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BMRB: 16954

2KYG

Structure of the AML1-ETO Nervy Domain - PKA(RIIa) complex and its contribution to AML1-ETO activity

Authors

Corpora, T.A., Cierpecki, T., Bushweller, J.

Assembly

NHR3/PKA(RIIa) Complex

Entity

1. PKA(RIIa) (polymer, Thiol state: not present), 50 monomers, 5616.383 × 2 Da Detail

GAMGSMSHIQ IPPGLTELLQ GYTVEVLRQQ PPDLVEFAVE YFTRLREARA

2. NHR3 (polymer, Thiol state: not present), 38 monomers, 4179.680 Da Detail

AMADIGSASG YVPEEIWKKA EEAVNEVKRQ AMTELQKA

Total weight

15412.445 Da

Max. entity weight

5616.383 Da

Source organism

Exptl. method

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 96.3 %, Completeness (bb): 95.4 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	96.3 % (977 of 1015)	98.3 % (520 of 529)	93.2 % (368 of 395)	97.8 % (89 of 91)
Backbone	95.4 % (494 of 518)	97.7 % (173 of 177)	93.0 % (240 of 258)	97.6 % (81 of 83)
Sidechain	96.4 % (558 of 579)	98.6 % (347 of 352)	92.7 % (203 of 219)	100.0 % (8 of 8)
Aromatic	96.7 % (58 of 60)	96.7 % (29 of 30)	96.6 % (28 of 29)	100.0 % (1 of 1)
Methyl	99.0 % (101 of 102)	100.0 % (51 of 51)	98.0 % (50 of 51)

1. PKA(RIIa)

GAMGSMSHIQ IPPGLTELLQ GYTVEVLRQQ PPDLVEFAVE YFTRLREARA

2. NHR3

AMADIGSASG YVPEEIWKKA EEAVNEVKRQ AMTELQKA

Show sample condition

Sample #1

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 K, pH 4.0, Details 20 mM NaPi pH=4.0 1 mM EDTA temp=30 C

#	Name	Isotope labeling	Type	Concentration
1	NHR3	[U-99% 13C; U-99% 15N]		2 mM
2	PKA(RIIa)	natural abundance		4 mM
3	NaPi	natural abundance		20 mM
4	EDTA	natural abundance		1 mM

Sample #2

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 K, pH 4.0, Details 20 mM NaPi pH=4.0 1 mM EDTA temp=30 C

#	Name	Isotope labeling	Type	Concentration
5	PKA(RIIa)	[U-99% 13C; U-99% 15N]		4 mM
6	NHR3	natural abundance		2 mM
7	NaPi	natural abundance		20 mM
8	EDTA	natural abundance		1 mM

Protein Blocks Logo

Calculated from 15 models in PDB: 2KYG, Strand ID: A, B, C Detail

Release date

2010-08-18

Citation

Structure of the AML1-ETO NHR3-PKA(RIIα) complex and its contribution to AML1-ETO activity
Corpora, T., Roudaia, L., Oo, Z., Chen, W., Manuylova, E., Cai, X., Chen, M.J., Cierpicki, T., Speck, N.A., Bushweller, J.H.
J. Mol. Biol. (2010), 402, 560-577, PubMed 20708017 , DOI 10.1016/j.jmb.2010.08.007 , Abstract

Related entities 1. PKA(RIIa), : 2 : 50 entities Detail

Related entities 2. NHR3, : 1 : 5 : 20 entities Detail

Interaction partners 1. PKA(RIIa), : 69 interactors Detail

More details for 69 interactors identified by 25 citations

Interaction partners 2. NHR3, : 2 interactors Detail

More details for 2 interactors identified by 1 citations

Experiments performed 18 experiments Detail

1 2D 1H-15N HSQC

Instrument

Varian Avance - 500 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 K, pH 4.0, Details 20 mM NaPi pH=4.0 1 mM EDTA temp=30 C

#	Name	Isotope labeling	Type	Concentration
1	NHR3	[U-99% 13C; U-99% 15N]		2 mM
2	PKA(RIIa)	natural abundance		4 mM
3	NaPi	natural abundance		20 mM
4	EDTA	natural abundance		1 mM

2 3D CBCA(CO)NH

Instrument

Varian Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 K, pH 4.0, Details 20 mM NaPi pH=4.0 1 mM EDTA temp=30 C

#	Name	Isotope labeling	Type	Concentration
1	NHR3	[U-99% 13C; U-99% 15N]		2 mM
2	PKA(RIIa)	natural abundance		4 mM
3	NaPi	natural abundance		20 mM
4	EDTA	natural abundance		1 mM

3 3D HNCO

Instrument

Varian Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 K, pH 4.0, Details 20 mM NaPi pH=4.0 1 mM EDTA temp=30 C

#	Name	Isotope labeling	Type	Concentration
1	NHR3	[U-99% 13C; U-99% 15N]		2 mM
2	PKA(RIIa)	natural abundance		4 mM
3	NaPi	natural abundance		20 mM
4	EDTA	natural abundance		1 mM

4 3D HNCACB

Instrument

Varian Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 K, pH 4.0, Details 20 mM NaPi pH=4.0 1 mM EDTA temp=30 C

#	Name	Isotope labeling	Type	Concentration
1	NHR3	[U-99% 13C; U-99% 15N]		2 mM
2	PKA(RIIa)	natural abundance		4 mM
3	NaPi	natural abundance		20 mM
4	EDTA	natural abundance		1 mM

5 3D HCCH-TOCSY

Instrument

Varian Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 K, pH 4.0, Details 20 mM NaPi pH=4.0 1 mM EDTA temp=30 C

#	Name	Isotope labeling	Type	Concentration
1	NHR3	[U-99% 13C; U-99% 15N]		2 mM
2	PKA(RIIa)	natural abundance		4 mM
3	NaPi	natural abundance		20 mM
4	EDTA	natural abundance		1 mM

6 3D HNHA

Instrument

Varian Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 K, pH 4.0, Details 20 mM NaPi pH=4.0 1 mM EDTA temp=30 C

#	Name	Isotope labeling	Type	Concentration
1	NHR3	[U-99% 13C; U-99% 15N]		2 mM
2	PKA(RIIa)	natural abundance		4 mM
3	NaPi	natural abundance		20 mM
4	EDTA	natural abundance		1 mM

7 3D H(CCO)NH

Instrument

Varian Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 K, pH 4.0, Details 20 mM NaPi pH=4.0 1 mM EDTA temp=30 C

#	Name	Isotope labeling	Type	Concentration
1	NHR3	[U-99% 13C; U-99% 15N]		2 mM
2	PKA(RIIa)	natural abundance		4 mM
3	NaPi	natural abundance		20 mM
4	EDTA	natural abundance		1 mM

8 3D 1H-15N NOESY

Instrument

Varian Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 K, pH 4.0, Details 20 mM NaPi pH=4.0 1 mM EDTA temp=30 C

#	Name	Isotope labeling	Type	Concentration
1	NHR3	[U-99% 13C; U-99% 15N]		2 mM
2	PKA(RIIa)	natural abundance		4 mM
3	NaPi	natural abundance		20 mM
4	EDTA	natural abundance		1 mM

9 3D 1H-13C NOESY

Instrument

Varian Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 K, pH 4.0, Details 20 mM NaPi pH=4.0 1 mM EDTA temp=30 C

#	Name	Isotope labeling	Type	Concentration
1	NHR3	[U-99% 13C; U-99% 15N]		2 mM
2	PKA(RIIa)	natural abundance		4 mM
3	NaPi	natural abundance		20 mM
4	EDTA	natural abundance		1 mM

10 2D 1H-15N HSQC

Instrument

Varian Avance - 500 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 K, pH 4.0, Details 20 mM NaPi pH=4.0 1 mM EDTA temp=30 C

#	Name	Isotope labeling	Type	Concentration
5	PKA(RIIa)	[U-99% 13C; U-99% 15N]		4 mM
6	NHR3	natural abundance		2 mM
7	NaPi	natural abundance		20 mM
8	EDTA	natural abundance		1 mM

11 3D CBCA(CO)NH

Instrument

Varian Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 K, pH 4.0, Details 20 mM NaPi pH=4.0 1 mM EDTA temp=30 C

#	Name	Isotope labeling	Type	Concentration
5	PKA(RIIa)	[U-99% 13C; U-99% 15N]		4 mM
6	NHR3	natural abundance		2 mM
7	NaPi	natural abundance		20 mM
8	EDTA	natural abundance		1 mM

12 3D HNCO

Instrument

Varian Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 K, pH 4.0, Details 20 mM NaPi pH=4.0 1 mM EDTA temp=30 C

#	Name	Isotope labeling	Type	Concentration
5	PKA(RIIa)	[U-99% 13C; U-99% 15N]		4 mM
6	NHR3	natural abundance		2 mM
7	NaPi	natural abundance		20 mM
8	EDTA	natural abundance		1 mM

13 3D HNCACB

Instrument

Varian Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 K, pH 4.0, Details 20 mM NaPi pH=4.0 1 mM EDTA temp=30 C

#	Name	Isotope labeling	Type	Concentration
5	PKA(RIIa)	[U-99% 13C; U-99% 15N]		4 mM
6	NHR3	natural abundance		2 mM
7	NaPi	natural abundance		20 mM
8	EDTA	natural abundance		1 mM

14 3D HCCH-TOCSY

Instrument

Varian Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 K, pH 4.0, Details 20 mM NaPi pH=4.0 1 mM EDTA temp=30 C

#	Name	Isotope labeling	Type	Concentration
5	PKA(RIIa)	[U-99% 13C; U-99% 15N]		4 mM
6	NHR3	natural abundance		2 mM
7	NaPi	natural abundance		20 mM
8	EDTA	natural abundance		1 mM

15 3D HNHA

Instrument

Varian Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 K, pH 4.0, Details 20 mM NaPi pH=4.0 1 mM EDTA temp=30 C

#	Name	Isotope labeling	Type	Concentration
5	PKA(RIIa)	[U-99% 13C; U-99% 15N]		4 mM
6	NHR3	natural abundance		2 mM
7	NaPi	natural abundance		20 mM
8	EDTA	natural abundance		1 mM

16 3D H(CCO)NH

Instrument

Varian Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 K, pH 4.0, Details 20 mM NaPi pH=4.0 1 mM EDTA temp=30 C

#	Name	Isotope labeling	Type	Concentration
5	PKA(RIIa)	[U-99% 13C; U-99% 15N]		4 mM
6	NHR3	natural abundance		2 mM
7	NaPi	natural abundance		20 mM
8	EDTA	natural abundance		1 mM

17 3D 1H-15N NOESY

Instrument

Varian Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 K, pH 4.0, Details 20 mM NaPi pH=4.0 1 mM EDTA temp=30 C

#	Name	Isotope labeling	Type	Concentration
5	PKA(RIIa)	[U-99% 13C; U-99% 15N]		4 mM
6	NHR3	natural abundance		2 mM
7	NaPi	natural abundance		20 mM
8	EDTA	natural abundance		1 mM

18 3D 1H-13C NOESY

Instrument

Varian Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 K, pH 4.0, Details 20 mM NaPi pH=4.0 1 mM EDTA temp=30 C

#	Name	Isotope labeling	Type	Concentration
5	PKA(RIIa)	[U-99% 13C; U-99% 15N]		4 mM
6	NHR3	natural abundance		2 mM
7	NaPi	natural abundance		20 mM
8	EDTA	natural abundance		1 mM

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints, RDC restraints	combined_16954_2kyg.nef
Input source #2: Coordindates	2kyg.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	Error

Disulfide bonds

None

Other bonds (neither disulfide, covalent nor hydrogen bonds, e.g. Zinc–sulphur bond)

None

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
A	0	.	Not matched with CCD	None
A	1	.	Not matched with CCD	None
B	0	.	Not matched with CCD	None
B	1	.	Not matched with CCD	None

Sequence alignments

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

----                                                
..GA                                                
  ||                                                
-.-AMGSMSHIQIPPGLTELLQGYTVEVLRQQPPDLVEFAVEYFTRLREARA
 - ---------10--------20--------30--------40--------

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

----                                                
..GA                                                
  ||                                                
-.-AMGSMSHIQIPPGLTELLQGYTVEVLRQQPPDLVEFAVEYFTRLREARA
 - ---------10--------20--------30--------40--------

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

--580-----590-------600-------610-----
AMADIGSASGYVPEEIWKKAEEAVNEVKRQAMTELQKA
||||||||||||||||||||||||||||||||||||||
AMADIGSASGYVPEEIWKKAEEAVNEVKRQAMTELQKA
--------10--------20--------30--------

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	50	2	0	100.0
B	B	50	2	0	100.0
C	C	38	0	0	100.0

Content subtype: combined_16954_2kyg.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Error	1038		100.0 (chain: C, length: 38)
1	Distance restraints	CNS/XPLOR_distance_constraints_3	Error	10171 (1)	noe	97.4 (chain: C, length: 38)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_2	Error	166 (166)	.	60.5 (chain: C, length: 38)
1	RDC restraints	CNS/XPLOR_dipolar_coupling_4	Error	286 (286)	.	65.8 (chain: C, length: 38)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Error
- Sequence coverage of experimental data
  - Entity_assembly_ID: C, Chain length: 38, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 581
  - ¹³C chemical shifts: 364
  - ¹⁵N chemical shifts: 93
- Completeness of assignments
  - Entity_assemble_ID: C
- 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: C

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_3
- Status: Error
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: C, Chain length: 38, Sequence coverage: 97.4%
- Total number of restraints: 9879
- Weight of restraints: 1.0 (9879)
- Potential type of restraints: square-well-parabolic (9879)
- Range of distance target values: 2.35, 3.65 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
  - Chain_ID: B
  - Chain_ID: C
- Distance restraints on contact map

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_2
- Status: Error
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: C, Chain length: 38, Sequence coverage: 60.5%
- Total number of restraints: 166
- Total number of restraints per polymer type: 166
- Weight of restraints: 1.0 (166)
- Potential type of restraints: square-well-parabolic (166)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: C

RDC restraints

Saveframe: CNS/XPLOR_dipolar_coupling_4
- Status: Error
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: C, Chain length: 38, Sequence coverage: 65.8%
- Total number of restraints: 286
- Potential type of restraints: undefined (286)
- Range of observed RDC values: 100.0, -100.0 (Hz)
- RDC restraints per residue
  - Chain_ID: C
    None