BMRB Entry 11463

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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/BMR11463
MolProbity Validation Chart

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NMR-STAR v3 text file.
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Title:
Solution structure of the bromodomain of human BRPF1 in complex with histone H4K5ac peptide
Deposition date:
2011-12-08
Original release date:
2013-03-26
Authors:
Qin, X. R.; Nagashima, T.; Umehara, T.; Hayashi, F.; Yokoyama, S.
Citation:

Citation: Qin, X. R.; Hayashi, F.; Yokoyama, S.. "Site-specific histone recognition by the bromodomain of Brpf1 and the role in MOZ/MORF histone acetyltransferase complexes"  .

Assembly members:

Assembly members:
An_acetylated-lysine_5_of_histone_4_peptide, polymer, 10 residues, 960.099 Da.
Bromodomain, polymer, 121 residues, 13777.645 Da.

Natural source:

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

Experimental source:

Experimental source:   Production method: chemical synthesis   Host organism: E. coli - cell free

Entity Sequences (FASTA):

Entity Sequences (FASTA):
An_acetylated-lysine_5_of_histone_4_peptide: SGRGXGGKGL
Bromodomain: GSSGSSGFLILLRKTLEQLQ EKDTGNIFSEPVPLSEVPDY LDHIKKPMDFFTMKQNLEAY RYLNFDDFEEDFNLIVSNCL KYNAKDTIFYRAAVRLREQG GAVLRQARRQAEKMGSGPSS G

Data sets:
Data typeCount
13C chemical shifts550
15N chemical shifts130
1H chemical shifts919

Additional metadata:

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

Entity Assembly IDEntity NameEntity ID
1An_acetylated-lysine_5_of_histone_4_peptide1
2Bromodomain2

Entities:

Entity 1, An_acetylated-lysine_5_of_histone_4_peptide 10 residues - 960.099 Da.

SGRG(ALY)GGKGL acetylated-lysine 5

1   SERGLYARGGLYALYGLYGLYLYSGLYLEU

Entity 2, Bromodomain 121 residues - 13777.645 Da.

41-47 and 156-161 represent a non-native affinity tag

1   GLYSERSERGLYSERSERGLYPHELEUILE
2   LEULEUARGLYSTHRLEUGLUGLNLEUGLN
3   GLULYSASPTHRGLYASNILEPHESERGLU
4   PROVALPROLEUSERGLUVALPROASPTYR
5   LEUASPHISILELYSLYSPROMETASPPHE
6   PHETHRMETLYSGLNASNLEUGLUALATYR
7   ARGTYRLEUASNPHEASPASPPHEGLUGLU
8   ASPPHEASNLEUILEVALSERASNCYSLEU
9   LYSTYRASNALALYSASPTHRILEPHETYR
10   ARGALAALAVALARGLEUARGGLUGLNGLY
11   GLYALAVALLEUARGGLNALAARGARGGLN
12   ALAGLULYSMETGLYSERGLYPROSERSER
13   GLY

Samples:

sample_1: entity_1 1.5 mM; entity_2, [U-99% 13C; U-99% 15N], 0.54 mM; H2O 90%; D2O 10%; sodium phosphate 50 mM; NaCl 50 mM; d-DTT 5 mM; NaN3 0.02%

sample_conditions_1: ionic strength: 100 mM; pH: 6.5; pressure: 1 atm; temperature: 288 K

Experiments:

NameSampleSample stateSample conditions
3D 1H-15N NOESYsample_1isotropicsample_conditions_1
3D 1H-13C NOESYsample_1isotropicsample_conditions_1
13C-edited (F1)sample_1isotropicsample_conditions_1
13C/15N-filtered (F3) 3D NOESYsample_1isotropicsample_conditions_1

Software:

NMRPipe v20100701, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

NMRView v5.0.4, Johnson, One Moon Scientific - processing

Kujira v0.9905, Kobayashi, N. - data analysis

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

AMBER v5, Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollm - refinement

NMR spectrometers:

  • Varian INOVA 800 MHz

Related Database Links:

EMBL P62805 CAD28495
PDB
DBJ BAC31528 BAE33691 BAG10583 BAG57257
GB AAB02119 AAF19605 AAH05647 AAH46521 AAI38362
REF NP_001178501 NP_001269055 NP_001269056 NP_004625 NP_084454
SP P55201
TPG DAA17219
AlphaFold P55201

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