BMRB Entry 34330

Name: Solution structure of TRIM28 RING domain
Published: 2019-04-24

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PDB ID: 6i9h
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR34330
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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:

Solution structure of TRIM28 RING domain

Deposition date:

2018-11-23

Original release date:

2019-04-24

Authors:

Stevens, R.; Esposito, D.; Rittinger, K.

Citation:

Citation: Stevens, R.; Esposito, D.; Rittinger, K.. "Characterisation of class VI TRIM RING domains: linking RING activity to C-terminal domain identity" Life Sci. Alliance 2, e201900295-e201900295 (2019).
PubMed: 31028095

Assembly members:

Assembly members:
entity_1, polymer, 94 residues, 9674.865 Da.
entity_ZN, non-polymer, 65.409 Da.

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: Escherichia coli

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: GPGGAEALELLEHCGVCRER LRPEREPRLLPCLHSACSAC LGPAAPAAANSSGDGGAAGD GTVVDCPVCKQQCFSKDIVE NYFMRDSGSKAATD

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
13C chemical shifts	369
15N chemical shifts	90
1H chemical shifts	579

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	entity_1	1
2	entity_2, 1	2
3	entity_2, 2	2

Entities:

Entity 1, entity_1 94 residues - 9674.865 Da.

1

GLY

PRO

GLY

ALA

GLU

ALA

LEU

GLU

LEU

2

LEU

GLU

HIS

CYS

GLY

VAL

CYS

ARG

GLU

ARG

3

LEU

ARG

PRO

GLU

ARG

GLU

PRO

ARG

LEU

4

PRO

CYS

LEU

HIS

SER

ALA

CYS

SER

ALA

CYS

5

LEU

GLY

PRO

ALA

PRO

ALA

ASN

6

SER

GLY

ASP

GLY

ALA

GLY

ASP

7

GLY

THR

VAL

ASP

CYS

PRO

VAL

CYS

LYS

8

GLN

CYS

PHE

SER

LYS

ASP

ILE

VAL

GLU

9

ASN

TYR

PHE

MET

ARG

ASP

SER

GLY

SER

LYS

10

ALA

THR

ASP

Entity 2, entity_2, 1 - Zn - 65.409 Da.

1

ZN

Samples:

sample_1: TRIM28 RING, [U-15N], 1 mM; MES 20 mM; NaCl 100 mM; TCEP 0.5 mM

sample_2: TRIM28 RING, [U-13C; U-15N], 1 mM; MES 20 mM; NaCl 100 mM; TCEP 0.5 mM

sample_conditions_1: ionic strength: 100 mM; pH: 6.2; pressure: 1 atm; temperature: 298 K

sample_conditions_2: ionic strength: 100 mM; pH: 6.2; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
3D HNCA	sample_2	isotropic	sample_conditions_2
3D HN(CO)CA	sample_2	isotropic	sample_conditions_2
3D CBCA(CO)NH	sample_2	isotropic	sample_conditions_2
3D HNCACB	sample_2	isotropic	sample_conditions_2
3D HNCO	sample_2	isotropic	sample_conditions_2
3D 1H-13C NOESY	sample_2	isotropic	sample_conditions_2
3D 1H-15N NOESY	sample_1	isotropic	sample_conditions_1
3D HCCH-TOCSY	sample_2	isotropic	sample_conditions_2
3D HN(CA)CO	sample_2	isotropic	sample_conditions_2
3D 1H-13C NOESY aromatic	sample_2	isotropic	sample_conditions_2
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_2	isotropic	sample_conditions_2

Software:

CcpNMR, CCPN - chemical shift assignment

ARIA, Linge, O'Donoghue and Nilges - structure calculation

X-PLOR NIH, Schwieters, Kuszewski, Tjandra and Clore - refinement

NMR spectrometers:

Bruker AvanceIII 700 MHz
Bruker AvanceIII 800 MHz
Bruker A 950 MHz

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