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Found 1 Document (1.023 seconds)

BMRB: 11504

2RT5

Structure of SPOC domain of the human transcriptional corepressor SHARP

Authors

Mikami, S., Kanaba, T., Mishima, M.

Assembly

SPOC domain of the human transcriptional corepressor SHARP in complex with SMRT

Entity

1. SHARP (polymer), 169 monomers, 18454.23 Da Detail

VDMVQLLKKY PIVWQGLLAL KNDTAAVQLH FVSGNNVLAH RSLPLSEGGP PLRIAQRMRL EATQLEGVAR RMTVETDYCL LLALPCGRDQ EDVVSQTESL KAAFITYLQA KQAAGIINVP NPGSNQPAYV LQIFPPCEFS ESHLSRLAPD LLASISNISP HLMIVIASV

2. SMRT (polymer, Thiol state: not present), 8 monomers, 1102.879 Da Detail

YETLXDXE

Total weight

19557.11 Da

Max. entity weight

18454.23 Da

Source organism

Homo sapiens

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 97.7 %, Completeness: 89.4 %, Completeness (bb): 96.7 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	89.4 % (1806 of 2020)	87.1 % (909 of 1044)	92.3 % (733 of 794)	90.1 % (164 of 182)
Backbone	96.7 % (992 of 1026)	96.2 % (333 of 346)	96.7 % (500 of 517)	97.5 % (159 of 163)
Sidechain	84.3 % (979 of 1161)	82.5 % (576 of 698)	89.6 % (398 of 444)	26.3 % (5 of 19)
Aromatic	33.3 % (36 of 108)	33.3 % (18 of 54)	34.0 % (18 of 53)	0.0 % (0 of 1)
Methyl	96.3 % (235 of 244)	95.9 % (117 of 122)	96.7 % (118 of 122)

1. SHARP

VDMVQLLKKY PIVWQGLLAL KNDTAAVQLH FVSGNNVLAH RSLPLSEGGP PLRIAQRMRL EATQLEGVAR RMTVETDYCL LLALPCGRDQ EDVVSQTESL KAAFITYLQA KQAAGIINVP NPGSNQPAYV LQIFPPCEFS ESHLSRLAPD LLASISNISP HLMIVIASV

2. SMRT

YETLXDXE

Show sample condition

Sample #1

Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 303 K, pH 7.5

#	Name	Isotope labeling	Type	Concentration
1	SHARP	[U-100% 13C; U-100% 15N]	protein	0.9 mM
2	SMRT	natural abundance	protein	0.9 mM
3	H2O		solvent	93 %
4	D2O		solvent	7 %

Sample #2

Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 303 K, pH 7.5

#	Name	Isotope labeling	Type	Concentration
5	SHARP	[U-15% 13C; U-100% 15N]	protein	0.9 mM
6	SMRT	natural abundance	protein	0.9 mM
7	H2O		solvent	93 %
8	D2O		solvent	7 %

Sample #3

Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 303 K, pH 7.5

#	Name	Isotope labeling	Type	Concentration
9	SMRT	[U-13C; U-15N]-Leu, Glu, Tyr, Asp	protein	0.9 mM
10	SHARP	natural abundance	protein	0.9 mM
11	H2O		solvent	93 %
12	D2O		solvent	7 %

Sample #4

Solvent system 100% D2O, Pressure 1 atm, Temperature 303 K, pH 7.5

#	Name	Isotope labeling	Type	Concentration
13	SHARP	[U-100% 13C; U-100% 15N]	protein	0.9 mM
14	SMRT	natural abundance	protein	0.9 mM
15	D2O		solvent	100 %

Protein Blocks Logo

Calculated from 20 models in PDB: 2RT5, Strand ID: A, B Detail

Release date

2013-12-01

Citation

Structural insights into the recruitment of SMRT by the corepressor SHARP under phosphorylative regulation
Mikami, S., Kanaba, T., Mishima, M.
Structure (2014), 22, 35-46, PubMed 24268649 , DOI 10.1016/j.str.2013.10.007 , Abstract

Related entities 1. SHARP, : 1 : 1 : 11 entities Detail

Experiments performed 15 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 303 K, pH 7.5

#	Name	Isotope labeling	Type	Concentration
1	SHARP	[U-100% 13C; U-100% 15N]	protein	0.9 mM
2	SMRT	natural abundance	protein	0.9 mM
3	H2O		solvent	93 %
4	D2O		solvent	7 %

2 3D HNCO

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 303 K, pH 7.5

#	Name	Isotope labeling	Type	Concentration
1	SHARP	[U-100% 13C; U-100% 15N]	protein	0.9 mM
2	SMRT	natural abundance	protein	0.9 mM
3	H2O		solvent	93 %
4	D2O		solvent	7 %

3 3D HNCACB

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 303 K, pH 7.5

#	Name	Isotope labeling	Type	Concentration
1	SHARP	[U-100% 13C; U-100% 15N]	protein	0.9 mM
2	SMRT	natural abundance	protein	0.9 mM
3	H2O		solvent	93 %
4	D2O		solvent	7 %

4 3D CBCA(CO)NH

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 303 K, pH 7.5

#	Name	Isotope labeling	Type	Concentration
1	SHARP	[U-100% 13C; U-100% 15N]	protein	0.9 mM
2	SMRT	natural abundance	protein	0.9 mM
3	H2O		solvent	93 %
4	D2O		solvent	7 %

5 3D HN(CA)CO

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 303 K, pH 7.5

#	Name	Isotope labeling	Type	Concentration
1	SHARP	[U-100% 13C; U-100% 15N]	protein	0.9 mM
2	SMRT	natural abundance	protein	0.9 mM
3	H2O		solvent	93 %
4	D2O		solvent	7 %

6 3D C(CO)NH

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 303 K, pH 7.5

#	Name	Isotope labeling	Type	Concentration
1	SHARP	[U-100% 13C; U-100% 15N]	protein	0.9 mM
2	SMRT	natural abundance	protein	0.9 mM
3	H2O		solvent	93 %
4	D2O		solvent	7 %

7 3D H(CCO)NH

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 303 K, pH 7.5

#	Name	Isotope labeling	Type	Concentration
1	SHARP	[U-100% 13C; U-100% 15N]	protein	0.9 mM
2	SMRT	natural abundance	protein	0.9 mM
3	H2O		solvent	93 %
4	D2O		solvent	7 %

8 3D HCCH-TOCSY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 303 K, pH 7.5

#	Name	Isotope labeling	Type	Concentration
1	SHARP	[U-100% 13C; U-100% 15N]	protein	0.9 mM
2	SMRT	natural abundance	protein	0.9 mM
3	H2O		solvent	93 %
4	D2O		solvent	7 %

9 4D HC(CO)NH

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 303 K, pH 7.5

#	Name	Isotope labeling	Type	Concentration
1	SHARP	[U-100% 13C; U-100% 15N]	protein	0.9 mM
2	SMRT	natural abundance	protein	0.9 mM
3	H2O		solvent	93 %
4	D2O		solvent	7 %

10 3D 13C edited NOESY-HSQC

Instrument

Bruker Avance - 900 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 303 K, pH 7.5

#	Name	Isotope labeling	Type	Concentration
13	SHARP	[U-100% 13C; U-100% 15N]	protein	0.9 mM
14	SMRT	natural abundance	protein	0.9 mM
15	D2O		solvent	100 %

11 2D 1H-13C HSQC aliphatic

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 303 K, pH 7.5

#	Name	Isotope labeling	Type	Concentration
5	SHARP	[U-15% 13C; U-100% 15N]	protein	0.9 mM
6	SMRT	natural abundance	protein	0.9 mM
7	H2O		solvent	93 %
8	D2O		solvent	7 %

12 3D HNHB

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 303 K, pH 7.5

#	Name	Isotope labeling	Type	Concentration
5	SHARP	[U-15% 13C; U-100% 15N]	protein	0.9 mM
6	SMRT	natural abundance	protein	0.9 mM
7	H2O		solvent	93 %
8	D2O		solvent	7 %

13 3D HN(CO)NB

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 303 K, pH 7.5

#	Name	Isotope labeling	Type	Concentration
5	SHARP	[U-15% 13C; U-100% 15N]	protein	0.9 mM
6	SMRT	natural abundance	protein	0.9 mM
7	H2O		solvent	93 %
8	D2O		solvent	7 %

14 15N edited NOESY-HSQC

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 303 K, pH 7.5

#	Name	Isotope labeling	Type	Concentration
1	SHARP	[U-100% 13C; U-100% 15N]	protein	0.9 mM
2	SMRT	natural abundance	protein	0.9 mM
3	H2O		solvent	93 %
4	D2O		solvent	7 %

15 2D 15N filtered 1H NOESY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 303 K, pH 7.5

#	Name	Isotope labeling	Type	Concentration
9	SMRT	[U-13C; U-15N]-Leu, Glu, Tyr, Asp	protein	0.9 mM
10	SHARP	natural abundance	protein	0.9 mM
11	H2O		solvent	93 %
12	D2O		solvent	7 %

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_11504_2rt5.nef
Input source #2: Coordindates	2rt5.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)
2:4:LEU:C	2:5:SEP:N	unknown	unknown	n/a
2:5:SEP:C	2:6:ASP:N	unknown	unknown	n/a
2:6:ASP:C	2:7:SEP:N	unknown	unknown	n/a
2:7:SEP:C	2:8:GLU:N	unknown	unknown	n/a

Non-standard residues

None

Sequence alignments

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

----3500---3510------3520------3530------3540------3550------3560------3570------3580------3590-----
VDMVQLLKKYPIVWQGLLALKNDTAAVQLHFVSGNNVLAHRSLPLSEGGPPLRIAQRMRLEATQLEGVARRMTVETDYCLLLALPCGRDQEDVVSQTESL
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
VDMVQLLKKYPIVWQGLLALKNDTAAVQLHFVSGNNVLAHRSLPLSEGGPPLRIAQRMRLEATQLEGVARRMTVETDYCLLLALPCGRDQEDVVSQTESL
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100

-3600------3610------3620------3630------3640------3650------3660--- 
KAAFITYLQAKQAAGIINVPNPGS..PAYVLQIFPPCEFSESHLSRLAPDLLASISNISPHLMIVIAS 
||||||||||||||||||||||||  |||||||||||||||||||||||||||||||||||||||||| 
KAAFITYLQAKQAAGIINVPNPGSNQPAYVLQIFPPCEFSESHLSRLAPDLLASISNISPHLMIVIASV
-------110-------120-------130-------140-------150-------160---------

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	169	3	0	98.2
B	B	8	6	0	25.0

Content subtype: combined_11504_2rt5.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1748		98.8 (chain: A, length: 168), 50.0 (chain: B, length: 4)
1	Distance restraints	CNS/XPLOR_distance_constraints_3	Warning	3480 (1)	noe	98.8 (chain: A, length: 168), 25.0 (chain: B, length: 4)
2	Distance restraints	CNS/XPLOR_distance_constraints_5	Warning	4 (1)	undefined	25.0 (chain: B, length: 4)
3	Distance restraints	CNS/XPLOR_distance_constraints_4	OK	188 (1)	hbond	72.6 (chain: A, length: 168)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_2	Warning	301 (301)	.	92.9 (chain: A, length: 168)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 168, Sequence coverage: 98.8%
  - Entity_assembly_ID: B, Chain length: 4, Sequence coverage: 50.0%
- Total number of assignments
  - ¹H chemical shifts: 877
  - ¹³C chemical shifts: 711
  - ¹⁵N chemical shifts: 160
- 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	990	871	88.0
¹³C chemical shifts	754	709	94.0
¹⁵N chemical shifts	179	159	88.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	328	326	99.4
¹³C chemical shifts	332	329	99.1
¹⁵N chemical shifts	154	153	99.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	662	545	82.3
¹³C chemical shifts	422	380	90.0
¹⁵N chemical shifts	25	6	24.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	121	120	99.2
¹³C chemical shifts	121	121	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	50	12	24.0
¹³C chemical shifts	49	12	24.5
¹⁵N chemical shifts	1	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	10	6	60.0
¹³C chemical shifts	6	2	33.3
¹⁵N chemical shifts	2	1	50.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	4	2	50.0
¹³C chemical shifts	3	0	0.0
¹⁵N chemical shifts	2	1	50.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	6	4	66.7
¹³C chemical shifts	3	2	66.7

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_3
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 168, Sequence coverage: 98.8%
  - Entity_assembly_ID: B, Chain length: 4, Sequence coverage: 25.0%
- Total number of restraints: 3480
- Weight of restraints: 1.0 (3480)
- Potential type of restraints: square-well-parabolic (3480)
- Range of distance target values: 2.16, 3.77 (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
- Saveframe: CNS/XPLOR_distance_constraints_5
  - Status: Warning
  - Experiment type: undefined
  - Sequence coverage of experimental data
    - Entity_assembly_ID: B, Chain length: 4, Sequence coverage: 25.0%
  - Total number of restraints: 4
  - Weight of restraints: 1.0 (4)
  - Potential type of restraints: square-well-parabolic (4)
  - Range of distance target values: 3.9, 3.9 (Å)
  - Distance restraints per residue
    - Chain_ID: A
    - Chain_ID: B
  - Distance restraints on contact map
  - Saveframe: CNS/XPLOR_distance_constraints_4
    - Status: OK
    - Experiment type: hbond
    - Sequence coverage of experimental data
      - Entity_assembly_ID: A, Chain length: 168, Sequence coverage: 72.6%
    - Total number of restraints: 188
    - Weight of restraints: 1.0 (188)
    - Potential type of restraints: square-well-parabolic (188)
    - Range of distance target values: 2.05, 2.55 (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_2
- Status: Warning
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 168, Sequence coverage: 92.9%
- Total number of restraints: 301
- Total number of restraints per polymer type: 301
- Weight of restraints: 1.0 (301)
- Potential type of restraints: square-well-parabolic (301)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords SHARP

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Found 1 Document (1.023 seconds)

BMRB: 11504

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Related entities 1. SHARP, : 1 : 1 : 11 entities Detail

Experiments performed 15 experiments Detail

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NMR combined restraints 5 contents Detail