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BMRB: 17653

2LD7

solution structure of the mSin3A PAH3-SAP30 SID complex

Authors

Xie, T., He, Y., Korkeamaki, H., Zhang, Y., Imhoff, R., Lohi, O., Radhakrishnan, I.

Assembly

SAP30 and PAH3

Entity

1. SAP30 (polymer, Thiol state: not present), 94 monomers, 10530.62 Da Detail

SNAGSDDDGG DSPVQDIDTP EVDLYQLQVN TLRRYKRHFK LPTRPGLNKA QLVEIVGCHF KSIPVNEKDT LTCFIYSVRN DKNKSDLKAD SGVH

2. SAP30 and PAH3, entity 2 (polymer, Thiol state: not present), 75 monomers, 8662.838 Da Detail

SNASKHGVGT ESLFFDKVRK ALRSAEAYEN FLRCLVIFNQ EVISRAELVQ LVSPFLGKFP ELFNWFKNFL GYKES

Total weight

19193.457 Da

Max. entity weight

10530.62 Da

Source organism

Mus musculus

Exptl. method

solution NMR

Refine. method

simulated annealing, torsion angle dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 98.8 %, Completeness: 88.8 %, Completeness (bb): 97.0 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	88.8 % (1788 of 2014)	86.7 % (911 of 1051)	89.7 % (702 of 783)	97.2 % (175 of 180)
Backbone	97.0 % (970 of 1000)	95.3 % (325 of 341)	98.0 % (487 of 497)	97.5 % (158 of 162)
Sidechain	83.1 % (975 of 1173)	82.5 % (586 of 710)	83.6 % (372 of 445)	94.4 % (17 of 18)
Aromatic	42.0 % (79 of 188)	58.5 % (55 of 94)	24.7 % (23 of 93)	100.0 % (1 of 1)
Methyl	100.0 % (176 of 176)	100.0 % (88 of 88)	100.0 % (88 of 88)

1. SAP30

SNAGSDDDGG DSPVQDIDTP EVDLYQLQVN TLRRYKRHFK LPTRPGLNKA QLVEIVGCHF KSIPVNEKDT LTCFIYSVRN DKNKSDLKAD SGVH

2. entity 2

SNASKHGVGT ESLFFDKVRK ALRSAEAYEN FLRCLVIFNQ EVISRAELVQ LVSPFLGKFP ELFNWFKNFL GYKES

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Temperature 273 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	entity_1	[U-100% 13C; U-100% 15N]	1 mM
2	entity_2	natural abundance	1 mM
3	H2O	natural abundance	90 %
4	D2O	natural abundance	10 %

Sample #2

Solvent system 90% H2O/10% D2O, Temperature 273 K, pH 6.5

#	Name	Isotope labeling	Concentration
5	entity_1	natural abundance	1 mM
6	entity_2	[U-100% 13C; U-100% 15N]	1 mM
7	H2O	natural abundance	90 %
8	D2O	natural abundance	10 %

Sample #3

Solvent system 100% D2O, Temperature 273 K, pH 6.5

#	Name	Isotope labeling	Concentration
9	entity_1	[U-100% 13C; U-100% 15N]	1 mM
10	entity_2	natural abundance	1 mM
11	D2O	natural abundance	100 %

Sample #4

Solvent system 100% D2O, Temperature 273 K, pH 6.5

#	Name	Isotope labeling	Concentration
12	entity_1	natural abundance	1 mM
13	entity_2	[U-100% 13C; U-100% 15N]	1 mM
14	D2O	natural abundance	100 %

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: -2.27 ppm, Outliers: 3 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: -2.27 ppm, Outliers: 3 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: 0.03 ppm, Outliers: 2 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: -2.49 ppm, Outliers: 2 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2LD7, Strand ID: A, B Detail

Release date

2011-10-25

Citation

Structure of the 30-kDa Sin3-associated protein (SAP30) in complex with the mammalian Sin3A corepressor and its role in nucleic acid binding
Xie, T., He, Y., Korkeamaki, H., Zhang, Y., Imhoff, R., Lohi, O., Radhakrishnan, I.
J. Biol. Chem. (2011), 286, 27814-27824, PubMed 21676866 , DOI 10.1074/jbc.M111.252494 , Abstract

Related entities 1. SAP30, : 1 : 1 : 7 entities Detail

Related entities 2. SAP30 and PAH3, entity 2, : 3 : 35 entities Detail

Interaction partners 2. SAP30 and PAH3, entity 2, : 34 interactors Detail

More details for 34 interactors identified by 21 citations

Experiments performed 20 experiments Detail

1 3D 1H-15N NOESY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Temperature 273 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	entity_1	[U-100% 13C; U-100% 15N]	1 mM
2	entity_2	natural abundance	1 mM
3	H2O	natural abundance	90 %
4	D2O	natural abundance	10 %

2 3D 1H-15N NOESY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Temperature 273 K, pH 6.5

#	Name	Isotope labeling	Concentration
5	entity_1	natural abundance	1 mM
6	entity_2	[U-100% 13C; U-100% 15N]	1 mM
7	H2O	natural abundance	90 %
8	D2O	natural abundance	10 %

3 3D 1H-13C NOESY aliphatic

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Temperature 273 K, pH 6.5

#	Name	Isotope labeling	Concentration
9	entity_1	[U-100% 13C; U-100% 15N]	1 mM
10	entity_2	natural abundance	1 mM
11	D2O	natural abundance	100 %

4 3D 1H-13C NOESY aliphatic

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Temperature 273 K, pH 6.5

#	Name	Isotope labeling	Concentration
12	entity_1	natural abundance	1 mM
13	entity_2	[U-100% 13C; U-100% 15N]	1 mM
14	D2O	natural abundance	100 %

5 2D 1H-15N HSQC

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Temperature 273 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	entity_1	[U-100% 13C; U-100% 15N]	1 mM
2	entity_2	natural abundance	1 mM
3	H2O	natural abundance	90 %
4	D2O	natural abundance	10 %

6 2D 1H-15N HSQC

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Temperature 273 K, pH 6.5

#	Name	Isotope labeling	Concentration
5	entity_1	natural abundance	1 mM
6	entity_2	[U-100% 13C; U-100% 15N]	1 mM
7	H2O	natural abundance	90 %
8	D2O	natural abundance	10 %

7 3D CBCA(CO)NH

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Temperature 273 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	entity_1	[U-100% 13C; U-100% 15N]	1 mM
2	entity_2	natural abundance	1 mM
3	H2O	natural abundance	90 %
4	D2O	natural abundance	10 %

8 3D CBCA(CO)NH

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Temperature 273 K, pH 6.5

#	Name	Isotope labeling	Concentration
5	entity_1	natural abundance	1 mM
6	entity_2	[U-100% 13C; U-100% 15N]	1 mM
7	H2O	natural abundance	90 %
8	D2O	natural abundance	10 %

9 3D HNCACB

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Temperature 273 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	entity_1	[U-100% 13C; U-100% 15N]	1 mM
2	entity_2	natural abundance	1 mM
3	H2O	natural abundance	90 %
4	D2O	natural abundance	10 %

10 3D HNCACB

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Temperature 273 K, pH 6.5

#	Name	Isotope labeling	Concentration
5	entity_1	natural abundance	1 mM
6	entity_2	[U-100% 13C; U-100% 15N]	1 mM
7	H2O	natural abundance	90 %
8	D2O	natural abundance	10 %

11 3D HNCO

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Temperature 273 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	entity_1	[U-100% 13C; U-100% 15N]	1 mM
2	entity_2	natural abundance	1 mM
3	H2O	natural abundance	90 %
4	D2O	natural abundance	10 %

12 3D HNCO

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Temperature 273 K, pH 6.5

#	Name	Isotope labeling	Concentration
5	entity_1	natural abundance	1 mM
6	entity_2	[U-100% 13C; U-100% 15N]	1 mM
7	H2O	natural abundance	90 %
8	D2O	natural abundance	10 %

13 3D HNCA

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Temperature 273 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	entity_1	[U-100% 13C; U-100% 15N]	1 mM
2	entity_2	natural abundance	1 mM
3	H2O	natural abundance	90 %
4	D2O	natural abundance	10 %

14 3D HNCA

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Temperature 273 K, pH 6.5

#	Name	Isotope labeling	Concentration
5	entity_1	natural abundance	1 mM
6	entity_2	[U-100% 13C; U-100% 15N]	1 mM
7	H2O	natural abundance	90 %
8	D2O	natural abundance	10 %

15 3D HCCH-COSY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Temperature 273 K, pH 6.5

#	Name	Isotope labeling	Concentration
9	entity_1	[U-100% 13C; U-100% 15N]	1 mM
10	entity_2	natural abundance	1 mM
11	D2O	natural abundance	100 %

16 3D HCCH-COSY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Temperature 273 K, pH 6.5

#	Name	Isotope labeling	Concentration
12	entity_1	natural abundance	1 mM
13	entity_2	[U-100% 13C; U-100% 15N]	1 mM
14	D2O	natural abundance	100 %

17 3D HCCH-TOCSY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Temperature 273 K, pH 6.5

#	Name	Isotope labeling	Concentration
9	entity_1	[U-100% 13C; U-100% 15N]	1 mM
10	entity_2	natural abundance	1 mM
11	D2O	natural abundance	100 %

18 3D HCCH-TOCSY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Temperature 273 K, pH 6.5

#	Name	Isotope labeling	Concentration
12	entity_1	natural abundance	1 mM
13	entity_2	[U-100% 13C; U-100% 15N]	1 mM
14	D2O	natural abundance	100 %

19 2D 1H-13C HSQC aromatic

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Temperature 273 K, pH 6.5

#	Name	Isotope labeling	Concentration
9	entity_1	[U-100% 13C; U-100% 15N]	1 mM
10	entity_2	natural abundance	1 mM
11	D2O	natural abundance	100 %

20 2D 1H-13C HSQC aromatic

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Temperature 273 K, pH 6.5

#	Name	Isotope labeling	Concentration
12	entity_1	natural abundance	1 mM
13	entity_2	[U-100% 13C; U-100% 15N]	1 mM
14	D2O	natural abundance	100 %

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_17653_2ld7.nef
Input source #2: Coordindates	2ld7.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

---130-----140-------150-------160-------170-------180-------190-------200-------210-------220
SNAGSDDDGGDSPVQDIDTPEVDLYQLQVNTLRRYKRHFKLPTRPGLNKAQLVEIVGCHFKSIPVNEKDTLTCFIYSVRNDKNKSDLKADSGVH
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
SNAGSDDDGGDSPVQDIDTPEVDLYQLQVNTLRRYKRHFKLPTRPGLNKAQLVEIVGCHFKSIPVNEKDTLTCFIYSVRNDKNKSDLKADSGVH
--------10--------20--------30--------40--------50--------60--------70--------80--------90----

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

----460-------470-------480-------490-------500-------510-------520--------
SNASKHGVGTESLFFDKVRKALRSAEAYENFLRCLVIFNQEVISRAELVQLVSPFLGKFPELFNWFKNFLGYKES
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
SNASKHGVGTESLFFDKVRKALRSAEAYENFLRCLVIFNQEVISRAELVQLVSPFLGKFPELFNWFKNFLGYKES
--------10--------20--------30--------40--------50--------60--------70-----

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	94	0	0	100.0
B	B	75	0	0	100.0

Content subtype: combined_17653_2ld7.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1783		98.9 (chain: A, length: 94), 98.7 (chain: B, length: 75)
1	Distance restraints	CNS/XPLOR_distance_constraints_3	Warning	5702 (1)	noe	95.7 (chain: A, length: 94), 97.3 (chain: B, length: 75)
2	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	106 (1)	hbond	38.3 (chain: A, length: 94), 58.7 (chain: B, length: 75)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_4	OK	168 (168)	.	51.1 (chain: A, length: 94), 74.7 (chain: B, length: 75)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 94, Sequence coverage: 98.9%
  - Entity_assembly_ID: B, Chain length: 75, Sequence coverage: 98.7%
- Total number of assignments
  - ¹H chemical shifts: 910
  - ¹³C chemical shifts: 699
  - ¹⁵N chemical shifts: 174
- 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

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
199	CYS	HG	5.98

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	566	483	85.3
¹³C chemical shifts	417	379	90.9
¹⁵N chemical shifts	104	94	90.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	189	178	94.2
¹³C chemical shifts	188	184	97.9
¹⁵N chemical shifts	89	85	95.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	377	305	80.9
¹³C chemical shifts	229	195	85.2
¹⁵N chemical shifts	15	9	60.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	48	48	100.0
¹³C chemical shifts	48	48	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	33	17	51.5
¹³C chemical shifts	33	0	0.0

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
486	ARG	HH12	7.82
486	ARG	HH11	5.99
486	ARG	NH1	86.89
487	CYS	HG	3.11

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	485	423	87.2
¹³C chemical shifts	366	320	87.4
¹⁵N chemical shifts	85	79	92.9

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	152	148	97.4
¹³C chemical shifts	150	145	96.7
¹⁵N chemical shifts	73	71	97.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	333	275	82.6
¹³C chemical shifts	216	175	81.0
¹⁵N chemical shifts	12	8	66.7

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

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	61	36	59.0
¹³C chemical shifts	60	21	35.0
¹⁵N chemical shifts	1	1	100.0

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_3
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 94, Sequence coverage: 95.7%
  - Entity_assembly_ID: B, Chain length: 75, Sequence coverage: 97.3%
- Total number of restraints: 5702
- Weight of restraints: 1.0 (5702)
- Potential type of restraints: square-well-parabolic (5702)
- 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
- Distance restraints on contact map
- Saveframe: CNS/XPLOR_distance_constraints_2
  - Status: OK
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 94, Sequence coverage: 38.3%
    - Entity_assembly_ID: B, Chain length: 75, Sequence coverage: 58.7%
  - Total number of restraints: 106
  - Weight of restraints: 1.0 (106)
  - Potential type of restraints: square-well-parabolic (106)
  - 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
  - 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: 94, Sequence coverage: 51.1%
  - Entity_assembly_ID: B, Chain length: 75, Sequence coverage: 74.7%
- Total number of restraints: 168
- Total number of restraints per polymer type: 168
- Weight of restraints: 1.0 (168)
- Potential type of restraints: square-well-parabolic (168)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A
  - Chain_ID: B

Keywords mSin3A PAH3-SAP30 SID complex, protein-protein interaction, solution NMR structure

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Found 1 Document (3.584 seconds)

BMRB: 17653

Sample #1

Sample #2

Sample #3

Sample #4

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. SAP30, : 1 : 1 : 7 entities Detail

Related entities 2. SAP30 and PAH3, entity 2, : 3 : 35 entities Detail

Interaction partners 2. SAP30 and PAH3, entity 2, : 34 interactors Detail

Experiments performed 20 experiments Detail

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NMR combined restraints 5 contents Detail