLU

Samples:

sample_2: sodium phosphate 100 mM; DTT, [U-100% 2H], 5 mM; D2O 10%; H2O 90%

sample_1: sodium phosphate 100 mM; DTT, [U-100% 2H], 5 mM; D2O 100%

sample_conditions_1: ionic strength: 100 mM; pH: 6.5; pressure: 1 atm; temperature: 298 K

Experiments:

NameSampleSample stateSample conditions
3D HNCACBsample_2isotropicsample_conditions_1
3D HN(CO)CACBsample_2isotropicsample_conditions_1
3D 1H-15N NOESYsample_2isotropicsample_conditions_1
3D 1H-13C NOESY aliphaticsample_1isotropicsample_conditions_1
3D 1H-13C NOESY aromaticsample_1isotropicsample_conditions_1
3D 13C-Edited-15N/13C filtered NOESYsample_1isotropicsample_conditions_1

Software:

ARIA v2.3, Linge, O'Donoghue and Nilges - refinement

NMRPipe v7.1, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - chemical shift calculation, processing

TALOS v3.70F1, Cornilescu, Delaglio and Bax - geometry optimization

NMRView v5.04, Johnson, One Moon Scientific - chemical shift assignment, data analysis, peak picking

CNS v1.21, Brunger, Adams, Clore, Gros, Nilges and Read - structure solution

NMR spectrometers:

  • Bruker Avance 800 MHz
  • Bruker Avance 900 MHz
  • Bruker Avance 600 MHz
  • Bruker DRX 500 MHz

Related Database Links:

BMRB 15057 19738
PDB
REF XP_004761195 XP_006524755 XP_006524756 XP_008763395

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