BMRB Entry 36153

Name: GB1 structure determination in living eukaryotic cells by in-cell NMR spectroscopy
Published: 2025-10-11

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PDB ID: 5z4b
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR36153
MolProbity Validation Chart

NMR-STAR file interactive viewer.
NMR-STAR v3 text file.
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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:

GB1 structure determination in living eukaryotic cells by in-cell NMR spectroscopy

Deposition date:

2018-01-10

Original release date:

2025-10-11

Authors:

Tanaka, T.; Teppei, I.; Kamoshida, H.; Mishima, M.; Shirakawa, M.; Guentert, P.; Ito, Y.

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:
Protein LG, polymer, 57 residues, 6258.835 Da.

Natural source:

Natural source: Common Name: Peptostreptococcus magnus Taxonomy ID: 1260 Superkingdom: Bacteria Kingdom: Bacillati Genus/species: Finegoldia magna

Experimental source:

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

Entity Sequences (FASTA):

Entity Sequences (FASTA):
Protein LG: MGTYKLILNGKTLKGETTTE AVDAATAEKVFKQYANDNGV DGEWTYDDATKTFTVTE

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
13C chemical shifts	177
15N chemical shifts	61
1H chemical shifts	238

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	entity_1	1

Entities:

Entity 1, entity_1 57 residues - 6258.835 Da.

1

MET

GLY

THR

TYR

LYS

LEU

ILE

LEU

ASN

GLY

2

LYS

THR

LEU

LYS

GLY

GLU

THR

GLU

3

ALA

VAL

ASP

ALA

THR

ALA

GLU

LYS

VAL

4

PHE

LYS

GLN

TYR

ALA

ASN

ASP

ASN

GLY

VAL

5

ASP

GLY

GLU

TRP

THR

TYR

ASP

ALA

THR

6

LYS

THR

PHE

THR

VAL

THR

GLU

Samples:

sample_1: GB1, [U-100% 15N], 50 ± 12 uM; H2O 90%; D2O, [U-2H], 10%

sample_2: GB1, [U-100% 13C; U-100% 15N], 50 ± 12 uM; H2O 90%; D2O, [U-2H], 10%

sample_conditions_1: ionic strength: 0 mM; pH: .; 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 - structure calculation

Analysis v2.4.2, CCPN - chemical shift assignment

TOPSPIN v3.0, Bruker Biospin - collection

AZARA v2.8.1, Boucher - processing

OPAL v1.4, Luginbuhl, Guntert, Billeter and Wuthrich - refinement

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