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Found 1 Document (1.549 seconds)

BMRB: 16127

2KDP

Solution Structure of the SAP30 zinc finger motif

Authors

Radhakrishnan, I., He, Y., Imhoff, R., Sahu, A.

Assembly

SAP30 ZnF

Entity

1. SAP30 ZnF (polymer, Thiol state: free and other bound), 71 monomers, 8106.241 Da Detail

SNAGQLCCLR EDGERCGRAA GNASFSKRIQ KSISQKKVKI ELDKSARHLY ICDYHKNLIQ SVRNRRKRKG S

2. ZN (non-polymer), 65.409 Da

Total weight

8171.6504 Da

Max. entity weight

8106.241 Da

Source organism

Homo sapiens

Exptl. method

solution NMR

Refine. method

molecular dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 89.8 %, Completeness (bb): 96.0 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	89.8 % (756 of 842)	85.2 % (385 of 452)	95.5 % (297 of 311)	93.7 % (74 of 79)
Backbone	96.0 % (409 of 426)	97.3 % (143 of 147)	96.2 % (200 of 208)	93.0 % (66 of 71)
Sidechain	85.5 % (412 of 482)	79.3 % (242 of 305)	95.9 % (162 of 169)	100.0 % (8 of 8)
Aromatic	64.7 % (22 of 34)	64.7 % (11 of 17)	64.7 % (11 of 17)
Methyl	100.0 % (58 of 58)	100.0 % (29 of 29)	100.0 % (29 of 29)

1. SAP30 ZnF

SNAGQLCCLR EDGERCGRAA GNASFSKRIQ KSISQKKVKI ELDKSARHLY ICDYHKNLIQ SVRNRRKRKG S

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Concentration
1	SAP30 ZnF	[U-95% 13C; U-95% 15N]	0.56 mM
2	TRIS	[U-13C; U-15N]	20 mM
3	acetic acid	[U-13C]	20 mM
4	DTT	[U-2H]	2 mM
5	Sodium Azide	natural abundance	0.2 %
6	zinc chloride	natural abundance	0.56 mM
7	H2O	natural abundance	90 %
8	D2O	natural abundance	10 %

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Concentration
9	SAP30 ZnF	[U-95% 13C; U-95% 15N]	0.56 mM
10	TRIS	[U-13C; U-15N]	20 mM
11	acetic acid	[U-13C]	20 mM
12	DTT	[U-2H]	2 mM
13	Sodium Azide	natural abundance	0.2 %
14	zinc chloride	natural abundance	0.56 mM
15	H2O	natural abundance	90 %
16	D2O	natural abundance	10 %

LACS Plot; CA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	null	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	null	indirect	0.1013291

Referencing offset: -0.2 ppm, Outliers: 1 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	null	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	null	indirect	0.1013291

Referencing offset: -0.2 ppm, Outliers: 1 Detail

LACS Plot; HA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	null	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	null	indirect	0.1013291

Referencing offset: 0.04 ppm, Outliers: 1 Detail

LACS Plot; CO

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	null	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	null	indirect	0.1013291

Referencing offset: -0.12 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 47 models in PDB: 2KDP, Strand ID: A Detail

Release date

2009-02-22

Citation

Solution structure of a novel zinc finger motif in the SAP30 polypeptide of the Sin3 corepressor complex and its potential role in nucleic acid recognition
He, Y., Imhoff, R., Sahu, A., Radhakrishnan, I.
Nucleic Acids Res. (2009), 37, 2142-2152, PubMed 19223330 , DOI 10.1093/nar/gkp051 , Abstract

Entries sharing articles Swiss-Prot: 1 entries Detail

Swiss-Prot: O75446 released on 2005-06-21
Title SAP30_HUMAN Entity Histone deacetylase complex subunit SAP30

Related entities 1. SAP30 ZnF, : 1 : 5 : 19 entities Detail

Interaction partners 1. SAP30 ZnF, : 19 interactors Detail

More details for 19 interactors identified by 11 citations

Experiments performed 10 experiments Detail

1 2D 1H-15N HSQC

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Concentration
1	SAP30 ZnF	[U-95% 13C; U-95% 15N]	0.56 mM
2	TRIS	[U-13C; U-15N]	20 mM
3	acetic acid	[U-13C]	20 mM
4	DTT	[U-2H]	2 mM
5	Sodium Azide	natural abundance	0.2 %
6	zinc chloride	natural abundance	0.56 mM
7	H2O	natural abundance	90 %
8	D2O	natural abundance	10 %

2 2D 1H-13C HSQC

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Concentration
9	SAP30 ZnF	[U-95% 13C; U-95% 15N]	0.56 mM
10	TRIS	[U-13C; U-15N]	20 mM
11	acetic acid	[U-13C]	20 mM
12	DTT	[U-2H]	2 mM
13	Sodium Azide	natural abundance	0.2 %
14	zinc chloride	natural abundance	0.56 mM
15	H2O	natural abundance	90 %
16	D2O	natural abundance	10 %

3 3D CBCA(CO)NH

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Concentration
1	SAP30 ZnF	[U-95% 13C; U-95% 15N]	0.56 mM
2	TRIS	[U-13C; U-15N]	20 mM
3	acetic acid	[U-13C]	20 mM
4	DTT	[U-2H]	2 mM
5	Sodium Azide	natural abundance	0.2 %
6	zinc chloride	natural abundance	0.56 mM
7	H2O	natural abundance	90 %
8	D2O	natural abundance	10 %

4 3D HNCO

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Concentration
1	SAP30 ZnF	[U-95% 13C; U-95% 15N]	0.56 mM
2	TRIS	[U-13C; U-15N]	20 mM
3	acetic acid	[U-13C]	20 mM
4	DTT	[U-2H]	2 mM
5	Sodium Azide	natural abundance	0.2 %
6	zinc chloride	natural abundance	0.56 mM
7	H2O	natural abundance	90 %
8	D2O	natural abundance	10 %

5 3D HNCACB

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Concentration
1	SAP30 ZnF	[U-95% 13C; U-95% 15N]	0.56 mM
2	TRIS	[U-13C; U-15N]	20 mM
3	acetic acid	[U-13C]	20 mM
4	DTT	[U-2H]	2 mM
5	Sodium Azide	natural abundance	0.2 %
6	zinc chloride	natural abundance	0.56 mM
7	H2O	natural abundance	90 %
8	D2O	natural abundance	10 %

6 3D H(CCO)NH

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Concentration
1	SAP30 ZnF	[U-95% 13C; U-95% 15N]	0.56 mM
2	TRIS	[U-13C; U-15N]	20 mM
3	acetic acid	[U-13C]	20 mM
4	DTT	[U-2H]	2 mM
5	Sodium Azide	natural abundance	0.2 %
6	zinc chloride	natural abundance	0.56 mM
7	H2O	natural abundance	90 %
8	D2O	natural abundance	10 %

7 3D HCCH-TOCSY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Concentration
9	SAP30 ZnF	[U-95% 13C; U-95% 15N]	0.56 mM
10	TRIS	[U-13C; U-15N]	20 mM
11	acetic acid	[U-13C]	20 mM
12	DTT	[U-2H]	2 mM
13	Sodium Azide	natural abundance	0.2 %
14	zinc chloride	natural abundance	0.56 mM
15	H2O	natural abundance	90 %
16	D2O	natural abundance	10 %

8 3D HCCH-COSY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Concentration
9	SAP30 ZnF	[U-95% 13C; U-95% 15N]	0.56 mM
10	TRIS	[U-13C; U-15N]	20 mM
11	acetic acid	[U-13C]	20 mM
12	DTT	[U-2H]	2 mM
13	Sodium Azide	natural abundance	0.2 %
14	zinc chloride	natural abundance	0.56 mM
15	H2O	natural abundance	90 %
16	D2O	natural abundance	10 %

9 3D 1H-15N NOESY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Concentration
1	SAP30 ZnF	[U-95% 13C; U-95% 15N]	0.56 mM
2	TRIS	[U-13C; U-15N]	20 mM
3	acetic acid	[U-13C]	20 mM
4	DTT	[U-2H]	2 mM
5	Sodium Azide	natural abundance	0.2 %
6	zinc chloride	natural abundance	0.56 mM
7	H2O	natural abundance	90 %
8	D2O	natural abundance	10 %

10 3D 1H-13C NOESY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Concentration
9	SAP30 ZnF	[U-95% 13C; U-95% 15N]	0.56 mM
10	TRIS	[U-13C; U-15N]	20 mM
11	acetic acid	[U-13C]	20 mM
12	DTT	[U-2H]	2 mM
13	Sodium Azide	natural abundance	0.2 %
14	zinc chloride	natural abundance	0.56 mM
15	H2O	natural abundance	90 %
16	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_16127_2kdp.nef
Input source #2: Coordindates	2kdp.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)
1:7:CYS:SG	2:1:ZN:ZN	unknown	unknown	n/a
1:16:CYS:SG	2:1:ZN:ZN	unknown	unknown	n/a
1:52:CYS:SG	2:1:ZN:ZN	unknown	unknown	n/a
1:55:HIS:ND1	2:1:ZN:ZN	unknown	unknown	n/a

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
B	1	ZN	ZINC ION	None

Sequence alignments

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

--------70--------80--------90-------100-------110-------120-------130-
SNAGQLCCLREDGERCGRAAGNASFSKRIQKSISQKKVKIELDKSARHLYICDYHKNLIQSVRNRRKRKGS
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
SNAGQLCCLREDGERCGRAAGNASFSKRIQKSISQKKVKIELDKSARHLYICDYHKNLIQSVRNRRKRKGS
--------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_16127_2kdp.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	4		No information
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	760		100.0 (chain: A, length: 71)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	Warning	1889 (1)	noe	97.2 (chain: A, length: 71)
2	Distance restraints	CNS/XPLOR_distance_constraints_3	Warning	18 (1)	hbond	23.9 (chain: A, length: 71)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_5	OK	54 (54)	.	52.1 (chain: A, length: 71)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 71, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 385
  - ¹³C chemical shifts: 297
  - ¹⁵N chemical shifts: 78
- Completeness of assignments
  - Entity_assemble_ID: A
- Redox state of CYS
- 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

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
68	CYS	HG	1.9
108	HIS	ND1	137.13
108	HIS	NE2	164.74
115	HIS	ND1	223.47
115	HIS	NE2	172.13

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	452	384	85.0
¹³C chemical shifts	311	297	95.5
¹⁵N chemical shifts	88	74	84.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	147	142	96.6
¹³C chemical shifts	142	135	95.1
¹⁵N chemical shifts	71	66	93.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	305	242	79.3
¹³C chemical shifts	169	162	95.9
¹⁵N chemical shifts	17	8	47.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	29	29	100.0
¹³C chemical shifts	29	29	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	17	11	64.7
¹³C chemical shifts	17	11	64.7

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 71, Sequence coverage: 97.2%
- Total number of restraints: 1889
- Weight of restraints: 1.0 (1889)
- Potential type of restraints: square-well-parabolic (1889)
- Range of distance target values: 1.65, 4.0 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
  - Chain_ID: B
    None
- Distance restraints on contact map
- Saveframe: CNS/XPLOR_distance_constraints_3
  - Status: Warning
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 71, Sequence coverage: 23.9%
  - Total number of restraints: 18
  - Weight of restraints: 1.0 (18)
  - Potential type of restraints: square-well-parabolic (18)
  - Range of distance target values: 1.9, 2.9 (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_5
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 71, Sequence coverage: 52.1%
- Total number of restraints: 54
- Total number of restraints per polymer type: 54
- Weight of restraints: 1.0 (54)
- Potential type of restraints: square-well-parabolic (54)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords nucleic acid interaction, sap30, sin3, zinc finger motif

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Found 1 Document (1.549 seconds)

BMRB: 16127

Sample #1

Sample #2

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Entries sharing articles Swiss-Prot: 1 entries Detail

Related entities 1. SAP30 ZnF, : 1 : 5 : 19 entities Detail

Interaction partners 1. SAP30 ZnF, : 19 interactors Detail

Experiments performed 10 experiments Detail

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NMR combined restraints 5 contents Detail