BMRBj - BMREntryMaster

Found 1 Document (0.803 seconds)

BMRB: 30206

5U5S

Solution structures of Brd2 second bromodomain in complex with stat3 peptide

Authors

Zeng, L., Zhou, M.

Assembly

Bromodomain-containing protein 2, Stat3 peptide

Entity

1. Bromodomain-containing protein 2, Stat3 peptide, entity 1 (polymer), 112 monomers, 13132.94 Da Detail

GKLSEQLKHC NGILKELLSK KHAAYAWPFY KPVDASALGL HDYHDIIKHP MDLSTVKRKM ENRDYRDAQE FAADVRLMFS NCYKYNPPDH DVVAMARKLQ DVFEFRYAKM PD

2. Bromodomain-containing protein 2, Stat3 peptide, entity 2 (polymer, Thiol state: not present), 12 monomers, 1538.791 Da Detail

HNLLRIXQFL QS

Total weight

14671.731 Da

Max. entity weight

13132.94 Da

Source organism

Homo sapiens

Exptl. method

solution NMR

Refine. method

torsion angle dynamics

Data set

assigned_chemical_shifts, spectral_peak_list

Chem. Shift Complete

Sequence coverage: 98.4 %, Completeness: 83.7 %, Completeness (bb): 78.0 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	83.7 % (1264 of 1510)	88.7 % (703 of 793)	77.9 % (459 of 589)	79.7 % (102 of 128)
Backbone	78.0 % (566 of 726)	90.9 % (221 of 243)	67.5 % (247 of 366)	83.8 % (98 of 117)
Sidechain	90.3 % (816 of 904)	87.6 % (482 of 550)	96.2 % (330 of 343)	36.4 % (4 of 11)
Aromatic	92.9 % (145 of 156)	96.2 % (75 of 78)	89.6 % (69 of 77)	100.0 % (1 of 1)
Methyl	96.6 % (112 of 116)	98.3 % (57 of 58)	94.8 % (55 of 58)

1. entity 1

GKLSEQLKHC NGILKELLSK KHAAYAWPFY KPVDASALGL HDYHDIIKHP MDLSTVKRKM ENRDYRDAQE FAADVRLMFS NCYKYNPPDH DVVAMARKLQ DVFEFRYAKM PD

2. entity 2

HNLLRIXQFL QS

Show sample condition

Sample #1

Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7.4, Details 10 mM sodium phosphate, 100 mM sodium chloride, 2 mM EDTA, 2 mM [U-2H] DTT, 100% D2O

#	Name	Isotope labeling	Concentration
1	DTT	[U-2H]	2 mM
2	EDTA	natural abundance	2 mM
3	sodium chloride	natural abundance	100 mM
4	sodium phosphate	natural abundance	10 mM
5	entity_1		0.0 ~ 0.0 mM
6	entity_2		0.0 ~ 0.0 mM

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.4, Details 10 mM sodium phosphate, 100 mM sodium chloride, 2 mM EDTA, 2 mM [U-2H] DTT, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
7	DTT	[U-2H]	2 mM
8	EDTA	natural abundance	2 mM
9	sodium chloride	natural abundance	100 mM
10	sodium phosphate	natural abundance	10 mM
11	entity_1		0.0 ~ 0.0 mM
12	entity_2		0.0 ~ 0.0 mM

Protein Blocks Logo

Calculated from 20 models in PDB: 5U5S, Strand ID: A, B Detail

Release date

2017-02-01

Citation

Distinct Roles of Brd2 and Brd4 in Potentiating the Transcriptional Program for Th17 Cell Differentiation
Cheung, K.L., Zhang, F., Jaganathan, A., Sharma, R., Zhang, Q., Konuma, T., Shen, T., Lee, J.-Y, J., Ren, C., Chen, C.-H, C., Lu, G., Olson, M.R., Zhang, W., Kaplan, M.H., Littman, D.R., Walsh, M.J., Xiong, H., Zeng, L., Zhou, M.
Mol. Cell (2017), 65, 1068-1080, PubMed 28262505 , DOI 10.1016/j.molcel.2016.12.022 , Abstract

Related entities 1. Bromodomain-containing protein 2, Stat3 peptide, entity 1, : 3 : 101 entities Detail

Experiments performed 7 experiments Detail

1 3D HNCACB

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.4, Details 10 mM sodium phosphate, 100 mM sodium chloride, 2 mM EDTA, 2 mM [U-2H] DTT, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
7	DTT	[U-2H]	2 mM
8	EDTA	natural abundance	2 mM
9	sodium chloride	natural abundance	100 mM
10	sodium phosphate	natural abundance	10 mM
11	entity_1		0.0 ~ 0.0 mM
12	entity_2		0.0 ~ 0.0 mM

2 3D HNCOCACB

Instrument

Bruker Avance - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
7	DTT	[U-2H]	2 mM
8	EDTA	natural abundance	2 mM
9	sodium chloride	natural abundance	100 mM
10	sodium phosphate	natural abundance	10 mM
11	entity_1		0.0 ~ 0.0 mM
12	entity_2		0.0 ~ 0.0 mM

3 3D 1H-15N NOESY

Instrument

Bruker Avance - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
7	DTT	[U-2H]	2 mM
8	EDTA	natural abundance	2 mM
9	sodium chloride	natural abundance	100 mM
10	sodium phosphate	natural abundance	10 mM
11	entity_1		0.0 ~ 0.0 mM
12	entity_2		0.0 ~ 0.0 mM

4 3D 1H-13C NOESY aliphatic

Instrument

Bruker Avance - 900 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7.4, Details 10 mM sodium phosphate, 100 mM sodium chloride, 2 mM EDTA, 2 mM [U-2H] DTT, 100% D2O

#	Name	Isotope labeling	Concentration
1	DTT	[U-2H]	2 mM
2	EDTA	natural abundance	2 mM
3	sodium chloride	natural abundance	100 mM
4	sodium phosphate	natural abundance	10 mM
5	entity_1		0.0 ~ 0.0 mM
6	entity_2		0.0 ~ 0.0 mM

5 3D 1H-13C NOESY aromatic

Instrument

Bruker Avance - 900 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7.4, Details 10 mM sodium phosphate, 100 mM sodium chloride, 2 mM EDTA, 2 mM [U-2H] DTT, 100% D2O

#	Name	Isotope labeling	Concentration
1	DTT	[U-2H]	2 mM
2	EDTA	natural abundance	2 mM
3	sodium chloride	natural abundance	100 mM
4	sodium phosphate	natural abundance	10 mM
5	entity_1		0.0 ~ 0.0 mM
6	entity_2		0.0 ~ 0.0 mM

6 3D 1H-13C filtered NOESY aliphatic

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7.4, Details 10 mM sodium phosphate, 100 mM sodium chloride, 2 mM EDTA, 2 mM [U-2H] DTT, 100% D2O

#	Name	Isotope labeling	Concentration
1	DTT	[U-2H]	2 mM
2	EDTA	natural abundance	2 mM
3	sodium chloride	natural abundance	100 mM
4	sodium phosphate	natural abundance	10 mM
5	entity_1		0.0 ~ 0.0 mM
6	entity_2		0.0 ~ 0.0 mM

7 3D 1H-13C filtered NOESY aromatic

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7.4, Details 10 mM sodium phosphate, 100 mM sodium chloride, 2 mM EDTA, 2 mM [U-2H] DTT, 100% D2O

#	Name	Isotope labeling	Concentration
1	DTT	[U-2H]	2 mM
2	EDTA	natural abundance	2 mM
3	sodium chloride	natural abundance	100 mM
4	sodium phosphate	natural abundance	10 mM
5	entity_1		0.0 ~ 0.0 mM
6	entity_2		0.0 ~ 0.0 mM

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_30206_5u5s.nef
Input source #2: Coordindates	5u5s.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	True (see coodinates for details)
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)

Ptnr_site_1	Ptnr_site_2	Redox_state_prediction_1	Redox_state_prediction_2	Distance (Å)
2:6:ILE:C	2:7:ALY:N	unknown	unknown	n/a
2:7:ALY:C	2:8:GLN:N	unknown	unknown	n/a

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
B	287	ALY	N(6)-ACETYLLYSINE	Assigned chemical shifts, Coordinates

Sequence alignments

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

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

-------110--
DVFEFRYAKMPD
||||||||||||
DVFEFRYAKMPD

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

-------290--
HNLLRIXQFLQS
||||||||||||
HNLLRIXQFLQS
--------10--

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	112	0	0	100.0
B	B	12	0	0	100.0

Content subtype: combined_30206_5u5s.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	2		No information
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	1256		99.1 (chain: A, length: 112), 100.0 (chain: B, length: 12)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	130 (1)	hbond	75.0 (chain: A, length: 112)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_3	OK	200 (200)	.	96.4 (chain: A, length: 112)

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 112, Sequence coverage: 99.1%
  - Entity_assembly_ID: B, Chain length: 12, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 708
  - ¹³C chemical shifts: 448
  - ¹⁵N chemical shifts: 100
- Completeness of assignments
  - Entity_assemble_ID: A
  - Entity_assemble_ID: B
- 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
  - Chain_ID: B

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	715	645	90.2
¹³C chemical shifts	533	404	75.8
¹⁵N chemical shifts	120	100	83.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	221	210	95.0
¹³C chemical shifts	224	106	47.3
¹⁵N chemical shifts	106	96	90.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	494	435	88.1
¹³C chemical shifts	309	298	96.4
¹⁵N chemical shifts	14	4	28.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	55	55	100.0
¹³C chemical shifts	55	54	98.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	71	68	95.8
¹³C chemical shifts	70	62	88.6
¹⁵N chemical shifts	1	1	100.0

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
287	ALY	HZ	7.919
287	ALY	CA	56.06
287	ALY	CB	33.07
287	ALY	CE	42.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	89	62	69.7
¹³C chemical shifts	58	41	70.7
¹⁵N chemical shifts	15	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	23	14	60.9
¹³C chemical shifts	22	7	31.8
¹⁵N chemical shifts	11	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	66	48	72.7
¹³C chemical shifts	36	34	94.4
¹⁵N chemical shifts	4	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	9	8	88.9
¹³C chemical shifts	9	6	66.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	7	7	100.0
¹³C chemical shifts	7	7	100.0

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: OK
- Experiment type: hbond
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 112, Sequence coverage: 75.0%
- Total number of restraints: 130
- Weight of restraints: 1.0 (130)
- Potential type of restraints: square-well-parabolic (130)
- Range of distance target values: 1.8, 3.2 (Å)
- Histogram of distance target values
- Distance restraints per residue
  - Chain_ID: A
  - Chain_ID: B
    None
- 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: 112, Sequence coverage: 96.4%
- Total number of restraints: 200
- Total number of restraints per polymer type: 200
- Weight of restraints: 1.0 (200)
- Potential type of restraints: square-well-parabolic (200)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords Brd2, Brd4, bromodomain, p300, stat3, th17

Search

Query history

Resources

Search for primary databases

Search for subsidiary databases

Display

Hits per page

Statistics

Query Changes will take effect after "OK" button is selected.

Maximum hits

Default conjunction operator

Omni-box

Search filter

Sequence search (BLAST)

E-value

Query sequence coverage

Miscellaneous

The number of previewed publications

Completeness of assigned chemical shift

Sequence chart about top aligned regions

Sequence chart about interacting regions

Hit context with highlight

Link destinations for BMRB, PDB and EMDB

Found 1 Document (0.803 seconds)

BMRB: 30206

Sample #1

Sample #2

Related entities 1. Bromodomain-containing protein 2, Stat3 peptide, entity 1, : 3 : 101 entities Detail

Experiments performed 7 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 4 contents Detail