BMRBj - BMREntryMaster

Found 1 Document (2.558 seconds)

BMRB: 34004

5L7B

Solution structure of the human SNF5/INI1 domain

Authors

Allen, M.D., Zinzalla, G., Bycroft, M.

Assembly

SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily B member 1

Entity

1. SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily B member 1 (polymer, Thiol state: all free), 78 monomers, 8816.904 Da Detail

GGSEVLVPIR LDMEIDGQKL RDAFTWNMNE KLMTPEMFSE ILCDDLDLNP LTFVPAIASA IRQQIESYPT DSILEDQS

Formula weight

8816.904 Da

Source organism

Homo sapiens

Exptl. method

solution NMR

Refine. method

torsion angle dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 98.7 %, Completeness: 90.5 %, Completeness (bb): 98.0 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	90.5 % (820 of 906)	97.9 % (461 of 471)	79.4 % (281 of 354)	96.3 % (78 of 81)
Backbone	98.0 % (449 of 458)	96.8 % (149 of 154)	98.7 % (228 of 231)	98.6 % (72 of 73)
Sidechain	85.5 % (447 of 523)	98.4 % (312 of 317)	65.2 % (129 of 198)	75.0 % (6 of 8)
Aromatic	50.0 % (25 of 50)	100.0 % (25 of 25)	0.0 % (0 of 24)	0.0 % (0 of 1)
Methyl	87.0 % (80 of 92)	95.7 % (44 of 46)	78.3 % (36 of 46)

1. SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily B member 1

GGSEVLVPIR LDMEIDGQKL RDAFTWNMNE KLMTPEMFSE ILCDDLDLNP LTFVPAIASA IRQQIESYPT DSILEDQS

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 6.5, Details 20 mM potassium phosphate, 100 mM sodium chloride, 5 mM [U-100% 2H] beta-mercaptoethanol, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	beta-mercaptoethanol	[U-100% 2H]	5 mM
2	potassium phosphate	natural abundance	20 mM
3	sodium chloride	natural abundance	100 mM
4	H2O	natural abundance	90 %
5	D2O	natural abundance	10 %

Sample #2

#	Name	Isotope labeling	Concentration
6	beta-mercaptoethanol	[U-100% 2H]	5 mM
7	potassium phosphate	natural abundance	20 mM
8	sodium chloride	natural abundance	100 mM
9	H2O	natural abundance	90 %
10	D2O	natural abundance	10 %

LACS Plot; CA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl carbons	internal	direct	1.0
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	liquid anhydrous ammonia	nitrogen	internal	indirect	1.0

Referencing offset: 0.09 ppm, Outliers: 1 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl carbons	internal	direct	1.0
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	liquid anhydrous ammonia	nitrogen	internal	indirect	1.0

Referencing offset: 0.09 ppm, Outliers: 1 Detail

LACS Plot; HA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl carbons	internal	direct	1.0
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	liquid anhydrous ammonia	nitrogen	internal	indirect	1.0

Referencing offset: 0.03 ppm, Outliers: 2 Detail

LACS Plot; CO

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl carbons	internal	direct	1.0
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	liquid anhydrous ammonia	nitrogen	internal	indirect	1.0

Referencing offset: 0.96 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 5L7B, Strand ID: A Detail

Release date

2016-06-15

Citation

The structure of INI1/hSNF5 RPT1 and its interactions with the c-MYC:MAX heterodimer provide insights into the interplay between MYC and the SWI/SNF chromatin remodeling complex
Sammak, S., Allen, M.D., Hamdani, N., Bycroft, M., Zinzalla, G.
FEBS J. (2018), 285, 4165-4180, PubMed 30222246 , DOI 10.1111/febs.14660 , Abstract

Entries sharing articles BMRB: 1 entries Detail

BMRB: 27571 released on 2018-08-05
Title Backbone 1H, 13C, and 15N Chemical Shift Assignments for the bHLHZip c-MYC:MAX complex.

Related entities 1. SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily B member 1, : 6 : 47 entities Detail

Interaction partners 1. SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily B member 1, : 17 interactors Detail

More details for 17 interactors identified by 10 citations

Experiments performed 11 experiments Detail

1 2D 1H-1H NOESY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 6.5, Details 20 mM potassium phosphate, 100 mM sodium chloride, 5 mM [U-100% 2H] beta-mercaptoethanol, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	beta-mercaptoethanol	[U-100% 2H]	5 mM
2	potassium phosphate	natural abundance	20 mM
3	sodium chloride	natural abundance	100 mM
4	H2O	natural abundance	90 %
5	D2O	natural abundance	10 %

2 2D 1H-1H TOCSY

Instrument

Bruker Avance - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	beta-mercaptoethanol	[U-100% 2H]	5 mM
2	potassium phosphate	natural abundance	20 mM
3	sodium chloride	natural abundance	100 mM
4	H2O	natural abundance	90 %
5	D2O	natural abundance	10 %

3 2D DQF-COSY

Instrument

Bruker Avance - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	beta-mercaptoethanol	[U-100% 2H]	5 mM
2	potassium phosphate	natural abundance	20 mM
3	sodium chloride	natural abundance	100 mM
4	H2O	natural abundance	90 %
5	D2O	natural abundance	10 %

4 3D HNCACB

Instrument

Bruker DRX - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
6	beta-mercaptoethanol	[U-100% 2H]	5 mM
7	potassium phosphate	natural abundance	20 mM
8	sodium chloride	natural abundance	100 mM
9	H2O	natural abundance	90 %
10	D2O	natural abundance	10 %

5 2D 1H-15N HSQC

Instrument

Bruker DRX - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
6	beta-mercaptoethanol	[U-100% 2H]	5 mM
7	potassium phosphate	natural abundance	20 mM
8	sodium chloride	natural abundance	100 mM
9	H2O	natural abundance	90 %
10	D2O	natural abundance	10 %

6 3D HBHA(CO)NH

Instrument

Bruker DRX - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
6	beta-mercaptoethanol	[U-100% 2H]	5 mM
7	potassium phosphate	natural abundance	20 mM
8	sodium chloride	natural abundance	100 mM
9	H2O	natural abundance	90 %
10	D2O	natural abundance	10 %

7 3D HNHB

Instrument

Bruker DRX - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
6	beta-mercaptoethanol	[U-100% 2H]	5 mM
7	potassium phosphate	natural abundance	20 mM
8	sodium chloride	natural abundance	100 mM
9	H2O	natural abundance	90 %
10	D2O	natural abundance	10 %

8 3D HNCACO

Instrument

Bruker DRX - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
6	beta-mercaptoethanol	[U-100% 2H]	5 mM
7	potassium phosphate	natural abundance	20 mM
8	sodium chloride	natural abundance	100 mM
9	H2O	natural abundance	90 %
10	D2O	natural abundance	10 %

9 3D HNCO

Instrument

Bruker DRX - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
6	beta-mercaptoethanol	[U-100% 2H]	5 mM
7	potassium phosphate	natural abundance	20 mM
8	sodium chloride	natural abundance	100 mM
9	H2O	natural abundance	90 %
10	D2O	natural abundance	10 %

10 3D CBCA(CO)NH

Instrument

Bruker DRX - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
6	beta-mercaptoethanol	[U-100% 2H]	5 mM
7	potassium phosphate	natural abundance	20 mM
8	sodium chloride	natural abundance	100 mM
9	H2O	natural abundance	90 %
10	D2O	natural abundance	10 %

11 2D 1H-13C HSQC

Instrument

Bruker DRX - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
6	beta-mercaptoethanol	[U-100% 2H]	5 mM
7	potassium phosphate	natural abundance	20 mM
8	sodium chloride	natural abundance	100 mM
9	H2O	natural abundance	90 %
10	D2O	natural abundance	10 %

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_34004_5l7b.nef
Input source #2: Coordindates	5l7b.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

-------190-------200-------210-------220-------230-------240-------250--------
GGSEVLVPIRLDMEIDGQKLRDAFTWNMNEKLMTPEMFSEILCDDLDLNPLTFVPAIASAIRQQIESYPTDSILEDQS
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GGSEVLVPIRLDMEIDGQKLRDAFTWNMNEKLMTPEMFSEILCDDLDLNPLTFVPAIASAIRQQIESYPTDSILEDQS
--------10--------20--------30--------40--------50--------60--------70--------

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	78	0	0	100.0

Content subtype: combined_34004_5l7b.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	818		97.4 (chain: A, length: 78)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	Warning	2735 (1)	noe	97.4 (chain: A, length: 78)
2	Distance restraints	CNS/XPLOR_distance_constraints_3	OK	81 (1)	hbond	61.5 (chain: A, length: 78)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_4	Warning	143 (143)	.	84.6 (chain: A, length: 78)

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 78, Sequence coverage: 97.4%
- Total number of assignments
  - ¹H chemical shifts: 468
  - ¹³C chemical shifts: 273
  - ¹⁵N chemical shifts: 77
- Completeness of assignments
  - Entity_assemble_ID: A
- 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

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
214	THR	HG1	6.042
223	CYS	HG	2.656
232	THR	HG1	5.243

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	471	464	98.5
¹³C chemical shifts	354	273	77.1
¹⁵N chemical shifts	84	77	91.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	154	147	95.5
¹³C chemical shifts	156	152	97.4
¹⁵N chemical shifts	73	71	97.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	317	317	100.0
¹³C chemical shifts	198	121	61.1
¹⁵N chemical shifts	11	6	54.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	50	50	100.0
¹³C chemical shifts	50	40	80.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	25	25	100.0
¹³C chemical shifts	24	0	0.0
¹⁵N chemical shifts	1	0	0.0

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 78, Sequence coverage: 97.4%
- Total number of restraints: 2717
- Weight of restraints: 1.0 (2717)
- Potential type of restraints: square-well-parabolic (2717)
- Range of distance target values: 2.3, 3.9 (Å)
- Histogram of 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: 78, Sequence coverage: 61.5%
  - Total number of restraints: 81
  - Weight of restraints: 1.0 (81)
  - Potential type of restraints: square-well-parabolic (81)
  - Range of distance target values: 1.95, 2.9 (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: Warning
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 78, Sequence coverage: 84.6%
- Total number of restraints: 143
- Total number of restraints per polymer type: 143
- Weight of restraints: 1.0 (143)
- Potential type of restraints: square-well-parabolic (143)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords DNA BINDING PROTEIN, SNF5/INI1 NMR structure

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Found 1 Document (2.558 seconds)

BMRB: 34004

Sample #1

Sample #2

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Entries sharing articles BMRB: 1 entries Detail

Related entities 1. SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily B member 1, : 6 : 47 entities Detail

Interaction partners 1. SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily B member 1, : 17 interactors Detail

Experiments performed 11 experiments Detail

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NMR combined restraints 5 contents Detail