BMRB Entry 25649

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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, SPARTA
BMRB Entry DOI: doi:10.13018/BMR25649
MolProbity Validation Chart

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Title:
Human Brd4 ET domain in complex with MLV Integrase C-term
Deposition date:
2015-06-03
Original release date:
2016-02-29
Authors:
Crowe, Brandon; Foster, Mark
Citation:

Citation: Crowe, Brandon; Larue, Ross; Yuan, Chunhua; Kvaratskhelia, Mamuka; Foster, Mark. "Structure of the Brd4 ET domain bound to a C-terminal motif from gamma-retroviral integrases reveals a conserved mechanism of interaction"  Proc. Natl. Acad. Sci. U. S. A. 113, 2086-2091 (2016).
PubMed: 26858406

Assembly members:

Assembly members:
Brd4_ET, polymer, 86 residues, 9291.632 Da.
MLV_IN_EBM, polymer, 17 residues, 2157.567 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: recombinant technology   Host organism: Escherichia coli   Vector: pEX-N-His

Entity Sequences (FASTA):

Entity Sequences (FASTA):
Brd4_ET: GAIAMESEEEDKCKPMSYEE KRQLSLDINKLPGEKLGRVV HIIQSREPSLKNSNPDEIEI DFETLKPSTLRELERYVTSC LRKKTR
MLV_IN_EBM: TWRVQRSQNPLKIRLTR

Data sets:
Data typeCount
13C chemical shifts354
15N chemical shifts86
1H chemical shifts551

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 86 residues - 9291.632 Da.

Residues 1-5 (GAIAM) are non-native cloning artifacts. Residues 6-84 are human Brd4 ET domain (600-678) Residues 85-86 (TR) are non native cloning artifacts.

1   GLYALAILEALAMETGLUSERGLUGLUGLU
2   ASPLYSCYSLYSPROMETSERTYRGLUGLU
3   LYSARGGLNLEUSERLEUASPILEASNLYS
4   LEUPROGLYGLULYSLEUGLYARGVALVAL
5   HISILEILEGLNSERARGGLUPROSERLEU
6   LYSASNSERASNPROASPGLUILEGLUILE
7   ASPPHEGLUTHRLEULYSPROSERTHRLEU
8   ARGGLULEUGLUARGTYRVALTHRSERCYS
9   LEUARGLYSLYSTHRARG

Entity 2, entity_2 17 residues - 2157.567 Da.

residues 1-17 are MLV Integrase C-term EBM(389-405)

1   THRTRPARGVALGLNARGSERGLNASNPRO
2   LEULYSILEARGLEUTHRARG

Samples:

U13C-15NBrd4_MLV_in_H2O: Brd4 ET, [U-99% 13C; U-99% 15N], 0.4 – 0.8 mM; MLV IN EBM0.4 – 0.8 mM; TRIS, [U-2H], 20 mM; sodium chloride 100 mM; sodium azide 0.002 % v/v; DSS 0.5 mM; DTT, [U-2H], 2 mM; H2O 90%; D2O 10%

U13C-15NBrd4_MLV_in_D2O: Brd4 ET, [U-99% 13C; U-99% 15N], 0.4 – 0.8 mM; MLV IN EBM0.4 – 0.8 mM; TRIS, [U-2H], 20 mM; sodium chloride 100 mM; sodium azide 0.002 % v/v; DSS 0.5 mM; DTT, [U-2H], 2 mM; D2O 100%

U15NBrd4_MLV_in_H2O: Brd4 ET, [U-99% 15N], 0.4 – 0.8 mM; MLV IN EBM0.4 – 0.8 mM; TRIS, [U-2H], 20 mM; sodium chloride 100 mM; sodium azide 0.002 % v/v; DSS 0.5 mM; DTT, [U-2H], 2 mM; H2O 90%; D2O 10%

U15NBrd4_free: Brd4 ET, [U-99% 15N], 0.4 – 0.8 mM; TRIS, [U-2H], 20 mM; sodium chloride 100 mM; sodium azide 0.002 % v/v; DSS 0.5 mM; DTT, [U-2H], 2 mM; H2O 90%; D2O 10%

MLV_IN_EBM_in_H2O: MLV IN EBM 1 mM; DSS 0.5 mM; sodium azide 0.002 % v/v; H2O 90%; D2O 10%

sample_conditions_1: ionic strength: 0.25 M; pH: 7.0; pressure: 1 atm; temperature: 298 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCU15NBrd4_freeisotropicsample_conditions_1
2D 1H-15N HSQCU15NBrd4_MLV_in_H2Oisotropicsample_conditions_1
2D 1H-15N HSQCU13C-15NBrd4_MLV_in_H2Oisotropicsample_conditions_1
2D 1H-13C HSQC aliphaticU13C-15NBrd4_MLV_in_H2Oisotropicsample_conditions_1
2D 1H-13C HSQC aliphaticU13C-15NBrd4_MLV_in_D2Oisotropicsample_conditions_1
1D 13C,15N-filtered watergate 1HMLV_IN_EBM_in_H2Oisotropicsample_conditions_1
1D 13C,15N-filtered watergate 1HU13C-15NBrd4_MLV_in_H2Oisotropicsample_conditions_1
3D HNCOU13C-15NBrd4_MLV_in_H2Oisotropicsample_conditions_1
3D HNCAU13C-15NBrd4_MLV_in_H2Oisotropicsample_conditions_1
3D HNCACBU13C-15NBrd4_MLV_in_H2Oisotropicsample_conditions_1
3D CBCA(CO)NHU13C-15NBrd4_MLV_in_H2Oisotropicsample_conditions_1
3D HBHA(CO)NHU13C-15NBrd4_MLV_in_H2Oisotropicsample_conditions_1
3D HCCH-TOCSYU13C-15NBrd4_MLV_in_H2Oisotropicsample_conditions_1
3D CC(CO)NH-TOCSYU13C-15NBrd4_MLV_in_H2Oisotropicsample_conditions_1
2D 13C,15N-filtered 1H-1H COSYU13C-15NBrd4_MLV_in_H2Oisotropicsample_conditions_1
2D 13C,15N-filtered 1H-1H TOCSYU13C-15NBrd4_MLV_in_H2Oisotropicsample_conditions_1
2D 13C,15N-filtered 1H-1H NOESYU13C-15NBrd4_MLV_in_H2Oisotropicsample_conditions_1
2D 13C,15N-filtered 1H-1H COSYU13C-15NBrd4_MLV_in_D2Oisotropicsample_conditions_1
2D 13C,15N-filtered 1H-1H TOCSYU13C-15NBrd4_MLV_in_D2Oisotropicsample_conditions_1
2D 13C,15N-filtered 1H-1H NOESYU13C-15NBrd4_MLV_in_D2Oisotropicsample_conditions_1
3D 1H-15N NOESYU13C-15NBrd4_MLV_in_H2Oisotropicsample_conditions_1
3D 1H-13C NOESY aliphaticU13C-15NBrd4_MLV_in_H2Oisotropicsample_conditions_1
3D 1H-13C NOESY aliphaticU13C-15NBrd4_MLV_in_D2Oisotropicsample_conditions_1
3D 13C,15N-filtered(f1) 1H-15N(f2) NOESYU13C-15NBrd4_MLV_in_H2Oisotropicsample_conditions_1
3D 13C,15N-filtered(f1) 1H-13C(f2) NOESY aliphaticU13C-15NBrd4_MLV_in_D2Oisotropicsample_conditions_1

Software:

xwinnmr, Bruker Biospin - collection

TOPSPIN, Bruker Biospin - collection

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

NMRViewJ v8.1.17, Johnson, One Moon Scientific - chemical shift assignment, data analysis, peak picking

PINE, Bahrami, Markley, Assadi, and Eghbalnia - chemical shift assignment

TALOS-N, Cornilescu, Delaglio and Bax - data analysis

CYANA v3.97, Guntert, Mumenthaler and Wuthrich - refinement, structure solution

PSVS, Bhattacharya and Montelione - data analysis

NMR spectrometers:

  • Bruker Avance III HD Ultrashield 600 MHz
  • Bruker Avance III HD Ascend 700 MHz
  • Bruker Avance III HD 800 MHz

Related Database Links:

NCBI NP_490597.1
GB AAC58562.1
UNP O10624
AlphaFold O10624

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