BMRB Entry 25288

Name: Solution structure of the TRIM19 B-box1 (B1) of human promyelocytic leukemia (PML)
Published: 2014-11-10

Click here to enlarge.

PDB ID: 2mvw
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS, SPARTA
BMRB Entry DOI: doi:10.13018/BMR25288
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:

Solution structure of the TRIM19 B-box1 (B1) of human promyelocytic leukemia (PML)

Deposition date:

2014-10-17

Original release date:

2014-11-10

Authors:

Huang, Shu-Yu; Naik, Mandar; Fan, Pei-Ju; Wang, Ying-Hui; Chang, Chi-Fon; Huang, Tai-Huang

Citation:

Citation: Huang, Shu-Yu; Naik, Mandar; Wang, Ying-Hui; Chang, Chi-Fon; Fan, Pei-Ju; Shih, Hsiu-Ming; Huang, Tai-Huang. "NMR structure note: The B-box 1 dimer of human promyelocytic leukemia protein" J. Biomol. NMR 60, 275-281 (2014).
PubMed: 25355412

Assembly members:

Assembly members:
entity_1, polymer, 51 residues, 5941.833 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 Vector: pGEX4T-1

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: GSRQIVDAQAVCTRCKESAD FWCFECEQLLCAKCFEAHQW FLKHEARPLAE

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	362
15N chemical shifts	108
1H chemical shifts	698

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
Hide all

Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	entity_1_1	1
2	entity_1_2	1
3	ZINC ION_1	2
4	ZINC ION_2	2
5	ZINC ION_3	2
6	ZINC ION_4	2

Entities:

Entity 1, entity_1_1 51 residues - 5941.833 Da.

GLY A 118, SER A 119, GLY B 118, SER B 119 come from expression tag.

1

GLY

SER

ARG

GLN

ILE

VAL

ASP

ALA

GLN

ALA

2

VAL

CYS

THR

ARG

CYS

LYS

GLU

SER

ALA

ASP

3

PHE

TRP

CYS

PHE

GLU

CYS

GLU

GLN

LEU

4

CYS

ALA

LYS

CYS

PHE

GLU

ALA

HIS

GLN

TRP

5

PHE

LEU

LYS

HIS

GLU

ALA

ARG

PRO

LEU

ALA

6

GLU

Entity 2, ZINC ION_1 - Zn - 65.409 Da.

1

ZN

Samples:

sample_1: PML B1 box, [U-99% 13C; U-99% 15N], 1 mM; TRIS, [U-98% 2H], 25 mM; sodium chloride 100 mM; TCEP 0.2 mM; zinc chloride 1 mM

sample_2: PML B1 box, [U-99% 13C; U-99% 15N], 1 mM; TRIS, [U-98% 2H], 25 mM; sodium chloride 100 mM; TCEP 0.2 mM; zinc chloride 1 mM

sample_3: PML B1 box, [U-99% 13C; U-99% 15N], 0.5 mM; PML B1 box 0.5 mM; TRIS, [U-98% 2H], 25 mM; sodium chloride 100 mM; TCEP 0.2 mM; zinc chloride 1 mM

sample_conditions_1: pH: 7.0; 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 CBCA(CO)NH	sample_1	isotropic	sample_conditions_1
3D HNCO	sample_1	isotropic	sample_conditions_1
3D HNCA	sample_1	isotropic	sample_conditions_1
3D H(CCO)NH	sample_1	isotropic	sample_conditions_1
3D C(CO)NH	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
2D 1H-1H COSY	sample_1	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY aliphatic	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY aliphatic	sample_2	isotropic	sample_conditions_1
13C-edited/12C-filtered 3D NOESY-HSQC	sample_3	isotropic	sample_conditions_1

Software:

CYANA v3.9, Guntert, Mumenthaler and Wuthrich - geometry optimization

X-PLOR_NIH v2.26, Schwieters, Kuszewski, Tjandra and Clore - refinement

SPARKY v3.114, Goddard - chemical shift assignment

Procheck v3.5.4, Laskowski, MacArthur, Smith, Jones, Hutchinson, Morris, Moss and Thornton - data analysis

TALOS v1.2009.0721.18, Cornilescu, Delaglio and Bax - Torsion angles prediction

NMR spectrometers:

Bruker Uniform NMR System 600 MHz
Bruker Uniform NMR System 800 MHz
Bruker Uniform NMR System 850 MHz

PDB	2MVW
DBJ	BAD92187 BAD92288 BAD92648 BAG10798 BAG62579
EMBL	CAA44841
GB	AAA59972 AAA60125 AAA60126 AAA60351 AAA60352
PIR	S42517 S42518 S44380
REF	NP_001035900 NP_001266170 NP_001266654 NP_001267024 NP_002666
SP	P29590
AlphaFold	P29590