BMRBj - BMREntryMaster

Found 1 Document (3.018 seconds)

BMRB: 30368

6BGH

Solution NMR structure of Brd3 ET domain bound to Brg1 peptide

Authors

Szyszka, T.N., Wai, D.C., Mackay, J.P.

Assembly

Bromodomain-containing protein 3, Brd3 ET

Entity

1. Bromodomain-containing protein 3, Brd3 ET, entity 1 (polymer, Thiol state: all free), 87 monomers, 10163.25 Da Detail

ASASYDSEEE EEGLPMSYDE KRQLSLDINR LPGEKLGRVV HIIQSREPSL RDSNPDEIEI DFETLKPTTL RELERYVKSC LQKKQRK

2. Bromodomain-containing protein 3, Brd3 ET, entity 2 (polymer, Thiol state: not present), 12 monomers, 1411.780 Da Detail

RSVKVKIKLG RK

Total weight

11575.03 Da

Max. entity weight

10163.25 Da

Source organism

Homo sapiens

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 99.0 %, Completeness: 83.8 %, Completeness (bb): 87.8 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	83.8 % (1008 of 1203)	89.3 % (576 of 645)	77.1 % (353 of 458)	79.0 % (79 of 100)
Backbone	87.8 % (513 of 584)	95.9 % (189 of 197)	84.6 % (248 of 293)	80.9 % (76 of 94)
Sidechain	81.0 % (578 of 714)	86.4 % (387 of 448)	72.3 % (188 of 260)	50.0 % (3 of 6)
Aromatic	42.1 % (16 of 38)	84.2 % (16 of 19)	0.0 % (0 of 19)
Methyl	89.8 % (88 of 98)	98.0 % (48 of 49)	81.6 % (40 of 49)

1. entity 1

ASASYDSEEE EEGLPMSYDE KRQLSLDINR LPGEKLGRVV HIIQSREPSL RDSNPDEIEI DFETLKPTTL RELERYVKSC LQKKQRK

2. entity 2

RSVKVKIKLG RK

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7, Details 300 uM Brd3_ET, 600 uM Brg1, 0.02 % Roche Complete Protease Inhibitor, 166 uM DSS, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	Brd3_ET	natural abundance	300 uM
2	Brg1	natural abundance	600 uM
3	Roche Complete Protease Inhibitor	natural abundance	0.02 %
4	DSS	natural abundance	166 uM
5	NaCl	natural abundance	50 mM

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7, Details 300 uM [U-15N] Brd3_ET, 600 uM Brg1, 0.02 % Roche Complete Protease Inhibitor, 166 uM DSS, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
6	Brd3_ET	[U-15N]	300 uM
7	Brg1	natural abundance	600 uM
8	Roche Complete Protease Inhibitor	natural abundance	0.02 %
9	DSS	natural abundance	166 uM
10	NaCl	natural abundance	50 mM

Sample #3

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7, Details 300 uM [U-13C; U-15N] Brd3_ET, 600 uM Brg1, 0.02 % Roche Complete Protease Inhibitor, 166 uM DSS, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
11	Brd3_ET	[U-13C; U-15N]	300 uM
12	Brg1	natural abundance	600 uM
13	Roche Complete Protease Inhibitor	natural abundance	0.02 %
14	DSS	natural abundance	166 uM
15	NaCl	natural abundance	50 mM

Protein Blocks Logo

Calculated from 20 models in PDB: 6BGH, Strand ID: A, B Detail

Release date

2018-01-31

Citation

The BRD3 ET domain recognizes a short peptide motif through a mechanism that is conserved across chromatin remodelers and transcriptional regulators
Wai, D., Szyszka, T.N., Campbell, A.E., Kwong, C., Wilkinson-White, L.E., Silva, A., Low, J., Kwan, A.H., Gamsjaeger, R., Chalmers, J.D., Patrick, W.M., Lu, B., Vakoc, C.R., Blobel, G.A., Mackay, J.P.
J. Biol. Chem. (2018), 293, 7160-7175, PubMed 29567837 , DOI 10.1074/jbc.RA117.000678 , Abstract

Entries sharing articles BMRB: 1 entries Detail

BMRB: 30367 released on 2017-11-13
Title Solution NMR structures of the BRD3 ET domain in complex with a CHD4 peptide

Related entities 1. Bromodomain-containing protein 3, Brd3 ET, entity 1, : 5 : 69 entities Detail

Related entities 2. Bromodomain-containing protein 3, Brd3 ET, entity 2, : 1 : 7 entities Detail

Interaction partners 1. Bromodomain-containing protein 3, Brd3 ET, entity 1, : 13 interactors Detail

More details for 13 interactors identified by 7 citations

Interaction partners 2. Bromodomain-containing protein 3, Brd3 ET, entity 2, : 104 interactors Detail

More details for 104 interactors identified by 48 citations

Experiments performed 17 experiments Detail

1 2D 1H-13C HSQC

Instrument

Bruker AvanceIII - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7, Details 300 uM [U-13C; U-15N] Brd3_ET, 600 uM Brg1, 0.02 % Roche Complete Protease Inhibitor, 166 uM DSS, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
11	Brd3_ET	[U-13C; U-15N]	300 uM
12	Brg1	natural abundance	600 uM
13	Roche Complete Protease Inhibitor	natural abundance	0.02 %
14	DSS	natural abundance	166 uM
15	NaCl	natural abundance	50 mM

2 3D 1H-13C NOESY

Instrument

Bruker AvanceIII - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
11	Brd3_ET	[U-13C; U-15N]	300 uM
12	Brg1	natural abundance	600 uM
13	Roche Complete Protease Inhibitor	natural abundance	0.02 %
14	DSS	natural abundance	166 uM
15	NaCl	natural abundance	50 mM

3 3D 1H-15N NOESY

Instrument

Bruker AvanceIII - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7, Details 300 uM [U-15N] Brd3_ET, 600 uM Brg1, 0.02 % Roche Complete Protease Inhibitor, 166 uM DSS, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
6	Brd3_ET	[U-15N]	300 uM
7	Brg1	natural abundance	600 uM
8	Roche Complete Protease Inhibitor	natural abundance	0.02 %
9	DSS	natural abundance	166 uM
10	NaCl	natural abundance	50 mM

4 3D 13C/15N (F2/F1) Filtered, 1H-1H NOESY

Instrument

Bruker AvanceIII - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
11	Brd3_ET	[U-13C; U-15N]	300 uM
12	Brg1	natural abundance	600 uM
13	Roche Complete Protease Inhibitor	natural abundance	0.02 %
14	DSS	natural abundance	166 uM
15	NaCl	natural abundance	50 mM

5 2D 13C/15N (F2/F1) Filtered, 1H-1H NOESY

Instrument

Bruker AvanceIII - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
11	Brd3_ET	[U-13C; U-15N]	300 uM
12	Brg1	natural abundance	600 uM
13	Roche Complete Protease Inhibitor	natural abundance	0.02 %
14	DSS	natural abundance	166 uM
15	NaCl	natural abundance	50 mM

6 2D 13C/15N (F2/F1) Filtered, 1H-1H TOCSY

Instrument

Bruker AvanceIII - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
11	Brd3_ET	[U-13C; U-15N]	300 uM
12	Brg1	natural abundance	600 uM
13	Roche Complete Protease Inhibitor	natural abundance	0.02 %
14	DSS	natural abundance	166 uM
15	NaCl	natural abundance	50 mM

7 3D HCCH-TOCSY

Instrument

Bruker AvanceIII - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
11	Brd3_ET	[U-13C; U-15N]	300 uM
12	Brg1	natural abundance	600 uM
13	Roche Complete Protease Inhibitor	natural abundance	0.02 %
14	DSS	natural abundance	166 uM
15	NaCl	natural abundance	50 mM

8 3D HCCH-COSY

Instrument

Bruker AvanceIII - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
11	Brd3_ET	[U-13C; U-15N]	300 uM
12	Brg1	natural abundance	600 uM
13	Roche Complete Protease Inhibitor	natural abundance	0.02 %
14	DSS	natural abundance	166 uM
15	NaCl	natural abundance	50 mM

9 2D 1H-1H TOCSY

Instrument

Bruker AvanceIII - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7, Details 300 uM Brd3_ET, 600 uM Brg1, 0.02 % Roche Complete Protease Inhibitor, 166 uM DSS, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	Brd3_ET	natural abundance	300 uM
2	Brg1	natural abundance	600 uM
3	Roche Complete Protease Inhibitor	natural abundance	0.02 %
4	DSS	natural abundance	166 uM
5	NaCl	natural abundance	50 mM

10 2D 1H-1H NOESY

Instrument

Bruker AvanceIII - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	Brd3_ET	natural abundance	300 uM
2	Brg1	natural abundance	600 uM
3	Roche Complete Protease Inhibitor	natural abundance	0.02 %
4	DSS	natural abundance	166 uM
5	NaCl	natural abundance	50 mM

11 3D HNCO

Instrument

Bruker AvanceIII - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
11	Brd3_ET	[U-13C; U-15N]	300 uM
12	Brg1	natural abundance	600 uM
13	Roche Complete Protease Inhibitor	natural abundance	0.02 %
14	DSS	natural abundance	166 uM
15	NaCl	natural abundance	50 mM

12 2D 1H-15N HSQC

Instrument

Bruker AvanceIII - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
6	Brd3_ET	[U-15N]	300 uM
7	Brg1	natural abundance	600 uM
8	Roche Complete Protease Inhibitor	natural abundance	0.02 %
9	DSS	natural abundance	166 uM
10	NaCl	natural abundance	50 mM

13 3D HN(CA)CO

Instrument

Bruker AvanceIII - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
11	Brd3_ET	[U-13C; U-15N]	300 uM
12	Brg1	natural abundance	600 uM
13	Roche Complete Protease Inhibitor	natural abundance	0.02 %
14	DSS	natural abundance	166 uM
15	NaCl	natural abundance	50 mM

14 3D H(CC)(CO)HN

Instrument

Bruker AvanceIII - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
11	Brd3_ET	[U-13C; U-15N]	300 uM
12	Brg1	natural abundance	600 uM
13	Roche Complete Protease Inhibitor	natural abundance	0.02 %
14	DSS	natural abundance	166 uM
15	NaCl	natural abundance	50 mM

15 3D HNCA

Instrument

Bruker AvanceIII - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
11	Brd3_ET	[U-13C; U-15N]	300 uM
12	Brg1	natural abundance	600 uM
13	Roche Complete Protease Inhibitor	natural abundance	0.02 %
14	DSS	natural abundance	166 uM
15	NaCl	natural abundance	50 mM

16 3D CBCA(CO)NH

Instrument

Bruker AvanceIII - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
11	Brd3_ET	[U-13C; U-15N]	300 uM
12	Brg1	natural abundance	600 uM
13	Roche Complete Protease Inhibitor	natural abundance	0.02 %
14	DSS	natural abundance	166 uM
15	NaCl	natural abundance	50 mM

17 3D HNCACB

Instrument

Bruker AvanceIII - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
11	Brd3_ET	[U-13C; U-15N]	300 uM
12	Brg1	natural abundance	600 uM
13	Roche Complete Protease Inhibitor	natural abundance	0.02 %
14	DSS	natural abundance	166 uM
15	NaCl	natural abundance	50 mM

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_30368_6bgh.nef
Input source #2: Coordindates	6bgh.cif
Diamagnetism of the molecular assembly	True (excluding Oxygen atoms)
Whether the assembly has a disulfide bond	None
Whether the assembly has a other bond	None
Whether the assembly contains a cyclic polymer	None
Overall data processing status	Warning

Disulfide bonds

None

Other bonds (neither disulfide, covalent nor hydrogen bonds, e.g. Zinc–sulphur bond)

None

Non-standard residues

None

Sequence alignments

Entity_assembly_ID (NMR): A vs Auth_asym_ID (model): A

---560-----570-------580-------590-------600-------610-------620-------630-------640---
ASASYDSEEEEEGLPMSYDEKRQLSLDINRLPGEKLGRVVHIIQSREPSLRDSNPDEIEIDFETLKPTTLRELERYVKSCLQKKQRK
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ASASYDSEEEEEGLPMSYDEKRQLSLDINRLPGEKLGRVVHIIQSREPSLRDSNPDEIEIDFETLKPTTLRELERYVKSCLQKKQRK
--------10--------20--------30--------40--------50--------60--------70--------80-------

Entity_assembly_ID (NMR): B vs Auth_asym_ID (model): B

------1600--
RSVKVKIKLGRK
||||||||||||
RSVKVKIKLGRK
--------10--

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	87	0	0	100.0
B	B	12	0	0	100.0

Content subtype: combined_30368_6bgh.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	1004		98.9 (chain: A, length: 87), 100.0 (chain: B, length: 12)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	Warning	1347 (1)	noe	94.3 (chain: A, length: 87), 50.0 (chain: B, length: 12)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_3	OK	141 (141)	.	94.3 (chain: A, length: 87)

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 87, Sequence coverage: 98.9%
  - Entity_assembly_ID: B, Chain length: 12, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 573
  - ¹³C chemical shifts: 352
  - ¹⁵N chemical shifts: 79
- Completeness of assignments
  - Entity_assemble_ID: A
  - Entity_assemble_ID: B
- Redox state of CYS
- Peptide bond of PRO
- Rotameric state of ILE , LEU, and VAL
- Histogram of normalized assigned chemical shifts
- Random coil index and derived parameters (S² and NMR RMSD)
  - Chain_ID: A
  - Chain_ID: B

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	556	501	90.1
¹³C chemical shifts	397	352	88.7
¹⁵N chemical shifts	96	79	82.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	172	164	95.3
¹³C chemical shifts	174	165	94.8
¹⁵N chemical shifts	82	76	92.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	384	337	87.8
¹³C chemical shifts	223	187	83.9
¹⁵N chemical shifts	14	3	21.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	42	41	97.6
¹³C chemical shifts	42	40	95.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	19	16	84.2
¹³C chemical shifts	19	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	89	71	79.8
¹³C chemical shifts	61	0	0.0
¹⁵N chemical shifts	14	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	25	24	96.0
¹³C chemical shifts	24	0	0.0
¹⁵N chemical shifts	12	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	64	47	73.4
¹³C chemical shifts	37	0	0.0
¹⁵N chemical shifts	2	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	8	7	87.5
¹³C chemical shifts	8	0	0.0

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 87, Sequence coverage: 94.3%
  - Entity_assembly_ID: B, Chain length: 12, Sequence coverage: 50.0%
- Total number of restraints: 1329
- Weight of restraints: 1.0 (1329)
- Potential type of restraints: upper-bound-parabolic (1329)
- Range of distance target values: 2.11, 5.5 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
  - Chain_ID: B
- Distance restraints on contact map

Dihedral angle restraints

Saveframe: DYANA/DIANA_dihedral_3
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 87, Sequence coverage: 94.3%
- Total number of restraints: 141
- Total number of restraints per polymer type: 141
- Weight of restraints: 1.0 (141)
- Potential type of restraints: square-well-parabolic (141)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords TRANSCRIPTION, Transcription Bromodomain BET protein

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Found 1 Document (3.018 seconds)

BMRB: 30368

Sample #1

Sample #2

Sample #3

Entries sharing articles BMRB: 1 entries Detail

Related entities 1. Bromodomain-containing protein 3, Brd3 ET, entity 1, : 5 : 69 entities Detail

Related entities 2. Bromodomain-containing protein 3, Brd3 ET, entity 2, : 1 : 7 entities Detail

Interaction partners 1. Bromodomain-containing protein 3, Brd3 ET, entity 1, : 13 interactors Detail

Interaction partners 2. Bromodomain-containing protein 3, Brd3 ET, entity 2, : 104 interactors Detail

Experiments performed 17 experiments Detail

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NMR combined restraints 4 contents Detail