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BMRB: 25066

2MR9

NMR structure of UBA domain of DNA-damage-inducible 1 protein (Ddi1)

Authors

Zhang, D., Fushman, D.

Assembly

UBA domain of DNA-damage-inducible 1 protein (Ddi1)

Entity

1. UBA domain of DNA-damage-inducible 1 protein (Ddi1) (polymer, Thiol state: not present), 44 monomers, 4741.333 Da Detail

GSATFPEQTI KQLMDLGFPR DAVVKALKQT NGNAEFAASL LFQS

Formula weight

4741.333 Da

Source organism

Saccharomyces cerevisiae

Exptl. method

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 93.2 %, Completeness: 93.6 %, Completeness (bb): 92.4 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹⁵N
All	93.6 % (291 of 311)	93.5 % (246 of 263)	93.8 % (45 of 48)
Backbone	92.4 % (121 of 131)	92.1 % (82 of 89)	92.9 % (39 of 42)
Sidechain	94.4 % (170 of 180)	94.3 % (164 of 174)	100.0 % (6 of 6)
Aromatic	90.0 % (18 of 20)	90.0 % (18 of 20)
Methyl	96.0 % (24 of 25)	96.0 % (24 of 25)

1. entity

GSATFPEQTI KQLMDLGFPR DAVVKALKQT NGNAEFAASL LFQS

Show sample condition

Sample #1

Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 298.2 K, pH 6.8, Details 1mM Ddi1UBA sample in pH6.8 20mM Sodium Phosphate Buffer, containing 7% D2O.

#	Name	Isotope labeling	Type	Concentration
1	UBA	[U-100% 15N]		1 mM
2	D2O	[U-99% 2H]		7 %
3	H2O	natural abundance		93 %
4	sodium phosphate	natural abundance		20 mM

Sample #2

Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 298.2 K, pH 6.8, Details 0.5mM Ddi1UBA sample in liquid crystalline medium

#	Name	Isotope labeling	Type	Concentration
5	UBA	[U-100% 15N]		0.5 mM
6	D2O	[U-99% 2H]		7 %
7	H2O	natural abundance		43 %
8	sodium phosphate	natural abundance		10 mM
9	C12E5	natural abundance		5 %
10	n-hexanol	natural abundance		45 %

Protein Blocks Logo

Calculated from 10 models in PDB: 2MR9, Strand ID: A Detail

Release date

2015-02-01

Citation

DNA-damage-inducible 1 protein (Ddi1) contains an uncharacteristic ubiquitin-like domain that binds ubiquitin
Nowicka, U., Zhang, D., Walker, O., Castaneda, C.A., Krutauz, D., Chen, T., Reis, N., Glickman, M.H., Fushman, D.
Structure (2015), 23, 542-557, PubMed 25703377 , DOI 10.1016/j.str.2015.01.010 , Abstract

Related entities 1. UBA domain of DNA-damage-inducible 1 protein (Ddi1), : 1 : 1 : 2 : 142 entities Detail

Interaction partners 1. UBA domain of DNA-damage-inducible 1 protein (Ddi1), : 11 interactors Detail

More details for 11 interactors identified by 8 citations

Experiments performed 7 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 298.2 K, pH 6.8, Details 1mM Ddi1UBA sample in pH6.8 20mM Sodium Phosphate Buffer, containing 7% D2O.

#	Name	Isotope labeling	Type	Concentration
1	UBA	[U-100% 15N]		1 mM
2	D2O	[U-99% 2H]		7 %
3	H2O	natural abundance		93 %
4	sodium phosphate	natural abundance		20 mM

2 2D 1H-1H TOCSY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 298.2 K, pH 6.8, Details 1mM Ddi1UBA sample in pH6.8 20mM Sodium Phosphate Buffer, containing 7% D2O.

#	Name	Isotope labeling	Type	Concentration
1	UBA	[U-100% 15N]		1 mM
2	D2O	[U-99% 2H]		7 %
3	H2O	natural abundance		93 %
4	sodium phosphate	natural abundance		20 mM

3 2D 1H-1H NOESY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 298.2 K, pH 6.8, Details 1mM Ddi1UBA sample in pH6.8 20mM Sodium Phosphate Buffer, containing 7% D2O.

#	Name	Isotope labeling	Type	Concentration
1	UBA	[U-100% 15N]		1 mM
2	D2O	[U-99% 2H]		7 %
3	H2O	natural abundance		93 %
4	sodium phosphate	natural abundance		20 mM

4 3D 1H-15N NOESY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 298.2 K, pH 6.8, Details 1mM Ddi1UBA sample in pH6.8 20mM Sodium Phosphate Buffer, containing 7% D2O.

#	Name	Isotope labeling	Type	Concentration
1	UBA	[U-100% 15N]		1 mM
2	D2O	[U-99% 2H]		7 %
3	H2O	natural abundance		93 %
4	sodium phosphate	natural abundance		20 mM

5 3D 1H-15N TOCSY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 298.2 K, pH 6.8, Details 1mM Ddi1UBA sample in pH6.8 20mM Sodium Phosphate Buffer, containing 7% D2O.

#	Name	Isotope labeling	Type	Concentration
1	UBA	[U-100% 15N]		1 mM
2	D2O	[U-99% 2H]		7 %
3	H2O	natural abundance		93 %
4	sodium phosphate	natural abundance		20 mM

6 RDC

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 298.2 K, pH 6.8, Details 0.5mM Ddi1UBA sample in liquid crystalline medium

#	Name	Isotope labeling	Type	Concentration
5	UBA	[U-100% 15N]		0.5 mM
6	D2O	[U-99% 2H]		7 %
7	H2O	natural abundance		43 %
8	sodium phosphate	natural abundance		10 mM
9	C12E5	natural abundance		5 %
10	n-hexanol	natural abundance		45 %

7 RDC

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 308.2 K, pH 6.8, Details 0.5mM Ddi1UBA sample in liquid crystalline medium

#	Name	Isotope labeling	Type	Concentration
5	UBA	[U-100% 15N]		0.5 mM
6	D2O	[U-99% 2H]		7 %
7	H2O	natural abundance		43 %
8	sodium phosphate	natural abundance		10 mM
9	C12E5	natural abundance		5 %
10	n-hexanol	natural abundance		45 %

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints, RDC restraints	combined_25066_2mr9.nef
Input source #2: Coordindates	2mr9.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----
GSATFPEQTIKQLMDLGFPRDAVVKALKQTNGNAEFAASLLFQS
||||||||||||||||||||||||||||||||||||||||||||
GSATFPEQTIKQLMDLGFPRDAVVKALKQTNGNAEFAASLLFQS

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	44	0	0	100.0

Content subtype: combined_25066_2mr9.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	291		93.2 (chain: A, length: 44)
1	Distance restraints	CNS/XPLOR_distance_constraints_3	Warning	8 (1)	hbond	18.2 (chain: A, length: 44)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_2	OK	76 (76)	.	93.2 (chain: A, length: 44)
1	RDC restraints	CNS/XPLOR_dipolar_coupling_4	OK	28 (28)	.	63.6 (chain: A, length: 44)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 44, Sequence coverage: 93.2%
- Total number of assignments
  - ¹H chemical shifts: 246
  - ¹⁵N chemical shifts: 45
- Completeness of assignments
  - Entity_assemble_ID: A
- 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_3
- Status: Warning
- Experiment type: hbond
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 44, Sequence coverage: 18.2%
- Total number of restraints: 8
- Weight of restraints: 1.0 (8)
- Potential type of restraints: square-well-parabolic (8)
- Range of distance target values: 1.7, 2.7 (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_2
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 44, Sequence coverage: 93.2%
- Total number of restraints: 76
- Total number of restraints per polymer type: 76
- Weight of restraints: 1.0 (76)
- Potential type of restraints: square-well-parabolic (76)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

RDC restraints

Saveframe: CNS/XPLOR_dipolar_coupling_4
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 44, Sequence coverage: 63.6%
- Total number of restraints: 28
- Potential type of restraints: undefined (28)
- Range of observed RDC values: 100.0, -100.0 (Hz)
- RDC restraints per residue
  - Chain_ID: A
    None

Keywords DNA-damage-inducible 1 protein, Ubiquitin associated domain, Ddi1, UBA, NMR