BMRB Entry 34106

Name: NMR solution structure of ubl5 domain from polyubiquitin locus of T.thermophila.
Published: 2018-03-16

Click here to enlarge.

PDB ID: 5n9v
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR34106
MolProbity Validation Chart

NMR-STAR file interactive viewer.
NMR-STAR v3 text file.
XML gzip file.
RDF gzip file.
All files associated with the entry

Nicholas Rego and David Koes
3Dmol.js: molecular visualization with WebGL
Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

Select model:

I am color blind

Download raw data. Direct link to this display. Help

Title:

NMR solution structure of ubl5 domain from polyubiquitin locus of T.thermophila.

Deposition date:

2017-02-27

Original release date:

2018-03-16

Authors:

Chiarini, V.; Tossavainen, H.

Citation:

Citation: Chiarini, Valerio; Tossavainen, Helena; Sharma, Vivek; Colotti, Gianni. "NMR structure of a non-conjugatable, ADP-ribosylation associated, ubiquitin-like domain from Tetrahymena thermophila polyubiquitin locus" Biochim. Biophys. Acta Gen. Subj. 1863, 749-759 (2019).
PubMed: 30690122

Assembly members:

Assembly members:
entity_1, polymer, 81 residues, 9457.851 Da.

Natural source:

Natural source: Common Name: Tetrahymena thermophila Taxonomy ID: 312017 Superkingdom: Eukaryota Kingdom: not available Genus/species: Tetrahymena thermophila

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: SHMQVSIEFQNGEKLKFNVQ PSHKILDIKEMIFKKTNINV KDQSLKFAGNEMINQKTLSD YSIIDSTEEFTLHLETKLDL M

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
13C chemical shifts	391
15N chemical shifts	89
1H chemical shifts	617

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
Hide all

Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	entity_1	1

Entities:

Entity 1, entity_1 81 residues - 9457.851 Da.

1

SER

HIS

MET

GLN

VAL

SER

ILE

GLU

PHE

GLN

2

ASN

GLY

GLU

LYS

LEU

LYS

PHE

ASN

VAL

GLN

3

PRO

SER

HIS

LYS

ILE

LEU

ASP

ILE

LYS

GLU

4

MET

ILE

PHE

LYS

THR

ASN

ILE

ASN

VAL

5

LYS

ASP

GLN

SER

LEU

LYS

PHE

ALA

GLY

ASN

6

GLU

MET

ILE

ASN

GLN

LYS

THR

LEU

SER

ASP

7

TYR

SER

ILE

ASP

SER

THR

GLU

PHE

8

THR

LEU

HIS

LEU

GLU

THR

LYS

LEU

ASP

LEU

9

MET

Samples:

sample_1: T.thermophila BUBL1-ubl5, [U-13C; U-15N], 4 mM; sodium phosphate 20 mM

sample_conditions_1: ionic strength: 0.06 M; pH: 6; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_1	isotropic	sample_conditions_1
3D 1H-15N TOCSY	sample_1	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY	sample_1	isotropic	sample_conditions_1
3D HNCO	sample_1	isotropic	sample_conditions_1
3D HNCACB	sample_1	isotropic	sample_conditions_1
3D HNCA	sample_1	isotropic	sample_conditions_1
3D CBCA(CO)NH	sample_1	isotropic	sample_conditions_1
3D HN(CO)CA	sample_1	isotropic	sample_conditions_1
3D HN(CA)CO	sample_1	isotropic	sample_conditions_1
3D HCC(CO)NH	sample_1	isotropic	sample_conditions_1
3D HCCH-COSY	sample_1	isotropic	sample_conditions_1

Software:

TOPSPIN, Bruker Biospin - collection, processing

CcpNMR, CCPN - data analysis

CYANA, Guntert, Mumenthaler and Wuthrich - structure calculation

AMBER, Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman - refinement

NMR spectrometers:

Bruker AvanceIII 850 MHz
Bruker AvanceIII 600 MHz

Download HSQC peak lists in one of the following formats:
CSV: Backbone or all simulated peaks
SPARKY: Backbone or all simulated peaks