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Found 1 Document (0.397 seconds)

BMRB: 34181

6EMQ

Solution structure of the LEDGF/p75 IBD - MLL1 (aa 111-160) complex

Authors

Veverka, V.

Assembly

PC4 and SFRS1-interacting protein,Histone-lysine N-methyltransferase 2A (E.C.2.1.1.43)

Entity

1. PC4 and SFRS1-interacting protein,Histone-lysine N-methyltransferase 2A (E.C.2.1.1.43) (polymer, Thiol state: all free), 165 monomers, 17941.01 Da Detail

SNAASWETSM DSRLQRIHAE IKNSLKIDNL DVNRCIEALD ELASLQVTMQ QAQKHTEMIT TLKKIRRFKV SQVIMEKSTM LYNKFKNMFL VGEGDSVITQ VLNKSGGSGS GSGSSGFDAA LQVSAAIGTN LRRFRAVFGE SGGGGGSGED EQFLGFGSDE EVRVR

Formula weight

17941.01 Da

Source organism

Homo sapiens

Exptl. method

solution NMR

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 93.3 %, Completeness: 90.6 %, Completeness (bb): 90.6 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	90.6 % (1684 of 1858)	91.1 % (880 of 966)	90.1 % (639 of 709)	90.2 % (165 of 183)
Backbone	90.6 % (897 of 990)	87.9 % (306 of 348)	92.2 % (440 of 477)	91.5 % (151 of 165)
Sidechain	91.2 % (926 of 1015)	92.9 % (574 of 618)	89.2 % (338 of 379)	77.8 % (14 of 18)
Aromatic	77.8 % (84 of 108)	94.4 % (51 of 54)	60.4 % (32 of 53)	100.0 % (1 of 1)
Methyl	97.1 % (165 of 170)	100.0 % (85 of 85)	94.1 % (80 of 85)

1. entity 1

SNAASWETSM DSRLQRIHAE IKNSLKIDNL DVNRCIEALD ELASLQVTMQ QAQKHTEMIT TLKKIRRFKV SQVIMEKSTM LYNKFKNMFL VGEGDSVITQ VLNKSGGSGS GSGSSGFDAA LQVSAAIGTN LRRFRAVFGE SGGGGGSGED EQFLGFGSDE EVRVR

Show sample condition

Sample

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7, Details 0.5 mM [U-13C; U-15N] LEDGF/p75 IBD-MLL1, 50 mM TRIS, 150 mM sodium chloride, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
1	LEDGF/p75 IBD-MLL1	[U-13C; U-15N]	0.5 mM
2	TRIS	natural abundance	50 mM
3	sodium chloride	natural abundance	150 mM

LACS Plot; CA

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

Referencing offset: -0.21 ppm, Outliers: 3 Detail

LACS Plot; CB

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

Referencing offset: -0.21 ppm, Outliers: 3 Detail

LACS Plot; HA

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

Referencing offset: 0.02 ppm, Outliers: 1 Detail

Release date

2018-07-16

Citation

Affinity switching of the LEDGF/p75 IBD interactome is governed by kinase-dependent phosphorylation
Sharma, S., Cermakova, K., De Rijck, J., Demeulemeester, J., Fabry, M., El Ashkar, S., Van Belle, S., Lepsik, M., Tesina, P., Duchoslav, V., Novak, P., Hubalek, M., Srb, P., Christ, F., Rezacova, P., Hodges, H.C., Debyser, Z., Veverka, V.
Proc. Natl. Acad. Sci. U. S. A. (2018), 115, E7053-E7062, PubMed 29997176 , DOI 10.1073/pnas.1803909115 , Abstract

Related entities 1. PC4 and SFRS1-interacting protein,Histone-lysine N-methyltransferase 2A (E.C.2.1.1.43), : 1 : 2 entities Detail

Experiments performed 3 experiments Detail

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_34181_6emq.nef
Input source #2: Coordindates	6emq.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	447	.	Not matched with CCD	None
A	443	.	Not matched with CCD	None
A	446	.	Not matched with CCD	None
A	445	.	Not matched with CCD	None
A	448	.	Not matched with CCD	None
A	444	.	Not matched with CCD	None

Sequence alignments

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

------480                                                                                           
......SNA                                                                                           
      |||                                                                                           
-.-.-.-N-A-WETSMDSRLQRIHAEIKNSLKIDNLDVNRCIEALDELASLQVTMQQAQKHTEMITTLKKIRRFKVSQVIMEKSTMLYNKFKNMFLVGEG
 - - - - - ---------10--------20--------30--------40--------50--------60--------70--------80--------

                                                                       
                                                                       
                                                                       
DSVITQVLNKSGGSGSGSGSSGFDAALQVSAAIGTNLRRFRAVFGESGGGGGSGEDEQFLGFGSDEEVRVR
90-------100-------110-------120-------130-------140-------150-------16

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	165	6	0	100.0

Content subtype: combined_34181_6emq.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	Error	1645		87.7 (chain: A, length: 171)
1	Distance restraints	CNS/XPLOR_distance_constraints_3	Error	3237 (1)	noe	78.9 (chain: A, length: 171)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_2	OK	180 (180)	.	59.1 (chain: A, length: 171)

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: Error
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 171, Sequence coverage: 87.7%
- Total number of assignments
  - ¹³C chemical shifts: 621
  - ¹H chemical shifts: 866
  - ¹⁵N chemical shifts: 158
- Completeness of assignments
- 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

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_3
- Status: Error
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 171, Sequence coverage: 78.9%
- Total number of restraints: 3237
- Weight of restraints: 1.0 (3237)
- Potential type of restraints: square-well-parabolic (3237)
- Range of distance target values: 1.3, 3.04 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
- Distance restraints on contact map

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_2
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 171, Sequence coverage: 59.1%
- Total number of restraints: 180
- Total number of restraints per polymer type: 180
- Weight of restraints: 1.0 (180)
- Potential type of restraints: square-well-parabolic (180)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue

Keywords TRANSCRIPTION, epigenetics, leukemia, protein-protein complex

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Found 1 Document (0.397 seconds)

BMRB: 34181

Sample

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. PC4 and SFRS1-interacting protein,Histone-lysine N-methyltransferase 2A (E.C.2.1.1.43), : 1 : 2 entities Detail

Experiments performed 3 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 4 contents Detail