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Found 1 Document (3.667 seconds)

BMRB: 17485

2L9S

Solution structure of Pf1 SID1-mSin3A PAH2 Complex

Authors

Senthil Kumar, G., Xie, T., Zhang, Y., Radhakrishnan, I.

Assembly

mSin3A PAH2-Pf1 SID1 Complex

Entity

1. mSin3A PAH2-Pf1 SID1 Complex, entity 1 (polymer), 45 monomers, 4990.581 Da Detail

SNADYVQPQL RRPFELLIAA AMERNPTQFQ LPNELTCTTA LPGSS

2. mSin3A PAH2-Pf1 SID1 Complex, entity 2 (polymer), 94 monomers, 10805.78 Da Detail

SNASLQNNQP VEFNHAINYV NKIKNRFQGQ PDIYKAFLEI LHTYQKEQRN AKEAGGNYTP ALTEQEVYAQ VARLFKNQED LLSEFGQFLP DANS

Total weight

15796.361 Da

Max. entity weight

10805.78 Da

Source organism

Homo sapiens , Mus musculus

Exptl. method

solution NMR

Refine. method

torsion angle dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 98.6 %, Completeness: 86.1 %, Completeness (bb): 96.3 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	86.1 % (1426 of 1656)	85.5 % (743 of 869)	86.6 % (545 of 629)	87.3 % (138 of 158)
Backbone	96.3 % (786 of 816)	97.1 % (266 of 274)	95.1 % (392 of 412)	98.5 % (128 of 130)
Sidechain	79.2 % (771 of 974)	80.2 % (477 of 595)	80.9 % (284 of 351)	35.7 % (10 of 28)
Aromatic	33.1 % (45 of 136)	55.9 % (38 of 68)	10.3 % (7 of 68)
Methyl	99.3 % (137 of 138)	100.0 % (69 of 69)	98.6 % (68 of 69)

1. entity 1

SNADYVQPQL RRPFELLIAA AMERNPTQFQ LPNELTCTTA LPGSS

2. entity 2

SNASLQNNQP VEFNHAINYV NKIKNRFQGQ PDIYKAFLEI LHTYQKEQRN AKEAGGNYTP ALTEQEVYAQ VARLFKNQED LLSEFGQFLP DANS

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.00

#	Name	Isotope labeling	Concentration
1	entity_1	[U-100% 13C; U-100% 15N]	0.75 ~ 1.7 mM
2	entity_2	[U-100% 13C; U-100% 15N]	0.75 ~ 1.7 mM
3	H2O	[U-100% 13C; U-100% 15N]	90 %
4	D2O	[U-100% 13C; U-100% 15N]	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: -0.13 ppm, Outliers: 2 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: -0.13 ppm, Outliers: 2 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: 0.24 ppm, Outliers: 2 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2L9S, Strand ID: A, B Detail

Release date

2011-02-23

Citation

Solution structure of the mSin3A PAH2-Pf1 SID1 complex: a Mad1/Mxd1-like interaction disrupted by MRG15 in the Rpd3S/Sin3S complex
Kumar, G., Xie, T., Zhang, Y., Radhakrishnan, I.
J. Mol. Biol. (2011), 408, 987-1000, PubMed 21440557 , DOI 10.1016/j.jmb.2011.03.043 , Abstract

Related entities 1. mSin3A PAH2-Pf1 SID1 Complex, entity 1, : 1 : 6 : 3 entities Detail

Related entities 2. mSin3A PAH2-Pf1 SID1 Complex, entity 2, : 5 : 119 entities Detail

Interaction partners 1. mSin3A PAH2-Pf1 SID1 Complex, entity 1, : 1 interactors Detail

More details for 1 interactors identified by 1 citations

Interaction partners 2. mSin3A PAH2-Pf1 SID1 Complex, entity 2, : 33 interactors Detail

More details for 33 interactors identified by 21 citations

Experiments performed 3 experiments Detail

NMR combined restraints 7 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_17485_2l9s.nef
Input source #2: Coordindates	2l9s.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

---200-----210-------220-------230-------240-
SNADYVQPQLRRPFELLIAAAMERNPTQFQLPNELTCTTALPGSS
|||||||||||||||||||||||||||||||||||||||||||||
SNADYVQPQLRRPFELLIAAAMERNPTQFQLPNELTCTTALPGSS
--------10--------20--------30--------40-----

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

------300-------310-------320-------330-------340-------350-------360-------370-------380-----
SNASLQNNQPVEFNHAINYVNKIKNRFQGQPDIYKAFLEILHTYQKEQRNAKEAGGNYTPALTEQEVYAQVARLFKNQEDLLSEFGQFLPDANS
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
SNASLQNNQPVEFNHAINYVNKIKNRFQGQPDIYKAFLEILHTYQKEQRNAKEAGGNYTPALTEQEVYAQVARLFKNQEDLLSEFGQFLPDANS
--------10--------20--------30--------40--------50--------60--------70--------80--------90----

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	45	0	0	100.0
B	B	94	0	0	100.0

Content subtype: combined_17485_2l9s.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1407		97.8 (chain: A, length: 45), 98.9 (chain: B, length: 94)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	Warning	3450 (1)	noe	97.8 (chain: A, length: 45), 98.9 (chain: B, length: 94)
2	Distance restraints	CNS/XPLOR_distance_constraints_3	Warning	74 (1)	noe	26.7 (chain: A, length: 45)
3	Distance restraints	CNS/XPLOR_distance_constraints_4	Warning	201 (1)	noe	33.3 (chain: A, length: 45), 23.4 (chain: B, length: 94)
4	Distance restraints	CNS/XPLOR_distance_constraints_5	Warning	92 (1)	hbond	22.2 (chain: A, length: 45), 59.6 (chain: B, length: 94)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_6	Warning	134 (134)	.	26.7 (chain: A, length: 45), 69.1 (chain: B, length: 94)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 45, Sequence coverage: 97.8%
  - Entity_assembly_ID: B, Chain length: 94, Sequence coverage: 98.9%
- Total number of assignments
  - ¹H chemical shifts: 726
  - ¹³C chemical shifts: 545
  - ¹⁵N chemical shifts: 136
- 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	271	233	86.0
¹³C chemical shifts	200	178	89.0
¹⁵N chemical shifts	50	47	94.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	86	82	95.3
¹³C chemical shifts	90	80	88.9
¹⁵N chemical shifts	40	38	95.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	185	151	81.6
¹³C chemical shifts	110	98	89.1
¹⁵N chemical shifts	10	9	90.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	26	26	100.0
¹³C chemical shifts	26	25	96.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	14	8	57.1
¹³C chemical shifts	14	7	50.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	598	493	82.4
¹³C chemical shifts	429	367	85.5
¹⁵N chemical shifts	114	89	78.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	188	185	98.4
¹³C chemical shifts	188	181	96.3
¹⁵N chemical shifts	90	88	97.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	410	308	75.1
¹³C chemical shifts	241	186	77.2
¹⁵N chemical shifts	24	1	4.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	44	44	100.0
¹³C chemical shifts	44	44	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	54	30	55.6
¹³C chemical shifts	54	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: 45, Sequence coverage: 97.8%
  - Entity_assembly_ID: B, Chain length: 94, Sequence coverage: 98.9%
- Total number of restraints: 3447
- Weight of restraints: 1.0 (3447)
- Potential type of restraints: square-well-parabolic (3447)
- 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_3
  - Status: Warning
  - Experiment type: noe
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 45, Sequence coverage: 26.7%
  - Total number of restraints: 71
  - Weight of restraints: 1.0 (71)
  - Potential type of restraints: square-well-parabolic (71)
  - Range of distance target values: 3.0, 3.0 (Å)
  - Distance restraints per residue
    - Chain_ID: A
    - Chain_ID: B
      None
  - Distance restraints on contact map
  - Saveframe: CNS/XPLOR_distance_constraints_4
    - Status: Warning
    - Experiment type: noe
    - Sequence coverage of experimental data
      - Entity_assembly_ID: A, Chain length: 45, Sequence coverage: 33.3%
      - Entity_assembly_ID: B, Chain length: 94, Sequence coverage: 23.4%
    - Total number of restraints: 201
    - Weight of restraints: 1.0 (201)
    - Potential type of restraints: square-well-parabolic (201)
    - Range of distance target values: 2.8, 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_5
      - Status: Warning
      - Experiment type: hbond
      - Sequence coverage of experimental data
        Entity_assembly_ID: A, Chain length: 45, Sequence coverage: 22.2%
        Entity_assembly_ID: B, Chain length: 94, Sequence coverage: 59.6%
        ------300-------310-------320-------330-------340-------350-------360-------370-------380----- SNASLQNNQPVEFNHAINYVNKIKNRFQGQPDIYKAFLEILHTYQKEQRNAKEAGGNYTPALTEQEVYAQVARLFKNQEDLLSEFGQFLPDANS ||||||||||||||| |||||||||||||||||||||| ||||||||||| |||||||| ..........VEFNHAINYVNKIKN......DIYKAFLEILHTYQKEQRNAKE..........EQEVYAQVARL....EDLLSEFG ------300-------310-------320-------330-------340-------350-------360-------370-------
      - Total number of restraints: 92
        Total hydrogen bond restraints: 92
        O...H-x: 46
        O...h-N: 46
      - Weight of restraints: 1.0 (92)
        Total hydrogen bond restraints: 1.0 (92)
        O...H-x: 1.0 (46)
        O...h-N: 1.0 (46)
      - Potential type of restraints: square-well-parabolic (92)
        Total hydrogen bond restraints: square-well-parabolic (92)
        O...H-x: square-well-parabolic (46)
        O...h-N: square-well-parabolic (46)
      - 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
        Chain_ID_1: B - Chain_ID_2: B

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_6
- Status: Warning
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 45, Sequence coverage: 26.7%
  - Entity_assembly_ID: B, Chain length: 94, Sequence coverage: 69.1%
- Total number of restraints: 134
- Total number of restraints per polymer type: 134
- Weight of restraints: 1.0 (134)
- Potential type of restraints: square-well-parabolic (134)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: B

Keywords Amphipathic Helix motif, Protein-Peptide Complex, Transcription

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Found 1 Document (3.667 seconds)

BMRB: 17485

Sample

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. mSin3A PAH2-Pf1 SID1 Complex, entity 1, : 1 : 6 : 3 entities Detail

Related entities 2. mSin3A PAH2-Pf1 SID1 Complex, entity 2, : 5 : 119 entities Detail

Interaction partners 1. mSin3A PAH2-Pf1 SID1 Complex, entity 1, : 1 interactors Detail

Interaction partners 2. mSin3A PAH2-Pf1 SID1 Complex, entity 2, : 33 interactors Detail

Experiments performed 3 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 7 contents Detail