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BMRB: 19488

2MDJ

Solution structure of WW domain with polyproline stretch (PP2WW) of HYPB

Authors

Gao, Y., Hu, H.

Assembly

WW domain with polyproline stretch (PP2WW) of HYPB

Entity

1. WW domain with polyproline stretch (PP2WW) of HYPB (polymer, Thiol state: not present), 56 monomers, 6328.956 Da Detail

GSDLPPPSPP KPKTIVLPPN WKTARDPEGK IYYYHVITRQ TQWDPPTWES PGDDAS

Formula weight

6328.956 Da

Source organism

Exptl. method

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 83.9 %, Completeness: 62.8 %, Completeness (bb): 80.1 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	62.8 % (417 of 664)	61.1 % (215 of 352)	59.5 % (156 of 262)	92.0 % (46 of 50)
Backbone	80.1 % (250 of 312)	79.6 % (82 of 103)	77.6 % (128 of 165)	90.9 % (40 of 44)
Sidechain	51.6 % (209 of 405)	53.4 % (133 of 249)	46.7 % (70 of 150)	100.0 % (6 of 6)
Aromatic	12.5 % (8 of 64)	15.6 % (5 of 32)	0.0 % (0 of 29)	100.0 % (3 of 3)
Methyl	73.8 % (31 of 42)	85.7 % (18 of 21)	61.9 % (13 of 21)

1. entity

GSDLPPPSPP KPKTIVLPPN WKTARDPEGK IYYYHVITRQ TQWDPPTWES PGDDAS

Show sample condition

Sample

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	PP2WW	[U-99% 13C; U-99% 15N]		500 uM
2	sodium phosphate	natural abundance		20 mM
3	sodium chloride	natural abundance		50 mM
4	sodium azide	natural abundance		0.05 % w/v

LACS Plot; CA

Referencing offset: 0.01 ppm, Outliers: 2 Detail

LACS Plot; CB

Referencing offset: 0.01 ppm, Outliers: 2 Detail

LACS Plot; HA

Referencing offset: 0.13 ppm, Outliers: 1 Detail

LACS Plot; CO

Referencing offset: 0.44 ppm, Outliers: 2 Detail

Protein Blocks Logo

Calculated from 15 models in PDB: 2MDJ, Strand ID: A Detail

Release date

2014-03-20

Citation

Autoinhibitory structure of the WW domain of HYPB/SETD2 regulates its interaction with the proline-rich region of huntingtin
Gao, Y., Yang, H., Zhao, J., Jiang, Y., Hu, H.
Structure (2014), 22, 378-386, PubMed 24412394 , DOI 10.1016/j.str.2013.12.005 , Abstract

Related entities 1. WW domain with polyproline stretch (PP2WW) of HYPB, : 1 : 7 : 30 entities Detail

Interaction partners 1. WW domain with polyproline stretch (PP2WW) of HYPB, : 1 interactors Detail

More details for 1 interactors identified by 1 citations

Experiments performed 9 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	PP2WW	[U-99% 13C; U-99% 15N]		500 uM
2	sodium phosphate	natural abundance		20 mM
3	sodium chloride	natural abundance		50 mM
4	sodium azide	natural abundance		0.05 % w/v

2 3D CBCA(CO)NH

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	PP2WW	[U-99% 13C; U-99% 15N]		500 uM
2	sodium phosphate	natural abundance		20 mM
3	sodium chloride	natural abundance		50 mM
4	sodium azide	natural abundance		0.05 % w/v

3 3D HNCACB

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	PP2WW	[U-99% 13C; U-99% 15N]		500 uM
2	sodium phosphate	natural abundance		20 mM
3	sodium chloride	natural abundance		50 mM
4	sodium azide	natural abundance		0.05 % w/v

4 3D HNCO

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	PP2WW	[U-99% 13C; U-99% 15N]		500 uM
2	sodium phosphate	natural abundance		20 mM
3	sodium chloride	natural abundance		50 mM
4	sodium azide	natural abundance		0.05 % w/v

5 3D HNHA

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	PP2WW	[U-99% 13C; U-99% 15N]		500 uM
2	sodium phosphate	natural abundance		20 mM
3	sodium chloride	natural abundance		50 mM
4	sodium azide	natural abundance		0.05 % w/v

6 3D C(CO)NH

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	PP2WW	[U-99% 13C; U-99% 15N]		500 uM
2	sodium phosphate	natural abundance		20 mM
3	sodium chloride	natural abundance		50 mM
4	sodium azide	natural abundance		0.05 % w/v

7 3D HCCH-COSY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	PP2WW	[U-99% 13C; U-99% 15N]		500 uM
2	sodium phosphate	natural abundance		20 mM
3	sodium chloride	natural abundance		50 mM
4	sodium azide	natural abundance		0.05 % w/v

8 3D 1H-15N NOESY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	PP2WW	[U-99% 13C; U-99% 15N]		500 uM
2	sodium phosphate	natural abundance		20 mM
3	sodium chloride	natural abundance		50 mM
4	sodium azide	natural abundance		0.05 % w/v

9 3D 1H-13C NOESY aliphatic

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	PP2WW	[U-99% 13C; U-99% 15N]		500 uM
2	sodium phosphate	natural abundance		20 mM
3	sodium chloride	natural abundance		50 mM
4	sodium azide	natural abundance		0.05 % w/v

NMR combined restraints 3 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_19488_2mdj.nef
Input source #2: Coordindates	2mdj.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------
GSDLPPPSPPKPKTIVLPPNWKTARDPEGKIYYYHVITRQTQWDPPTWESPGDDAS
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GSDLPPPSPPKPKTIVLPPNWKTARDPEGKIYYYHVITRQTQWDPPTWESPGDDAS

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	56	0	0	100.0

Content subtype: combined_19488_2mdj.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	404		82.1 (chain: A, length: 56)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	Warning	360 (1)	noe	76.8 (chain: A, length: 56)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 56, Sequence coverage: 82.1%
- Total number of assignments
  - ¹H chemical shifts: 208
  - ¹³C chemical shifts: 150
  - ¹⁵N chemical shifts: 46
- Completeness of assignments
  - Entity_assemble_ID: A
- 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_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 56, Sequence coverage: 76.8%
- Total number of restraints: 360
- Weight of restraints: 1.0 (360)
- Potential type of restraints: square-well-parabolic (360)
- Range of distance target values: 1.62, 22.66 (Å)
- Histogram of distance target values
- Distance restraints per residue
  - Chain_ID: A
- Distance restraints on contact map

Keywords HYPB, polyproline, WW domain