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Found 1 Document (0.426 seconds)

BMRB: 34180

6EMP

Solution structure of the LEDGF/p75 IBD - POGZ (aa 1370-1404) complex

Authors

Veverka, V.

Assembly

PC4 and SFRS1-interacting protein,Pogo transposable element with ZNF domain

Entity

1. PC4 and SFRS1-interacting protein,Pogo transposable element with ZNF domain (polymer, Thiol state: all free), 139 monomers, 16015.92 Da Detail

SNAASWETSM DSRLQRIHAE IKNSLKIDNL DVNRCIEALD ELASLQVTMQ QAQKHTEMIT TLKKIRRFKV SQVIMEKSTM LYNKFKNMFL VGEGDSVITQ VLNKRPRSSP EETIEPESLH QLFEGESETE SFYGFEEAD

Formula weight

16015.92 Da

Source organism

Homo sapiens

Exptl. method

solution NMR

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 97.8 %, Completeness: 92.8 %, Completeness (bb): 95.4 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	92.8 % (1535 of 1654)	93.3 % (809 of 867)	92.6 % (588 of 635)	90.8 % (138 of 152)
Backbone	95.4 % (790 of 828)	95.3 % (266 of 279)	95.6 % (395 of 413)	94.9 % (129 of 136)
Sidechain	91.2 % (876 of 961)	92.3 % (543 of 588)	90.8 % (324 of 357)	56.3 % (9 of 16)
Aromatic	82.0 % (82 of 100)	100.0 % (50 of 50)	63.3 % (31 of 49)	100.0 % (1 of 1)
Methyl	97.9 % (141 of 144)	100.0 % (72 of 72)	95.8 % (69 of 72)

1. entity 1

SNAASWETSM DSRLQRIHAE IKNSLKIDNL DVNRCIEALD ELASLQVTMQ QAQKHTEMIT TLKKIRRFKV SQVIMEKSTM LYNKFKNMFL VGEGDSVITQ VLNKRPRSSP EETIEPESLH QLFEGESETE SFYGFEEAD

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-POGZ, 50 mM TRIS, 150 mM sodium chloride, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
1	LEDGF/p75 IBD-POGZ	[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: -0.23 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: -0.23 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: 1 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: 0.09 ppm, Outliers: 2 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,Pogo transposable element with ZNF domain, : 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_34180_6emp.nef
Input source #2: Coordindates	6emp.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

-340-----350-------360-------370-------380-------390-------400-------410-------420-------430-------4
SNAASWETSMDSRLQRIHAEIKNSLKIDNLDVNRCIEALDELASLQVTMQQAQKHTEMITTLKKIRRFKVSQVIMEKSTMLYNKFKNMFLVGEGDSVITQ
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
SNAASWETSMDSRLQRIHAEIKNSLKIDNLDVNRCIEALDELASLQVTMQQAQKHTEMITTLKKIRRFKVSQVIMEKSTMLYNKFKNMFLVGEGDSVITQ
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100

41370------1380------1390------1400----
VLNKRPRSSPEETIEPESLHQLFEGESETESFYGFEEAD
|||||||||||||||||||||||||||||||||||||||
VLNKRPRSSPEETIEPESLHQLFEGESETESFYGFEEAD
-------110-------120-------130---------

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	139	0	0	100.0

Content subtype: combined_34180_6emp.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	1517		97.8 (chain: A, length: 139)
1	Distance restraints	CNS/XPLOR_distance_constraints_3	Warning	3636 (1)	noe	89.2 (chain: A, length: 139)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_2	OK	182 (182)	.	74.1 (chain: A, length: 139)

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 139, Sequence coverage: 97.8%
- Total number of assignments
  - ¹³C chemical shifts: 584
  - ¹H chemical shifts: 800
  - ¹⁵N chemical shifts: 133
- Completeness of assignments
  - Entity_assemble_ID: A
- 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

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
373	CYS	HG	1.436
386	THR	HG1	5.545
416	SER	HG	4.239
417	THR	HG1	5.646

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	635	584	92.0
¹H chemical shifts	867	796	91.8
¹⁵N chemical shifts	159	133	83.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	278	263	94.6
¹H chemical shifts	279	260	93.2
¹⁵N chemical shifts	136	125	91.9

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	357	321	89.9
¹H chemical shifts	588	536	91.2
¹⁵N chemical shifts	23	8	34.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	78	74	94.9
¹H chemical shifts	78	78	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	49	30	61.2
¹H chemical shifts	50	50	100.0
¹⁵N chemical shifts	1	1	100.0

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_3
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 139, Sequence coverage: 89.2%
- Total number of restraints: 3636
- Weight of restraints: 1.0 (3636)
- Potential type of restraints: square-well-parabolic (3636)
- Range of distance target values: 1.26, 2.75 (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: 139, Sequence coverage: 74.1%
- Total number of restraints: 182
- Total number of restraints per polymer type: 182
- Weight of restraints: 1.0 (182)
- Potential type of restraints: square-well-parabolic (182)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords TRANSCRIPTION, epigenetics, leukemia, protein-protein complex

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Found 1 Document (0.426 seconds)

BMRB: 34180

Sample

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. PC4 and SFRS1-interacting protein,Pogo transposable element with ZNF domain, : 1 : 2 entities Detail

Experiments performed 3 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 4 contents Detail