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BMRB: 30444

6CUI

Solution structure of the Extraterminal (ET) Domain of BRD2

Authors

Houliston, S., Lemak, A., Picaud, S., Filippakopoulos, P., Arrowsmith, C.H.

Assembly

Bromodomain-containing protein 2

Entity

1. Bromodomain-containing protein 2 (polymer, Thiol state: all free), 132 monomers, 15248.22 Da Detail

SMKTAPPALP TGYDSEEEEE SRPMSYDEKR QLSLDINKLP GEKLGRVVHI IQAREPSLRD SNPEEIEIDF ETLKPSTLRE LERYVLSCLR KKPRKPYTIK KPVGKTKEEL ALEKKRELEK RLQDVSGQLN ST

Formula weight

15248.22 Da

Source organism

Exptl. method

Refine. method

molecular dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 94.7 %, Completeness: 86.1 %, Completeness (bb): 91.2 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	86.1 % (1376 of 1598)	85.1 % (729 of 857)	86.5 % (530 of 613)	91.4 % (117 of 128)
Backbone	91.2 % (702 of 770)	92.2 % (238 of 258)	89.8 % (351 of 391)	93.4 % (113 of 121)
Sidechain	82.8 % (791 of 955)	82.0 % (491 of 599)	84.8 % (296 of 349)	57.1 % (4 of 7)
Aromatic	71.7 % (33 of 46)	91.3 % (21 of 23)	52.2 % (12 of 23)
Methyl	97.7 % (127 of 130)	98.5 % (64 of 65)	96.9 % (63 of 65)

1. entity 1

SMKTAPPALP TGYDSEEEEE SRPMSYDEKR QLSLDINKLP GEKLGRVVHI IQAREPSLRD SNPEEIEIDF ETLKPSTLRE LERYVLSCLR KKPRKPYTIK KPVGKTKEEL ALEKKRELEK RLQDVSGQLN ST

Show sample condition

Sample

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5, Details 250 uM [U-13C; U-15N] BRD2-ET, 95% H2O/5% D2O

#	Name	Isotope labeling	Type	Concentration
1	BRD2-ET	[U-13C; U-15N]		250 uM
2	NaCl	natural abundance		500 mM

LACS Plot; CA

Referencing offset: -0.15 ppm, Outliers: 2 Detail

LACS Plot; CB

Referencing offset: -0.15 ppm, Outliers: 2 Detail

LACS Plot; HA

Referencing offset: 0.03 ppm, Outliers: 3 Detail

LACS Plot; CO

Referencing offset: -0.39 ppm, Outliers: 2 Detail

Protein Blocks Logo

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

Release date

2018-04-10

Citation

A common binding motif in the ET domain of BRD3 forms polymorphic structural interfaces with host and viral proteins
Houliston, S., Lemak, A., Picaud, S., Filippakopoulos, P., Arrowsmith, C.H.
Structure (2021), 29, 886-898, PubMed 33592170 , DOI 10.1016/j.str.2021.01.010 , Abstract

Related entities 1. Bromodomain-containing protein 2, : 1 : 30 entities Detail

Interaction partners 1. Bromodomain-containing protein 2, : 11 interactors Detail

More details for 11 interactors identified by 10 citations

Experiments performed 9 experiments Detail

1 3D 1H-15N NOESY

Instrument

Bruker AvanceII - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5, Details 250 uM [U-13C; U-15N] BRD2-ET, 95% H2O/5% D2O

#	Name	Isotope labeling	Type	Concentration
1	BRD2-ET	[U-13C; U-15N]		250 uM
2	NaCl	natural abundance		500 mM

2 3D 1H-13C NOESY

Instrument

Bruker AvanceII - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5, Details 250 uM [U-13C; U-15N] BRD2-ET, 95% H2O/5% D2O

#	Name	Isotope labeling	Type	Concentration
1	BRD2-ET	[U-13C; U-15N]		250 uM
2	NaCl	natural abundance		500 mM

3 3D CBCA(CO)NH

Instrument

Bruker AvanceIII - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5, Details 250 uM [U-13C; U-15N] BRD2-ET, 95% H2O/5% D2O

#	Name	Isotope labeling	Type	Concentration
1	BRD2-ET	[U-13C; U-15N]		250 uM
2	NaCl	natural abundance		500 mM

4 3D HNCO

Instrument

Bruker AvanceIII - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5, Details 250 uM [U-13C; U-15N] BRD2-ET, 95% H2O/5% D2O

#	Name	Isotope labeling	Type	Concentration
1	BRD2-ET	[U-13C; U-15N]		250 uM
2	NaCl	natural abundance		500 mM

5 3D HBHA(CO)NH

Instrument

Bruker AvanceIII - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5, Details 250 uM [U-13C; U-15N] BRD2-ET, 95% H2O/5% D2O

#	Name	Isotope labeling	Type	Concentration
1	BRD2-ET	[U-13C; U-15N]		250 uM
2	NaCl	natural abundance		500 mM

6 2D 1H-13C HSQC aliphatic

Instrument

Bruker AvanceII - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5, Details 250 uM [U-13C; U-15N] BRD2-ET, 95% H2O/5% D2O

#	Name	Isotope labeling	Type	Concentration
1	BRD2-ET	[U-13C; U-15N]		250 uM
2	NaCl	natural abundance		500 mM

7 2D 1H-15N HSQC

Instrument

Bruker AvanceII - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5, Details 250 uM [U-13C; U-15N] BRD2-ET, 95% H2O/5% D2O

#	Name	Isotope labeling	Type	Concentration
1	BRD2-ET	[U-13C; U-15N]		250 uM
2	NaCl	natural abundance		500 mM

8 3D HNCA

Instrument

Bruker AvanceIII - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5, Details 250 uM [U-13C; U-15N] BRD2-ET, 95% H2O/5% D2O

#	Name	Isotope labeling	Type	Concentration
1	BRD2-ET	[U-13C; U-15N]		250 uM
2	NaCl	natural abundance		500 mM

9 3D HCCH-TOCSY

Instrument

Bruker AvanceII - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5, Details 250 uM [U-13C; U-15N] BRD2-ET, 95% H2O/5% D2O

#	Name	Isotope labeling	Type	Concentration
1	BRD2-ET	[U-13C; U-15N]		250 uM
2	NaCl	natural abundance		500 mM

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_30444_6cui.nef
Input source #2: Coordindates	6cui.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

--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100
SMKTAPPALPTGYDSEEEEESRPMSYDEKRQLSLDINKLPGEKLGRVVHIIQAREPSLRDSNPEEIEIDFETLKPSTLRELERYVLSCLRKKPRKPYTIK
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
SMKTAPPALPTGYDSEEEEESRPMSYDEKRQLSLDINKLPGEKLGRVVHIIQAREPSLRDSNPEEIEIDFETLKPSTLRELERYVLSCLRKKPRKPYTIK

-------110-------120-------130--
KPVGKTKEELALEKKRELEKRLQDVSGQLNST
||||||||||||||||||||||||||||||||
KPVGKTKEELALEKKRELEKRLQDVSGQLNST

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	132	0	0	100.0

Content subtype: combined_30444_6cui.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	1380		93.9 (chain: A, length: 132)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	1519 (1)	noe	90.2 (chain: A, length: 132)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_3	OK	175 (175)	.	76.5 (chain: A, length: 132)

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 132, Sequence coverage: 93.9%
- Total number of assignments
  - ¹H chemical shifts: 736
  - ¹³C chemical shifts: 528
  - ¹⁵N chemical shifts: 116
- Completeness of assignments
  - Entity_assemble_ID: A
- Redox state of CYS
- Peptide bond of PRO
- Tautomeric state of HIS
- 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

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 132, Sequence coverage: 90.2%
- Total number of restraints: 1519
- Weight of restraints: 1.0 (1519)
- Potential type of restraints: square-well-parabolic (1519)
- Range of distance target values: 2.25, 3.9 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
- Distance restraints on contact map

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_3
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 132, Sequence coverage: 76.5%
- Total number of restraints: 175
- Total number of restraints per polymer type: 175
- Weight of restraints: 1.0 (175)
- Potential type of restraints: square-well-parabolic (175)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords TRANSCRIPTION