BMRBj - BMREntryMaster

Found 1 Document (5.381 seconds)

BMRB: 34475

6TVM

LEDGF/p75 dimer (residues 345-467)

Authors

Lux, V., Veverka, V.

Assembly

PC4 and SFRS1-interacting protein

Entity

1. PC4 and SFRS1-interacting protein (polymer), 128 monomers, 14619.64 × 2 Da Detail

SNAASETSMD SRLQRIHAEI KNSLKIDNLD VNRCIEALDE LASLQVTMQQ AQKHTEMITT LKKIRRFKVS QVIMEKSTML YNKFKNMFLV GEGDSVITQV LNKSLAEQRQ HEEANKTKDQ GKKGPNKK

Total weight

29239.28 Da

Max. entity weight

14619.64 Da

Source organism

Homo sapiens

Exptl. method

solution NMR

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 98.4 %, Completeness: 91.3 %, Completeness (bb): 97.0 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	91.3 % (1409 of 1544)	90.0 % (733 of 814)	94.5 % (546 of 578)	85.5 % (130 of 152)
Backbone	97.0 % (743 of 766)	96.9 % (251 of 259)	97.4 % (370 of 380)	96.1 % (122 of 127)
Sidechain	86.7 % (782 of 902)	86.1 % (478 of 555)	91.9 % (296 of 322)	32.0 % (8 of 25)
Aromatic	60.0 % (30 of 50)	80.0 % (20 of 25)	40.0 % (10 of 25)
Methyl	99.3 % (135 of 136)	100.0 % (68 of 68)	98.5 % (67 of 68)

1. entity 1

SNAASETSMD SRLQRIHAEI KNSLKIDNLD VNRCIEALDE LASLQVTMQQ AQKHTEMITT LKKIRRFKVS QVIMEKSTML YNKFKNMFLV GEGDSVITQV LNKSLAEQRQ HEEANKTKDQ GKKGPNKK

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, 20 mM HEPES, 100 mM sodium chloride, 1 mM TCEP, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
1	LEDGF	[U-13C; U-15N]	0.5 mM
2	HEPES	natural abundance	20 mM
3	sodium chloride	natural abundance	100 mM
4	TCEP	natural abundance	1 mM

Release date

2020-07-13

Citation

Molecular Mechanism of LEDGF/p75 Dimerization
Lux, V., Brouns, T., Cermakova, K., Srb, P., Fabry, M., Madlikova, M., Horejsi, M., Kukacka, Z., Novak, P., Kugler, M., Brynda, J., DeRijck, J., Christ, F., Debyser, Z., Veverka, V.
Structure (2020), 28, 1288-1299, PubMed 32946742 , DOI 10.1016/j.str.2020.08.012 , Abstract

Related entities 1. PC4 and SFRS1-interacting protein, : 1 : 17 : 16 entities Detail

Interaction partners 1. PC4 and SFRS1-interacting protein, : 13 interactors Detail

More details for 13 interactors identified by 3 citations

Experiments performed 8 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker AVANCE - 850 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7, Details 0.5 mM [U-13C; U-15N] LEDGF, 20 mM HEPES, 100 mM sodium chloride, 1 mM TCEP, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
1	LEDGF	[U-13C; U-15N]	0.5 mM
2	HEPES	natural abundance	20 mM
3	sodium chloride	natural abundance	100 mM
4	TCEP	natural abundance	1 mM

2 2D 1H-13C HSQC

Instrument

Bruker AVANCE - 850 MHz

Sample

#	Name	Isotope labeling	Concentration
1	LEDGF	[U-13C; U-15N]	0.5 mM
2	HEPES	natural abundance	20 mM
3	sodium chloride	natural abundance	100 mM
4	TCEP	natural abundance	1 mM

3 3D HNCACB

Instrument

Bruker AVANCE - 850 MHz

Sample

#	Name	Isotope labeling	Concentration
1	LEDGF	[U-13C; U-15N]	0.5 mM
2	HEPES	natural abundance	20 mM
3	sodium chloride	natural abundance	100 mM
4	TCEP	natural abundance	1 mM

4 3D CBCA(CO)NH

Instrument

Bruker AVANCE - 850 MHz

Sample

#	Name	Isotope labeling	Concentration
1	LEDGF	[U-13C; U-15N]	0.5 mM
2	HEPES	natural abundance	20 mM
3	sodium chloride	natural abundance	100 mM
4	TCEP	natural abundance	1 mM

5 3D HNCO

Instrument

Bruker AVANCE - 850 MHz

Sample

#	Name	Isotope labeling	Concentration
1	LEDGF	[U-13C; U-15N]	0.5 mM
2	HEPES	natural abundance	20 mM
3	sodium chloride	natural abundance	100 mM
4	TCEP	natural abundance	1 mM

6 3D HCCH-TOCSY

Instrument

Bruker AVANCE - 850 MHz

Sample

#	Name	Isotope labeling	Concentration
1	LEDGF	[U-13C; U-15N]	0.5 mM
2	HEPES	natural abundance	20 mM
3	sodium chloride	natural abundance	100 mM
4	TCEP	natural abundance	1 mM

7 3D 1H-15N NOESY

Instrument

Bruker AVANCE - 850 MHz

Sample

#	Name	Isotope labeling	Concentration
1	LEDGF	[U-13C; U-15N]	0.5 mM
2	HEPES	natural abundance	20 mM
3	sodium chloride	natural abundance	100 mM
4	TCEP	natural abundance	1 mM

8 3D 1H-13C NOESY

Instrument

Bruker AVANCE - 850 MHz

Sample

#	Name	Isotope labeling	Concentration
1	LEDGF	[U-13C; U-15N]	0.5 mM
2	HEPES	natural abundance	20 mM
3	sodium chloride	natural abundance	100 mM
4	TCEP	natural abundance	1 mM

Chemical shift validation 3 contents Detail

Properties

Input source #1: Assigned chemical shifts - Assigned chemical shifts	bmr34475_3.str
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

Content subtype: bmr34475_3.str

#	Content subtype	Saveframe	Status	# of rows	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	1561		98.4 (chain: 1, length: 128)
1	Chemical shift references	chem_shift_reference_1	OK	3		No information

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: 1, Chain length: 128, Sequence coverage: 98.4%
- Total number of assignments
  - ¹H chemical shifts: 882
  - ¹³C chemical shifts: 549
  - ¹⁵N chemical shifts: 130
- Completeness of assignments
  - Entity_assemble_ID: 1
- 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: 1

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
47	THR	HG1	5.57
78	THR	HG1	5.617

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	814	732	89.9
¹³C chemical shifts	578	549	95.0
¹⁵N chemical shifts	152	130	85.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	259	252	97.3
¹³C chemical shifts	256	252	98.4
¹⁵N chemical shifts	127	122	96.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	555	480	86.5
¹³C chemical shifts	322	297	92.2
¹⁵N chemical shifts	25	8	32.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	74	74	100.0
¹³C chemical shifts	74	73	98.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	25	20	80.0
¹³C chemical shifts	25	10	40.0

Keywords TRANSCRIPTION, domain-swapped dimer, epigenetic reader, integrase-binding domain

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Found 1 Document (5.381 seconds)

BMRB: 34475

Sample

Related entities 1. PC4 and SFRS1-interacting protein, : 1 : 17 : 16 entities Detail

Interaction partners 1. PC4 and SFRS1-interacting protein, : 13 interactors Detail

Experiments performed 8 experiments Detail

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Chemical shift validation 3 contents Detail