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BMRB: 19474

2MD5

Structure of uninhibited ETV6 ETS domain

Authors

De, S., McIntosh, L.P., Chan, A.C. K., Coyne, H.J., Okon, M., Graves, B.J., Murphy, M.E. P.

Assembly

uninhibited ETV6 ETS domain

Entity

1. uninhibited ETV6 ETS domain (polymer, Thiol state: not present), 102 monomers, 12427.16 Da Detail

GSHMGRIADS RLLWDYVYQL LSDSRYENFI RWEDKESKIF RIVDPNGLAR LWGNHKNRTN MTYEKMSRAL RHYYKLNIIR KEPGQRLLFR FMKTPDEIMS GR

Formula weight

12427.16 Da

Source organism

Exptl. method

Refine. method

torsion angle dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 98.0 %, Completeness: 85.3 %, Completeness (bb): 81.4 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	85.3 % (1098 of 1287)	92.2 % (630 of 683)	74.3 % (367 of 494)	91.8 % (101 of 110)
Backbone	81.4 % (493 of 606)	92.8 % (192 of 207)	69.7 % (209 of 300)	92.9 % (92 of 99)
Sidechain	90.0 % (699 of 777)	92.0 % (438 of 476)	86.9 % (252 of 290)	81.8 % (9 of 11)
Aromatic	83.1 % (113 of 136)	86.8 % (59 of 68)	78.5 % (51 of 65)	100.0 % (3 of 3)
Methyl	100.0 % (88 of 88)	100.0 % (44 of 44)	100.0 % (44 of 44)

1. u ETV6 ETS

GSHMGRIADS RLLWDYVYQL LSDSRYENFI RWEDKESKIF RIVDPNGLAR LWGNHKNRTN MTYEKMSRAL RHYYKLNIIR KEPGQRLLFR FMKTPDEIMS GR

Show sample condition

Sample

Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	uninhibited ETV6 ETS domain	[U-99% 13C; U-99% 15N]		0.6 mM
2	sodium phosphate	natural abundance		0.02 mM
3	sodium chloride	natural abundance		0.05 mM
4	H2O	natural abundance		93 %
5	D2O	natural abundance		7 %

LACS Plot; CA

Referencing offset: -0.29 ppm, Outliers: 1 Detail

LACS Plot; CB

Referencing offset: -0.29 ppm, Outliers: 1 Detail

LACS Plot; HA

Referencing offset: -0.03 ppm, Outliers: 2 Detail

Protein Blocks Logo

Calculated from 10 models in PDB: 2MD5, Strand ID: A Detail

Release date

2013-09-26

Citation

Steric mechanism of auto-inhibitory regulation of specific and non-specific DNA binding by the ETS transcriptional repressor ETV6
De, S., Chan, A.C.K., Coyne, H., Bhachech, N., Hermsdorf, U., Okon, M., Murphy, M.E.P., Graves, B.J., McIntosh, L.P.
J. Mol. Biol. (2014), 426, 1390-1406, PubMed 24333486 , DOI 10.1016/j.jmb.2013.11.031 , Abstract

Related entities 1. uninhibited ETV6 ETS domain, : 1 : 1 : 126 entities Detail

Interaction partners 1. uninhibited ETV6 ETS domain, : 17 interactors Detail

More details for 17 interactors identified by 10 citations

Experiments performed 10 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	uninhibited ETV6 ETS domain	[U-99% 13C; U-99% 15N]		0.6 mM
2	sodium phosphate	natural abundance		0.02 mM
3	sodium chloride	natural abundance		0.05 mM
4	H2O	natural abundance		93 %
5	D2O	natural abundance		7 %

2 2D 1H-13C HSQC aliphatic

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	uninhibited ETV6 ETS domain	[U-99% 13C; U-99% 15N]		0.6 mM
2	sodium phosphate	natural abundance		0.02 mM
3	sodium chloride	natural abundance		0.05 mM
4	H2O	natural abundance		93 %
5	D2O	natural abundance		7 %

3 2D 1H-13C HSQC aromatic

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	uninhibited ETV6 ETS domain	[U-99% 13C; U-99% 15N]		0.6 mM
2	sodium phosphate	natural abundance		0.02 mM
3	sodium chloride	natural abundance		0.05 mM
4	H2O	natural abundance		93 %
5	D2O	natural abundance		7 %

4 3D H(CCO)NH

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	uninhibited ETV6 ETS domain	[U-99% 13C; U-99% 15N]		0.6 mM
2	sodium phosphate	natural abundance		0.02 mM
3	sodium chloride	natural abundance		0.05 mM
4	H2O	natural abundance		93 %
5	D2O	natural abundance		7 %

5 3D (H)CC(CO)NH

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	uninhibited ETV6 ETS domain	[U-99% 13C; U-99% 15N]		0.6 mM
2	sodium phosphate	natural abundance		0.02 mM
3	sodium chloride	natural abundance		0.05 mM
4	H2O	natural abundance		93 %
5	D2O	natural abundance		7 %

6 3D HCCH-TOCSY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	uninhibited ETV6 ETS domain	[U-99% 13C; U-99% 15N]		0.6 mM
2	sodium phosphate	natural abundance		0.02 mM
3	sodium chloride	natural abundance		0.05 mM
4	H2O	natural abundance		93 %
5	D2O	natural abundance		7 %

7 3D HNCACB

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	uninhibited ETV6 ETS domain	[U-99% 13C; U-99% 15N]		0.6 mM
2	sodium phosphate	natural abundance		0.02 mM
3	sodium chloride	natural abundance		0.05 mM
4	H2O	natural abundance		93 %
5	D2O	natural abundance		7 %

8 3D 1H-15N NOESY

Instrument

Bruker Avance - 850 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	uninhibited ETV6 ETS domain	[U-99% 13C; U-99% 15N]		0.6 mM
2	sodium phosphate	natural abundance		0.02 mM
3	sodium chloride	natural abundance		0.05 mM
4	H2O	natural abundance		93 %
5	D2O	natural abundance		7 %

9 2D 1H-13C HSQC aliphatic

Instrument

Bruker Avance - 850 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	uninhibited ETV6 ETS domain	[U-99% 13C; U-99% 15N]		0.6 mM
2	sodium phosphate	natural abundance		0.02 mM
3	sodium chloride	natural abundance		0.05 mM
4	H2O	natural abundance		93 %
5	D2O	natural abundance		7 %

10 2D 1H-13C HSQC aromatic

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	uninhibited ETV6 ETS domain	[U-99% 13C; U-99% 15N]		0.6 mM
2	sodium phosphate	natural abundance		0.02 mM
3	sodium chloride	natural abundance		0.05 mM
4	H2O	natural abundance		93 %
5	D2O	natural abundance		7 %

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_19474_2md5.nef
Input source #2: Coordindates	2md5.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

---330-------340-------350-------360-------370-------380-------390-------400-------410-------420----
GSHMGRIADSRLLWDYVYQLLSDSRYENFIRWEDKESKIFRIVDPNGLARLWGNHKNRTNMTYEKMSRALRHYYKLNIIRKEPGQRLLFRFMKTPDEIMS
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GSHMGRIADSRLLWDYVYQLLSDSRYENFIRWEDKESKIFRIVDPNGLARLWGNHKNRTNMTYEKMSRALRHYYKLNIIRKEPGQRLLFRFMKTPDEIMS
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100

--
GR
||
GR
--

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	102	0	0	100.0

Content subtype: combined_19474_2md5.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1082		98.0 (chain: A, length: 102)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	OK	2441 (1)	noe	97.1 (chain: A, length: 102)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_3	OK	173 (173)	.	89.2 (chain: A, length: 102)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 102, Sequence coverage: 98.0%
- Total number of assignments
  - ¹H chemical shifts: 632
  - ¹³C chemical shifts: 349
  - ¹⁵N chemical shifts: 101
- Completeness of assignments
  - Entity_assemble_ID: A
- 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

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 102, Sequence coverage: 97.1%
- Total number of restraints: 2441
- Weight of restraints: 1.0 (2441)
- Potential type of restraints: upper-bound-parabolic (2441)
- Range of distance target values: 2.6, 5.5 (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: DYANA/DIANA_dihedral_3
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 102, Sequence coverage: 89.2%
- Total number of restraints: 173
- Total number of restraints per polymer type: 173
- Weight of restraints: 1.0 (173)
- Potential type of restraints: square-well-parabolic (173)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords Auto-inhibition, Protein, Transcription