BMRB Entry 27356

Name: 1H, 13C, and 15N Chemical Shift Assignments for ubiquitin in sf9 cells by in-cell NMR spectroscopy
Published: 2020-05-29

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PDB ID: 5zd0
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR27356
MolProbity Validation Chart

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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:

1H, 13C, and 15N Chemical Shift Assignments for ubiquitin in sf9 cells by in-cell NMR spectroscopy

Deposition date:

2018-01-10

Original release date:

2020-05-29

Authors:

Tanaka, Takashi; Ikeya, Teppei; Kamoshida, Hajime; Mishima, Masaki; Shirakawa, Masahiro; Guentert, Peter; Ito, Yutaka

Citation:

Citation: Tanaka, Takashi; Ikeya, Teppei; Kamoshida, Hajime; Suemoto, Yusuke; Mishima, Masaki; Shirakawa, Masahiro; Guntert, Peter; Ito, Yutaka. "High-Resolution Protein 3D Structure Determination in Living Eukaryotic Cells" Angew. Chem. Int. Ed. Engl. 58, 7284-7288 (2019).
PubMed: 30938016

Assembly members:

Assembly members:
ubiquitin3A, polymer, 76 residues, Formula weight is not available

Natural source:

Natural source: Common Name: Human Taxonomy ID: 9606 Superkingdom: Eukaryota Kingdom: Metazoa Genus/species: Homo sapiens

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Spodoptera frugiperda Vector: pFastBac

Entity Sequences (FASTA):

Entity Sequences (FASTA):
ubiquitin3A: MQIFVKTATGKTITLEVEPS DTIENVKAKIQDKEGIPPDQ QRLAFAGKQLEDGRTLSDYN IQKESTLHLALRLRGG

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	109
15N chemical shifts	70
1H chemical shifts	393

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	ubiquitin3A	1

Entities:

Entity 1, ubiquitin3A 76 residues - Formula weight is not available

1

MET

GLN

ILE

PHE

VAL

LYS

THR

ALA

THR

GLY

2

LYS

THR

ILE

THR

LEU

GLU

VAL

GLU

PRO

SER

3

ASP

THR

ILE

GLU

ASN

VAL

LYS

ALA

LYS

ILE

4

GLN

ASP

LYS

GLU

GLY

ILE

PRO

ASP

GLN

5

GLN

ARG

LEU

ALA

PHE

ALA

GLY

LYS

GLN

LEU

6

GLU

ASP

GLY

ARG

THR

LEU

SER

ASP

TYR

ASN

7

ILE

GLN

LYS

GLU

SER

THR

LEU

HIS

LEU

ALA

8

LEU

ARG

LEU

ARG

GLY

Samples:

sample_1: ubiquitin3A, [U-100% 15N], 50 ± 12 uM; ubiquitin3A, [U-100% 13C; U-100% 15N], 50 ± 12 uM

sample_conditions_1: pressure: 1 atm; temperature: 300 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 HNCO	sample_1	isotropic	sample_conditions_1
3D HNCA	sample_1	isotropic	sample_conditions_1
3D HN(CO)CA	sample_1	isotropic	sample_conditions_1
3D CBCA(CO)NH	sample_1	isotropic	sample_conditions_1
3D HBHA(CO)NH	sample_1	isotropic	sample_conditions_1
3D HCCH-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

Software:

CYANA v3.98, Guntert, Mumenthaler and Wuthrich - data analysis

TOPSPIN v3.0, Bruker Biospin - collection

AZARA v2.8.1, Boucher - refinement

Analysis v2.4.2, CCPN - chemical shift assignment

TALOS-N v4.12, Cornilescu, Delaglio and Bax - data analysis

Molmol v2.6, Koradi, Billeter and Wuthrich - data analysis

NMR spectrometers:

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