BMRB Entry 25066

Name: NMR structure of UBA domain of DNA-damage-inducible 1 protein (Ddi1)
Published: 2015-02-02

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PDB ID: 2mr9
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, SPARTA
BMRB Entry DOI: doi:10.13018/BMR25066
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Nicholas Rego and David Koes
3Dmol.js: molecular visualization with WebGL
Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

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

Deposition date:

2014-07-02

Original release date:

2015-02-02

Authors:

Zhang, Daoning; Fushman, David

Citation:

Citation: Nowicka, Urszula; Zhang, Daoning; Walker, Olivier; Castaneda, Calos; Krutauz, Daria; Chen, Tony; Reis, Noa; Glickman, Michael; Fushman, David. "DNA-damage-inducible 1 protein (Ddi1) contains an uncharacteristic ubiquitin-like domain" Structure ., .-..

Assembly members:

Assembly members:
entity, polymer, 44 residues, 4745.415 Da.

Natural source:

Natural source: Common Name: Baker's yeast Taxonomy ID: 4932 Superkingdom: Eukaryota Kingdom: Fungi Genus/species: Saccharomyces cerevisiae

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli Vector: pGEX 4T2

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity: GSATFPEQTIKQLMDLGFPR DAVVKALKQTNGNAEFAASL LFQS

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
1H chemical shifts	296
15N chemical shifts	45

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	UBA domain of DNA-damage-inducible 1 protein (Ddi1)	1

Entities:

Entity 1, UBA domain of DNA-damage-inducible 1 protein (Ddi1) 44 residues - 4745.415 Da.

First three residues 'GSA' represent a non-native affinity tag. Residue 4T represents 389T in the Ddi1 sequence.

1

GLY

SER

ALA

THR

PHE

PRO

GLU

GLN

THR

ILE

2

LYS

GLN

LEU

MET

ASP

LEU

GLY

PHE

PRO

ARG

3

ASP

ALA

VAL

LYS

ALA

LEU

LYS

GLN

THR

4

ASN

GLY

ASN

ALA

GLU

PHE

ALA

SER

LEU

5

LEU

PHE

GLN

SER

Samples:

sample_1: UBA, [U-100% 15N], 1 mM; D2O, [U-99% 2H], 7%; H2O 93%; sodium phosphate 20 mM

sample_2: UBA, [U-100% 15N], 0.5 mM; D2O, [U-99% 2H], 7%; H2O 43%; sodium phosphate 10 mM; C12E5 5%; n-hexanol 45%

sample_conditions_1: temperature: 298.2 K; pH: 6.8; pressure: 1 atm; ionic strength: 10 mM

sample_conditions_2: temperature: 308.2 K; pH: 6.8; pressure: 1 atm; ionic strength: 10 mM

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
2D 1H-1H TOCSY	sample_1	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_1	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_1	isotropic	sample_conditions_1
3D 1H-15N TOCSY	sample_1	isotropic	sample_conditions_1
RDC	sample_2	isotropic	sample_conditions_1
RDC	sample_2	isotropic	sample_conditions_2

Software:

CARA v1.8.1, Keller and Wuthrich - peak picking, chemical shift assignment

TOPSPIN v2.1, Bruker Biospin - collection, processing, data analysis

ARIA v2.1, Linge, O'Donoghue and Nilges - chemical shift calculation, structure solution, refinement

NMR spectrometers:

Bruker Avance 600 MHz

GB	EDN63120.1 AAB64670 AAB82066 AAC18522 AAT92964 AHY75700
PDB	2MR9 2MRO
DBJ	GAA22973
EMBL	CAY79329
REF	NP_011070
SP	P40087
TPG	DAA07804
AlphaFold	P40087