BMRBj - BMREntryMaster

Found 1 Document (1.591 seconds)

BMRB: 34185

6ER0

6th KOW domain of human hSpt5

Authors

Hahn, L., Schweimer, K., Roesch, P., Woehrl, B.M.

Assembly

Transcription elongation factor SPT5

Entity

1. Transcription elongation factor SPT5 (polymer), 127 monomers, 13842.49 Da Detail

GGYNPHTPGS GIEQNSSDWV TTDIQVKVRD TYLDTQVVGQ TGVIRSVTGG MCSVYLKDSE KVVSISSEHL EPITPTKNNK VKVILGEDRE ATGVLLSIDG EDGIVRMDLD EQLKILNLRF LGKLLEA

Formula weight

13842.49 Da

Source organism

Homo sapiens

Exptl. method

solution NMR

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 92.0 %, Completeness (bb): 97.2 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	92.0 % (1316 of 1431)	90.4 % (668 of 739)	93.4 % (521 of 558)	94.8 % (127 of 134)
Backbone	97.2 % (733 of 754)	97.3 % (256 of 263)	96.2 % (354 of 368)	100.0 % (123 of 123)
Sidechain	88.1 % (697 of 791)	86.6 % (412 of 476)	92.4 % (281 of 304)	36.4 % (4 of 11)
Aromatic	75.9 % (41 of 54)	100.0 % (27 of 27)	50.0 % (13 of 26)	100.0 % (1 of 1)
Methyl	94.6 % (159 of 168)	90.5 % (76 of 84)	98.8 % (83 of 84)

1. entity 1

GGYNPHTPGS GIEQNSSDWV TTDIQVKVRD TYLDTQVVGQ TGVIRSVTGG MCSVYLKDSE KVVSISSEHL EPITPTKNNK VKVILGEDRE ATGVLLSIDG EDGIVRMDLD EQLKILNLRF LGKLLEA

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.4, Details 0.44 mM [U-99% 13C; U-99% 15N] KOW6, 20 mM sodium phosphate, 20 mM sodium chloride, 0.5 mM DTT, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	KOW6	[U-99% 13C; U-99% 15N]	0.44 mM
2	sodium phosphate	natural abundance	20 mM
3	sodium chloride	natural abundance	20 mM
4	DTT	natural abundance	0.5 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: -0.12 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: -0.12 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: -0.08 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: 0.41 ppm, Outliers: 1 Detail

Release date

2018-10-22

Citation

Structure and nucleic acid binding properties of KOW domains 4 and 6-7 of human transcription elongation factor DSIF
Zuber, P.K., Hahn, L., Reinl, A., Schweimer, K., Knauer, S.H., Gottesman, M.E., Rosch, P., Wohrl, B.M.
Sci. Rep. (2018), 8, 11660-11660, PubMed 30076330 , DOI 10.1038/s41598-018-30042-3 , Abstract

Related entities 1. Transcription elongation factor SPT5, : 1 : 5 : 2 : 20 entities Detail

Interaction partners 1. Transcription elongation factor SPT5, : 55 interactors Detail

More details for 55 interactors identified by 20 citations

Experiments performed 13 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker AvanceIII - na MHz cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.4, Details 0.44 mM [U-99% 13C; U-99% 15N] KOW6, 20 mM sodium phosphate, 20 mM sodium chloride, 0.5 mM DTT, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	KOW6	[U-99% 13C; U-99% 15N]	0.44 mM
2	sodium phosphate	natural abundance	20 mM
3	sodium chloride	natural abundance	20 mM
4	DTT	natural abundance	0.5 mM

2 2D 1H-13C HSQC aliphatic

Instrument

Bruker AvanceIII - na MHz cryoprobe

Sample

#	Name	Isotope labeling	Concentration
1	KOW6	[U-99% 13C; U-99% 15N]	0.44 mM
2	sodium phosphate	natural abundance	20 mM
3	sodium chloride	natural abundance	20 mM
4	DTT	natural abundance	0.5 mM

3 2D 1H-13C HSQC aromatic

Instrument

Bruker AvanceIII - 700 MHz cryoprobe

Sample

#	Name	Isotope labeling	Concentration
1	KOW6	[U-99% 13C; U-99% 15N]	0.44 mM
2	sodium phosphate	natural abundance	20 mM
3	sodium chloride	natural abundance	20 mM
4	DTT	natural abundance	0.5 mM

4 3D HNCO

Instrument

Bruker AvanceIII - 700 MHz cryoprobe

Sample

#	Name	Isotope labeling	Concentration
1	KOW6	[U-99% 13C; U-99% 15N]	0.44 mM
2	sodium phosphate	natural abundance	20 mM
3	sodium chloride	natural abundance	20 mM
4	DTT	natural abundance	0.5 mM

5 3D HNCA

Instrument

Bruker AvanceIII - 700 MHz cryoprobe

Sample

#	Name	Isotope labeling	Concentration
1	KOW6	[U-99% 13C; U-99% 15N]	0.44 mM
2	sodium phosphate	natural abundance	20 mM
3	sodium chloride	natural abundance	20 mM
4	DTT	natural abundance	0.5 mM

6 3D 1H-13C NOESY aromatic

Instrument

Bruker AvanceIII - na MHz cryoprobe

Sample

#	Name	Isotope labeling	Concentration
1	KOW6	[U-99% 13C; U-99% 15N]	0.44 mM
2	sodium phosphate	natural abundance	20 mM
3	sodium chloride	natural abundance	20 mM
4	DTT	natural abundance	0.5 mM

7 3D 1H-13C NOESY aliphatic

Instrument

Bruker AvanceIII - na MHz cryoprobe

Sample

#	Name	Isotope labeling	Concentration
1	KOW6	[U-99% 13C; U-99% 15N]	0.44 mM
2	sodium phosphate	natural abundance	20 mM
3	sodium chloride	natural abundance	20 mM
4	DTT	natural abundance	0.5 mM

8 3D 1H-15N NOESY

Instrument

Bruker AvanceIII - na MHz cryoprobe

Sample

#	Name	Isotope labeling	Concentration
1	KOW6	[U-99% 13C; U-99% 15N]	0.44 mM
2	sodium phosphate	natural abundance	20 mM
3	sodium chloride	natural abundance	20 mM
4	DTT	natural abundance	0.5 mM

9 3D CCH-TOCSY

Instrument

Bruker AvanceIII - 700 MHz cryoprobe

Sample

#	Name	Isotope labeling	Concentration
1	KOW6	[U-99% 13C; U-99% 15N]	0.44 mM
2	sodium phosphate	natural abundance	20 mM
3	sodium chloride	natural abundance	20 mM
4	DTT	natural abundance	0.5 mM

10 3D HCCH-TOCSY

Instrument

Bruker AvanceIII - 700 MHz cryoprobe

Sample

#	Name	Isotope labeling	Concentration
1	KOW6	[U-99% 13C; U-99% 15N]	0.44 mM
2	sodium phosphate	natural abundance	20 mM
3	sodium chloride	natural abundance	20 mM
4	DTT	natural abundance	0.5 mM

11 3D C(CO)NH

Instrument

Bruker AvanceIII - 700 MHz cryoprobe

Sample

#	Name	Isotope labeling	Concentration
1	KOW6	[U-99% 13C; U-99% 15N]	0.44 mM
2	sodium phosphate	natural abundance	20 mM
3	sodium chloride	natural abundance	20 mM
4	DTT	natural abundance	0.5 mM

12 3D CBCA(CO)NH

Instrument

Bruker AvanceIII - 700 MHz cryoprobe

Sample

#	Name	Isotope labeling	Concentration
1	KOW6	[U-99% 13C; U-99% 15N]	0.44 mM
2	sodium phosphate	natural abundance	20 mM
3	sodium chloride	natural abundance	20 mM
4	DTT	natural abundance	0.5 mM

13 3D HNCACB

Instrument

Bruker AvanceIII - 700 MHz cryoprobe

Sample

#	Name	Isotope labeling	Concentration
1	KOW6	[U-99% 13C; U-99% 15N]	0.44 mM
2	sodium phosphate	natural abundance	20 mM
3	sodium chloride	natural abundance	20 mM
4	DTT	natural abundance	0.5 mM

NMR combined restraints 6 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints, RDC restraints	combined_34185_6er0.nef
Input source #2: Coordindates	6er0.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

--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100
GGYNPHTPGSGIEQNSSDWVTTDIQVKVRDTYLDTQVVGQTGVIRSVTGGMCSVYLKDSEKVVSISSEHLEPITPTKNNKVKVILGEDREATGVLLSIDG
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GGYNPHTPGSGIEQNSSDWVTTDIQVKVRDTYLDTQVVGQTGVIRSVTGGMCSVYLKDSEKVVSISSEHLEPITPTKNNKVKVILGEDREATGVLLSIDG

-------110-------120-------
EDGIVRMDLDEQLKILNLRFLGKLLEA
|||||||||||||||||||||||||||
EDGIVRMDLDEQLKILNLRFLGKLLEA

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	127	0	0	100.0

Content subtype: combined_34185_6er0.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	1301		100.0 (chain: A, length: 127)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	Warning	635 (1)	noe	85.0 (chain: A, length: 127)
2	Distance restraints	CNS/XPLOR_distance_constraints_3	OK	96 (1)	hbond	49.6 (chain: A, length: 127)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_4	OK	124 (124)	.	76.4 (chain: A, length: 127)
1	RDC restraints	CNS/XPLOR_dipolar_coupling_5	OK	80 (80)	.	63.0 (chain: A, length: 127)

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 127, Sequence coverage: 100.0%
- Total number of assignments
  - ¹³C chemical shifts: 516
  - ¹H chemical shifts: 661
  - ¹⁵N chemical shifts: 124
- Completeness of assignments
  - Entity_assemble_ID: A
- 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

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	558	516	92.5
¹H chemical shifts	739	661	89.4
¹⁵N chemical shifts	139	124	89.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	254	238	93.7
¹H chemical shifts	263	256	97.3
¹⁵N chemical shifts	123	121	98.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	304	278	91.4
¹H chemical shifts	476	405	85.1
¹⁵N chemical shifts	16	3	18.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	86	85	98.8
¹H chemical shifts	86	78	90.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	26	13	50.0
¹H chemical shifts	27	27	100.0
¹⁵N chemical shifts	1	1	100.0

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 127, Sequence coverage: 85.0%
- Total number of restraints: 634
- Weight of restraints: 1.0 (634)
- Potential type of restraints: square-well-parabolic (634)
- Range of distance target values: 1.35, 3.0 (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
- Saveframe: CNS/XPLOR_distance_constraints_3
  - Status: OK
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 127, Sequence coverage: 49.6%
  - Total number of restraints: 96
  - Weight of restraints: 1.0 (96)
  - Potential type of restraints: square-well-parabolic (96)
  - Range of distance target values: 1.15, 1.65 (Å)
  - Histogram of distance target values
  - Distance restraints per residue
    - Chain_ID: A
  - Distance restraints on contact map

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_4
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 127, Sequence coverage: 76.4%
- Total number of restraints: 124
- Total number of restraints per polymer type: 124
- Weight of restraints: 1.0 (124)
- Potential type of restraints: square-well-parabolic (124)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

RDC restraints

Saveframe: CNS/XPLOR_dipolar_coupling_5

Status: OK
Experiment type: .

Sequence coverage of experimental data

Entity_assembly_ID: A, Chain length: 127, Sequence coverage: 63.0%

--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100
GGYNPHTPGSGIEQNSSDWVTTDIQVKVRDTYLDTQVVGQTGVIRSVTGGMCSVYLKDSEKVVSISSEHLEPITPTKNNKVKVILGEDREATGVLLSIDG
                 ||||||| |||||||  ||| | || || |     ||||||||||||||  ||| || || |||||||| ||  || ||||||
.................DWVTTDI.VKVRDTY..TQV.G.TG.IR.V.....SVYLKDSEKVVSIS..HLE.IT.TK.NKVKVILG.DR..TG.LLSIDG
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100

-------110-------120-------
EDGIVRMDLDEQLKILNLRFLGKLLEA
|   |||| ||||| |||||| ||   
E...VRMD.DEQLK.LNLRFL.KL   
-------110-------120----

Total number of restraints: 80
Potential type of restraints: undefined (80)
Range of observed RDC values: 100.0, -100.0 (Hz)
RDC restraints per residue
- Chain_ID: A
  None

Keywords DSIF. transcription elongation, TRANSCRIPTION, hSpt5

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Found 1 Document (1.591 seconds)

BMRB: 34185

Sample

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. Transcription elongation factor SPT5, : 1 : 5 : 2 : 20 entities Detail

Interaction partners 1. Transcription elongation factor SPT5, : 55 interactors Detail

Experiments performed 13 experiments Detail

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NMR combined restraints 6 contents Detail