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BMRB: 25307

2MW8

solution structure of SATB1 homeodomain

Authors

Yamasaki, K., Yamasaki, T.

Assembly

SATB1 homeodomain

Entity

1. SATB1 homeodomain (polymer, Thiol state: not present), 71 monomers, 8302.479 Da Detail

GSHMNRQKTR PRTKISVEAL GILQSFIQDV GLYPDEEAIQ TLSAQLDLPK YTIIKFFQNQ RYYLKHHGKL K

Formula weight

8302.479 Da

Source organism

Exptl. method

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 90.1 %, Completeness: 34.4 %, Completeness (bb): 63.5 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹⁵N
All	34.4 % (188 of 547)	24.5 % (115 of 470)	94.8 % (73 of 77)
Backbone	63.5 % (134 of 211)	49.0 % (70 of 143)	94.1 % (64 of 68)
Sidechain	16.1 % (54 of 336)	13.8 % (45 of 327)	100.0 % (9 of 9)
Aromatic	8.1 % (3 of 37)	8.1 % (3 of 37)
Methyl	0.0 % (0 of 39)	0.0 % (0 of 39)

1. SATB1

GSHMNRQKTR PRTKISVEAL GILQSFIQDV GLYPDEEAIQ TLSAQLDLPK YTIIKFFQNQ RYYLKHHGKL K

Show sample condition

Sample #1

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 5.5

#	Name	Isotope labeling	Type	Concentration
1	SATB1 homeodomain	[U-15N]		0.3 mM
2	sodium phosphate	natural abundance		50 mM
3	sodium chloride	natural abundance		50 mM
4	DSS	natural abundance		0.5 mM
5	H2O	natural abundance		95 %
6	D2O	natural abundance		5 %

Sample #2

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 5.5

#	Name	Isotope labeling	Type	Concentration
7	SATB1 homeodomain	[U-15N]		0.7 ~ 1.2 mM
8	sodium phosphate	natural abundance		50 mM
9	sodium chloride	natural abundance		200 mM
10	DSS	natural abundance		0.5 mM
11	H2O	natural abundance		90 %
12	D2O	natural abundance		5 %

Sample #3

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 5.5

#	Name	Isotope labeling	Type	Concentration
13	SATB1 homeodomain	[U-15N]		0.7 ~ 1.2 mM
14	sodium phosphate	natural abundance		50 mM
15	sodium chloride	natural abundance		200 mM
16	DSS	natural abundance		0.5 mM
17	H2O	natural abundance		95 %
18	D2O	natural abundance		5 %

Protein Blocks Logo

Calculated from 20 models in PDB: 2MW8, Strand ID: A Detail

Release date

2015-11-01

Citation

The combination of sequence-specific and nonspecific DNA-binding modes of transcription factor SATB1
Yamasaki, K., Yamasaki, T.
Biochem. J. (2016), 473, 3321-3339, PubMed 27462121 , DOI 10.1042/BCJ20160236 , Abstract

Related entities 1. SATB1 homeodomain, : 1 : 5 : 149 entities Detail

Interaction partners 1. SATB1 homeodomain, : 32 interactors Detail

More details for 32 interactors identified by 9 citations

Experiments performed 7 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 5.5

#	Name	Isotope labeling	Type	Concentration
1	SATB1 homeodomain	[U-15N]		0.3 mM
2	sodium phosphate	natural abundance		50 mM
3	sodium chloride	natural abundance		50 mM
4	DSS	natural abundance		0.5 mM
5	H2O	natural abundance		95 %
6	D2O	natural abundance		5 %

2 2D 1H-15N HSQC

Instrument

Bruker DMX - 750 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 5.5

#	Name	Isotope labeling	Type	Concentration
7	SATB1 homeodomain	[U-15N]		0.7 ~ 1.2 mM
8	sodium phosphate	natural abundance		50 mM
9	sodium chloride	natural abundance		200 mM
10	DSS	natural abundance		0.5 mM
11	H2O	natural abundance		90 %
12	D2O	natural abundance		5 %

3 3D 1H-15N NOESY

Instrument

Bruker DMX - 500 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 5.5

#	Name	Isotope labeling	Type	Concentration
7	SATB1 homeodomain	[U-15N]		0.7 ~ 1.2 mM
8	sodium phosphate	natural abundance		50 mM
9	sodium chloride	natural abundance		200 mM
10	DSS	natural abundance		0.5 mM
11	H2O	natural abundance		90 %
12	D2O	natural abundance		5 %

4 3D 1H-15N TOCSY

Instrument

Bruker DMX - 500 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 5.5

#	Name	Isotope labeling	Type	Concentration
7	SATB1 homeodomain	[U-15N]		0.7 ~ 1.2 mM
8	sodium phosphate	natural abundance		50 mM
9	sodium chloride	natural abundance		200 mM
10	DSS	natural abundance		0.5 mM
11	H2O	natural abundance		90 %
12	D2O	natural abundance		5 %

5 2D 1H-1H NOESY

Instrument

Bruker DMX - 750 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 5.5

#	Name	Isotope labeling	Type	Concentration
13	SATB1 homeodomain	[U-15N]		0.7 ~ 1.2 mM
14	sodium phosphate	natural abundance		50 mM
15	sodium chloride	natural abundance		200 mM
16	DSS	natural abundance		0.5 mM
17	H2O	natural abundance		95 %
18	D2O	natural abundance		5 %

6 2D DQF-COSY

Instrument

Bruker DMX - 750 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 5.5

#	Name	Isotope labeling	Type	Concentration
13	SATB1 homeodomain	[U-15N]		0.7 ~ 1.2 mM
14	sodium phosphate	natural abundance		50 mM
15	sodium chloride	natural abundance		200 mM
16	DSS	natural abundance		0.5 mM
17	H2O	natural abundance		95 %
18	D2O	natural abundance		5 %

7 2D 1H-1H TOCSY

Instrument

Bruker DMX - 750 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 5.5

#	Name	Isotope labeling	Type	Concentration
13	SATB1 homeodomain	[U-15N]		0.7 ~ 1.2 mM
14	sodium phosphate	natural abundance		50 mM
15	sodium chloride	natural abundance		200 mM
16	DSS	natural abundance		0.5 mM
17	H2O	natural abundance		95 %
18	D2O	natural abundance		5 %

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_25307_2mw8.nef
Input source #2: Coordindates	2mw8.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

---640-----650-------660-------670-------680-------690-------700-------
GSHMNRQKTRPRTKISVEALGILQSFIQDVGLYPDEEAIQTLSAQLDLPKYTIIKFFQNQRYYLKHHGKLK
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GSHMNRQKTRPRTKISVEALGILQSFIQDVGLYPDEEAIQTLSAQLDLPKYTIIKFFQNQRYYLKHHGKLK
--------10--------20--------30--------40--------50--------60--------70-

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	71	0	0	100.0

Content subtype: combined_25307_2mw8.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	OK	155		90.1 (chain: A, length: 71)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	1000 (1)	noe	94.4 (chain: A, length: 71)
2	Distance restraints	CNS/XPLOR_distance_constraints_3	OK	64 (1)	hbond	57.7 (chain: A, length: 71)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_4	OK	57 (57)	.	67.6 (chain: A, length: 71)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: OK
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 71, Sequence coverage: 90.1%
- Total number of assignments
  - ¹H chemical shifts: 82
  - ¹⁵N chemical shifts: 73
- Completeness of assignments
  - Entity_assemble_ID: A
- 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: 71, Sequence coverage: 94.4%
- Total number of restraints: 997
- Weight of restraints: 1.0 (997)
- Potential type of restraints: square-well-parabolic (997)
- Range of distance target values: 2.15, 4.25 (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
- Saveframe: CNS/XPLOR_distance_constraints_3
  - Status: OK
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 71, Sequence coverage: 57.7%
  - Total number of restraints: 64
  - Weight of restraints: 1.0 (64)
  - Potential type of restraints: square-well-parabolic (64)
  - Range of distance target values: 2.0, 3.0 (Å)
  - Histogram of distance target values
  - Distance restraints per residue
    - Chain_ID: A
  - Distance restraints on contact map

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_4
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 71, Sequence coverage: 67.6%
- Total number of restraints: 57
- Total number of restraints per polymer type: 57
- Weight of restraints: 1.0 (57)
- Potential type of restraints: square-well-parabolic (57)
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords protein