BMRBj - BMREntryMaster

Found 1 Document (1.109 seconds)

BMRB: 19516

2MV7

Solution NMR structure of Dot1L in complex with AF9 (Dot1L-AF9).

Authors

Kuntimaddi, A., Bushweller, J.H.

Assembly

Dot1L-AF9 complex

Entity

1. Protein AF-9 (polymer, Thiol state: all free), 69 monomers, 8135.118 Da Detail

DKAYLDELVE LHRRLMTLRE RHILQQIVNL IEETGHFHIT NTTFDFDLCS LDKTTVRKLQ SYLETSGTS

2. Dot1L Histone-lysine N-methyltransferase (polymer, Thiol state: not present), 25 monomers, 2663.080 Da Detail

TNKLPVSIPL ASVVLPSRAE RARST

Total weight

10798.198 Da

Max. entity weight

8135.118 Da

Source organism

Exptl. method

Refine. method

simulated annealing, SIMULATED ANNEALING, SIMULATED ANNEALING

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 91.8 %, Completeness (bb): 97.1 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	91.8 % (1015 of 1106)	90.2 % (516 of 572)	93.8 % (410 of 437)	91.8 % (89 of 97)
Backbone	97.1 % (542 of 558)	96.8 % (181 of 187)	97.1 % (272 of 280)	97.8 % (89 of 91)
Sidechain	88.1 % (564 of 640)	87.0 % (335 of 385)	92.0 % (229 of 249)	0.0 % (0 of 6)
Aromatic	87.1 % (54 of 62)	90.3 % (28 of 31)	83.9 % (26 of 31)
Methyl	86.2 % (112 of 130)	86.2 % (56 of 65)	86.2 % (56 of 65)

1. Protein AF-9

DKAYLDELVE LHRRLMTLRE RHILQQIVNL IEETGHFHIT NTTFDFDLCS LDKTTVRKLQ SYLETSGTS

2. Dot1L Histone-lysine N-methyltransferase

TNKLPVSIPL ASVVLPSRAE RARST

Show sample condition

Sample

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

#	Name	Isotope labeling	Type	Concentration
1	Protein AF-9	[U-100% 13C; U-100% 15N]		750 uM
2	Histone-lysine N-methyltransferase, H3 lysine-79 specific	[U-100% 13C; U-100% 15N]		750 uM
3	Bis-Tris	natural abundance		9.3 mM
4	MES	natural abundance		15.8 mM
5	sodium chloride	natural abundance		100 mM
6	DTT	natural abundance		1 mM
7	D2O	natural abundance		10 %
8	H2O	natural abundance		95 %

Protein Blocks Logo

Calculated from 10 models in PDB: 2MV7, Strand ID: A, B Detail

Release date

2015-04-19

Citation

Degree of recruitment of DOT1L to MLL-AF9 defines level of H3K79 Di- and tri-methylation on target genes and transformation potential
Kuntimaddi, A., Bushweller, J.H.
Cell Rep. (2015), 11, 808-820, PubMed 25921540 , DOI 10.1016/j.celrep.2015.04.004 , Abstract

Related entities 1. Protein AF-9, : 5 : 20 entities Detail

Related entities 2. Dot1L Histone-lysine N-methyltransferase, : 4 : 3 entities Detail

Interaction partners 1. Protein AF-9, : 3 : 1 interactors Detail

More details for 4 interactors identified by 1 citations

Interaction partners 2. Dot1L Histone-lysine N-methyltransferase, : 19 : 1 interactors Detail

More details for 20 interactors identified by 4 citations

Experiments performed 15 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 600 MHz Cryoprobe

Sample

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

#	Name	Isotope labeling	Type	Concentration
1	Protein AF-9	[U-100% 13C; U-100% 15N]		750 uM
2	Histone-lysine N-methyltransferase, H3 lysine-79 specific	[U-100% 13C; U-100% 15N]		750 uM
3	Bis-Tris	natural abundance		9.3 mM
4	MES	natural abundance		15.8 mM
5	sodium chloride	natural abundance		100 mM
6	DTT	natural abundance		1 mM
7	D2O	natural abundance		10 %
8	H2O	natural abundance		95 %

2 2D 1H-15N HSQC

Instrument

Varian INOVA - 600 MHz Cryoprobe

Sample

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

#	Name	Isotope labeling	Type	Concentration
1	Protein AF-9	[U-100% 13C; U-100% 15N]		750 uM
2	Histone-lysine N-methyltransferase, H3 lysine-79 specific	[U-100% 13C; U-100% 15N]		750 uM
3	Bis-Tris	natural abundance		9.3 mM
4	MES	natural abundance		15.8 mM
5	sodium chloride	natural abundance		100 mM
6	DTT	natural abundance		1 mM
7	D2O	natural abundance		10 %
8	H2O	natural abundance		95 %

3 2D 1H-13C HSQC

Instrument

Varian INOVA - 600 MHz Cryoprobe

Sample

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

#	Name	Isotope labeling	Type	Concentration
1	Protein AF-9	[U-100% 13C; U-100% 15N]		750 uM
2	Histone-lysine N-methyltransferase, H3 lysine-79 specific	[U-100% 13C; U-100% 15N]		750 uM
3	Bis-Tris	natural abundance		9.3 mM
4	MES	natural abundance		15.8 mM
5	sodium chloride	natural abundance		100 mM
6	DTT	natural abundance		1 mM
7	D2O	natural abundance		10 %
8	H2O	natural abundance		95 %

4 3D CBCA(CO)NH

Instrument

Varian INOVA - 600 MHz Cryoprobe

Sample

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

#	Name	Isotope labeling	Type	Concentration
1	Protein AF-9	[U-100% 13C; U-100% 15N]		750 uM
2	Histone-lysine N-methyltransferase, H3 lysine-79 specific	[U-100% 13C; U-100% 15N]		750 uM
3	Bis-Tris	natural abundance		9.3 mM
4	MES	natural abundance		15.8 mM
5	sodium chloride	natural abundance		100 mM
6	DTT	natural abundance		1 mM
7	D2O	natural abundance		10 %
8	H2O	natural abundance		95 %

5 3D C(CO)NH

Instrument

Varian INOVA - 600 MHz Cryoprobe

Sample

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

#	Name	Isotope labeling	Type	Concentration
1	Protein AF-9	[U-100% 13C; U-100% 15N]		750 uM
2	Histone-lysine N-methyltransferase, H3 lysine-79 specific	[U-100% 13C; U-100% 15N]		750 uM
3	Bis-Tris	natural abundance		9.3 mM
4	MES	natural abundance		15.8 mM
5	sodium chloride	natural abundance		100 mM
6	DTT	natural abundance		1 mM
7	D2O	natural abundance		10 %
8	H2O	natural abundance		95 %

6 3D HNCO

Instrument

Varian INOVA - 600 MHz Cryoprobe

Sample

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

#	Name	Isotope labeling	Type	Concentration
1	Protein AF-9	[U-100% 13C; U-100% 15N]		750 uM
2	Histone-lysine N-methyltransferase, H3 lysine-79 specific	[U-100% 13C; U-100% 15N]		750 uM
3	Bis-Tris	natural abundance		9.3 mM
4	MES	natural abundance		15.8 mM
5	sodium chloride	natural abundance		100 mM
6	DTT	natural abundance		1 mM
7	D2O	natural abundance		10 %
8	H2O	natural abundance		95 %

7 3D HNCA

Instrument

Varian INOVA - 600 MHz Cryoprobe

Sample

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

#	Name	Isotope labeling	Type	Concentration
1	Protein AF-9	[U-100% 13C; U-100% 15N]		750 uM
2	Histone-lysine N-methyltransferase, H3 lysine-79 specific	[U-100% 13C; U-100% 15N]		750 uM
3	Bis-Tris	natural abundance		9.3 mM
4	MES	natural abundance		15.8 mM
5	sodium chloride	natural abundance		100 mM
6	DTT	natural abundance		1 mM
7	D2O	natural abundance		10 %
8	H2O	natural abundance		95 %

8 3D HNCACB

Instrument

Varian INOVA - 600 MHz Cryoprobe

Sample

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

#	Name	Isotope labeling	Type	Concentration
1	Protein AF-9	[U-100% 13C; U-100% 15N]		750 uM
2	Histone-lysine N-methyltransferase, H3 lysine-79 specific	[U-100% 13C; U-100% 15N]		750 uM
3	Bis-Tris	natural abundance		9.3 mM
4	MES	natural abundance		15.8 mM
5	sodium chloride	natural abundance		100 mM
6	DTT	natural abundance		1 mM
7	D2O	natural abundance		10 %
8	H2O	natural abundance		95 %

9 3D HCCH-TOCSY

Instrument

Varian INOVA - 600 MHz Cryoprobe

Sample

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

#	Name	Isotope labeling	Type	Concentration
1	Protein AF-9	[U-100% 13C; U-100% 15N]		750 uM
2	Histone-lysine N-methyltransferase, H3 lysine-79 specific	[U-100% 13C; U-100% 15N]		750 uM
3	Bis-Tris	natural abundance		9.3 mM
4	MES	natural abundance		15.8 mM
5	sodium chloride	natural abundance		100 mM
6	DTT	natural abundance		1 mM
7	D2O	natural abundance		10 %
8	H2O	natural abundance		95 %

10 3D HNHA

Instrument

Varian INOVA - 600 MHz Cryoprobe

Sample

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

#	Name	Isotope labeling	Type	Concentration
1	Protein AF-9	[U-100% 13C; U-100% 15N]		750 uM
2	Histone-lysine N-methyltransferase, H3 lysine-79 specific	[U-100% 13C; U-100% 15N]		750 uM
3	Bis-Tris	natural abundance		9.3 mM
4	MES	natural abundance		15.8 mM
5	sodium chloride	natural abundance		100 mM
6	DTT	natural abundance		1 mM
7	D2O	natural abundance		10 %
8	H2O	natural abundance		95 %

11 3D 1H-15N NOESY

Instrument

Varian INOVA - 600 MHz Cryoprobe

Sample

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

#	Name	Isotope labeling	Type	Concentration
1	Protein AF-9	[U-100% 13C; U-100% 15N]		750 uM
2	Histone-lysine N-methyltransferase, H3 lysine-79 specific	[U-100% 13C; U-100% 15N]		750 uM
3	Bis-Tris	natural abundance		9.3 mM
4	MES	natural abundance		15.8 mM
5	sodium chloride	natural abundance		100 mM
6	DTT	natural abundance		1 mM
7	D2O	natural abundance		10 %
8	H2O	natural abundance		95 %

12 3D 1H-13C NOESY aliphatic

Instrument

Varian INOVA - 600 MHz Cryoprobe

Sample

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

#	Name	Isotope labeling	Type	Concentration
1	Protein AF-9	[U-100% 13C; U-100% 15N]		750 uM
2	Histone-lysine N-methyltransferase, H3 lysine-79 specific	[U-100% 13C; U-100% 15N]		750 uM
3	Bis-Tris	natural abundance		9.3 mM
4	MES	natural abundance		15.8 mM
5	sodium chloride	natural abundance		100 mM
6	DTT	natural abundance		1 mM
7	D2O	natural abundance		10 %
8	H2O	natural abundance		95 %

13 3D 1H-13C NOESY aromatic

Instrument

Varian INOVA - 600 MHz Cryoprobe

Sample

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

#	Name	Isotope labeling	Type	Concentration
1	Protein AF-9	[U-100% 13C; U-100% 15N]		750 uM
2	Histone-lysine N-methyltransferase, H3 lysine-79 specific	[U-100% 13C; U-100% 15N]		750 uM
3	Bis-Tris	natural abundance		9.3 mM
4	MES	natural abundance		15.8 mM
5	sodium chloride	natural abundance		100 mM
6	DTT	natural abundance		1 mM
7	D2O	natural abundance		10 %
8	H2O	natural abundance		95 %

14 3D HNCO IPAP

Instrument

Bruker Avance - 600 MHz Cryoprobe

Sample

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

#	Name	Isotope labeling	Type	Concentration
9	Protein AF-9	[U-100% 13C; U-100% 15N]		750 uM
10	Histone-lysine N-methyltransferase, H3 lysine-79 specific	[U-100% 13C; U-100% 15N]		750 uM
11	Bis-Tris	natural abundance		9.3 mM
12	MES	natural abundance		15.8 mM
13	sodium chloride	natural abundance		100 mM
14	DTT	natural abundance		1 mM
15	D2O	natural abundance		10 %
16	H2O	natural abundance		95 %
17	(3-acrylamidopropyl)-trimethylammonium chloride	natural abundance		3.5 %
18	acrylic acid	natural abundance		3.5 %

15 3D HNCO IPAP

Instrument

Bruker Avance - 600 MHz Cryoprobe

Sample

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

#	Name	Isotope labeling	Type	Concentration
19	Protein AF-9	[U-100% 13C; U-100% 15N]		750 uM
20	Histone-lysine N-methyltransferase, H3 lysine-79 specific	[U-100% 13C; U-100% 15N]		750 uM
21	Bis-Tris	natural abundance		9.3 mM
22	MES	natural abundance		15.8 mM
23	sodium chloride	natural abundance		100 mM
24	DTT	natural abundance		1 mM
25	D2O	natural abundance		10 %
26	H2O	natural abundance		95 %
27	(3-acrylamidopropyl)-trimethylammonium chloride	natural abundance		3.5 %
28	acrylamide	natural abundance		3.5 %

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_19516_2mv7.nef
Input source #2: Coordindates	2mv7.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

500-----510-------520-------530-------540-------550-------560--------
DKAYLDELVELHRRLMTLRERHILQQIVNLIEETGHFHITNTTFDFDLCSLDKTTVRKLQSYLETSGTS
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
DKAYLDELVELHRRLMTLRERHILQQIVNLIEETGHFHITNTTFDFDLCSLDKTTVRKLQSYLETSGTS
--------10--------20--------30--------40--------50--------60---------

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

--880-------890-------900
TNKLPVSIPLASVVLPSRAERARST
|||||||||||||||||||||||||
TNKLPVSIPLASVVLPSRAERARST
--------10--------20-----

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	69	0	0	100.0
B	B	25	0	0	100.0

Content subtype: combined_19516_2mv7.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1025		100.0 (chain: A, length: 69), 100.0 (chain: B, length: 25)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	2662 (1)	noe	98.6 (chain: A, length: 69), 96.0 (chain: B, length: 25)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_3	OK	139 (139)	.	91.3 (chain: A, length: 69), 64.0 (chain: B, length: 25)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 69, Sequence coverage: 100.0%
  - Entity_assembly_ID: B, Chain length: 25, Sequence coverage: 100.0%
- Total number of assignments
  - ¹³C chemical shifts: 414
  - ¹H chemical shifts: 522
  - ¹⁵N chemical shifts: 89
- 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

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 69, Sequence coverage: 98.6%
  - Entity_assembly_ID: B, Chain length: 25, Sequence coverage: 96.0%
- Total number of restraints: 2557
- Weight of restraints: 1.0 (2557)
- Potential type of restraints: square-well-parabolic (2557)
- Range of distance target values: 2.3, 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
- Distance restraints on contact map

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_3
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 69, Sequence coverage: 91.3%
  - Entity_assembly_ID: B, Chain length: 25, Sequence coverage: 64.0%
- Total number of restraints: 139
- Total number of restraints per polymer type: 139
- Weight of restraints: 1.0 (139)
- Potential type of restraints: square-well-parabolic (139)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A
  - Chain_ID: B

Keywords AF4, AF9, Animals, Bone Marrow Cells, ChIP, ChIP-Seq, Chromatin Immunoprecipitation, Dot1, Dot1L, Epigenetics, H3K79, Histone H3-K79 methyltransferase, Histone methyltransferases, Histone-lysine N-methyltransferase, H3 lysine-79 specific, IDP, Intrinsically Disordered Protein, KMT4, Leukemia, MLL, MLL-AF9, MLLT3, Mice, Mixed Lineage Leukemia, Mutagenesis, Myeloid-Lymphoid Leukemia Protein, NMR, Non Linear Repeat Motifs, Protein AF-9, Protein Structure, Reverse Transcriptase Polymerase Chain Reaction, YEATS3