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Found 1 Document (0.565 seconds)

BMRB: 34179

6EMO

Solution structure of the LEDGF/p75 IBD - JPO2 (aa 1-32) complex

Authors

Veverka, V.

Assembly

PC4 and SFRS1-interacting protein,LEDGF/p75 IBD-JPO2 M1

Entity

1. PC4 and SFRS1-interacting protein,LEDGF/p75 IBD-JPO2 M1 (polymer, Thiol state: all free), 136 monomers, 15674.75 Da Detail

SNAASWETSM DSRLQRIHAE IKNSLKIDNL DVNRCIEALD ELASLQVTMQ QAQKHTEMIT TLKKIRRFKV SQVIMEKSTM LYNKFKNMFL VGEGDSVITQ VLNKMELATR YQIPKEVADI FNAPSDDEEF VGFRDD

Formula weight

15674.75 Da

Source organism

Homo sapiens

Exptl. method

solution NMR

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 99.3 %, Completeness: 96.5 %, Completeness (bb): 97.9 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	96.5 % (1569 of 1626)	97.6 % (830 of 850)	94.7 % (592 of 625)	97.4 % (147 of 151)
Backbone	97.9 % (795 of 812)	98.2 % (268 of 273)	97.8 % (396 of 405)	97.8 % (131 of 134)
Sidechain	95.7 % (906 of 947)	97.4 % (562 of 577)	92.9 % (328 of 353)	94.1 % (16 of 17)
Aromatic	81.3 % (78 of 96)	100.0 % (48 of 48)	61.7 % (29 of 47)	100.0 % (1 of 1)
Methyl	98.1 % (151 of 154)	100.0 % (77 of 77)	96.1 % (74 of 77)

1. entity 1

SNAASWETSM DSRLQRIHAE IKNSLKIDNL DVNRCIEALD ELASLQVTMQ QAQKHTEMIT TLKKIRRFKV SQVIMEKSTM LYNKFKNMFL VGEGDSVITQ VLNKMELATR YQIPKEVADI FNAPSDDEEF VGFRDD

Show sample condition

Sample

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details 0.5 mM [U-13C; U-15N] LEDGF/p75 IBD-JPO2 M1, 50 mM TRIS, 150 mM sodium chloride, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
1	LEDGF/p75 IBD-JPO2 M1	[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: -0.09 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: -0.09 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: 0.0 ppm, Outliers: 3 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: 0.18 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,LEDGF/p75 IBD-JPO2 M1, : 1 : 6 entities Detail

Experiments performed 11 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker AvanceIII - 850 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details 0.5 mM [U-13C; U-15N] LEDGF/p75 IBD-JPO2 M1, 50 mM TRIS, 150 mM sodium chloride, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
1	LEDGF/p75 IBD-JPO2 M1	[U-13C; U-15N]	0.5 mM
2	TRIS	natural abundance	50 mM
3	sodium chloride	natural abundance	150 mM

2 2D 1H-13C HMQC

Instrument

Bruker AvanceIII - 850 MHz

Sample

#	Name	Isotope labeling	Concentration
1	LEDGF/p75 IBD-JPO2 M1	[U-13C; U-15N]	0.5 mM
2	TRIS	natural abundance	50 mM
3	sodium chloride	natural abundance	150 mM

3 3D HNCACB

Instrument

Bruker AvanceIII - 850 MHz

Sample

#	Name	Isotope labeling	Concentration
1	LEDGF/p75 IBD-JPO2 M1	[U-13C; U-15N]	0.5 mM
2	TRIS	natural abundance	50 mM
3	sodium chloride	natural abundance	150 mM

4 3D CBCA(CO)NH

Instrument

Bruker AvanceIII - 850 MHz

Sample

#	Name	Isotope labeling	Concentration
1	LEDGF/p75 IBD-JPO2 M1	[U-13C; U-15N]	0.5 mM
2	TRIS	natural abundance	50 mM
3	sodium chloride	natural abundance	150 mM

5 3D HNCO

Instrument

Bruker AvanceIII - 850 MHz

Sample

#	Name	Isotope labeling	Concentration
1	LEDGF/p75 IBD-JPO2 M1	[U-13C; U-15N]	0.5 mM
2	TRIS	natural abundance	50 mM
3	sodium chloride	natural abundance	150 mM

6 3D HN(CA)CO

Instrument

Bruker AvanceIII - 850 MHz

Sample

#	Name	Isotope labeling	Concentration
1	LEDGF/p75 IBD-JPO2 M1	[U-13C; U-15N]	0.5 mM
2	TRIS	natural abundance	50 mM
3	sodium chloride	natural abundance	150 mM

7 3D HBHA(CO)NH

Instrument

Bruker AvanceIII - 850 MHz

Sample

#	Name	Isotope labeling	Concentration
1	LEDGF/p75 IBD-JPO2 M1	[U-13C; U-15N]	0.5 mM
2	TRIS	natural abundance	50 mM
3	sodium chloride	natural abundance	150 mM

8 3D HCCH-TOCSY

Instrument

Bruker AvanceIII - 850 MHz

Sample

#	Name	Isotope labeling	Concentration
1	LEDGF/p75 IBD-JPO2 M1	[U-13C; U-15N]	0.5 mM
2	TRIS	natural abundance	50 mM
3	sodium chloride	natural abundance	150 mM

9 3D C(CO)NH

Instrument

Bruker AvanceIII - 850 MHz

Sample

#	Name	Isotope labeling	Concentration
1	LEDGF/p75 IBD-JPO2 M1	[U-13C; U-15N]	0.5 mM
2	TRIS	natural abundance	50 mM
3	sodium chloride	natural abundance	150 mM

10 3D 1H-15N NOESY

Instrument

Bruker AvanceIII - 850 MHz

Sample

#	Name	Isotope labeling	Concentration
1	LEDGF/p75 IBD-JPO2 M1	[U-13C; U-15N]	0.5 mM
2	TRIS	natural abundance	50 mM
3	sodium chloride	natural abundance	150 mM

11 3D 1H-13C NOESY

Instrument

Bruker AvanceIII - 850 MHz

Sample

#	Name	Isotope labeling	Concentration
1	LEDGF/p75 IBD-JPO2 M1	[U-13C; U-15N]	0.5 mM
2	TRIS	natural abundance	50 mM
3	sodium chloride	natural abundance	150 mM

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_34179_6emo.nef
Input source #2: Coordindates	6emo.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	450	.	Not matched with CCD	None
A	443	.	Not matched with CCD	None
A	446	.	Not matched with CCD	None
A	449	.	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

---------                                                                                           
........S                                                                                           
        |                                                                                           
-.-.-.-.-N-A-W-TSMDSRLQRIHAEIKNSLKIDNLDVNRCIEALDELASLQVTMQQAQKHTEMITTLKKIRRFKVSQVIMEKSTMLYNKFKNMFLVG
 - - - - - - - ---------10--------20--------30--------40--------50--------60--------70--------80----

                                            
                                            
                                            
EGDSVITQVLNKMELATRYQIPKEVADIFNAPSDDEEFVGFRDD
----90-------100-------110-------120-------1

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	136	8	0	100.0

Content subtype: combined_34179_6emo.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	Error	1564		93.8 (chain: A, length: 144)
1	Distance restraints	CNS/XPLOR_distance_constraints_3	Error	4042 (1)	noe	90.3 (chain: A, length: 144)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_2	OK	178 (178)	.	72.2 (chain: A, length: 144)

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: Error
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 144, Sequence coverage: 93.8%
- Total number of assignments
  - ¹H chemical shifts: 829
  - ¹³C chemical shifts: 590
  - ¹⁵N chemical shifts: 145
- Completeness of assignments
- 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

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_3
- Status: Error
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 144, Sequence coverage: 90.3%
- Total number of restraints: 4042
- Weight of restraints: 1.0 (4042)
- Potential type of restraints: square-well-parabolic (4042)
- Range of distance target values: 1.18, 3.31 (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: 144, Sequence coverage: 72.2%
- Total number of restraints: 178
- Total number of restraints per polymer type: 178
- Weight of restraints: 1.0 (178)
- Potential type of restraints: square-well-parabolic (178)
- 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 (0.565 seconds)

BMRB: 34179

Sample

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. PC4 and SFRS1-interacting protein,LEDGF/p75 IBD-JPO2 M1, : 1 : 6 entities Detail

Experiments performed 11 experiments Detail

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NMR combined restraints 4 contents Detail