BMRB Entry 34822

Name: Structural characterization of PHOX2B and its DNA interactions shed lights into the molecular basis of the + 7Ala variant pathogenicity in CCHS
Published: 2024-05-07

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PDB ID: 8p7g
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR34822
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:

Structural characterization of PHOX2B and its DNA interactions shed lights into the molecular basis of the + 7Ala variant pathogenicity in CCHS

Deposition date:

2023-05-30

Original release date:

2024-05-07

Authors:

Russo, L.; Diana, D.; Fattorusso, R.

Citation:

Citation: Diana, Donatella; Pirone, Luciano; Russo, Luigi; D'Abrosca, Gianluca; Madheswaran, Manoj; Benfante, Roberta; Di Lascio, Simona; Caldinelli, Laura; Fornasari, Diego; Acconcia, Clementina; Corvino, Andrea; Ventserova, Nataliia; Pollegioni, Loredano; Isernia, Carla; Di Gaetano, Sonia; Malgieri, Gaetano; Pedone, Emilia; Fattorusso, Roberto. "Structural characterization of PHOX2B and its DNA interaction shed light on the molecular basis of the +7Ala variant pathogenicity in CCHS" Chem. Sci. 15, 8858-8872 (2024).
PubMed: 38873078

Assembly members:

Assembly members:
entity_1, polymer, 63 residues, 7741.804 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 'BL21-Gold(DE3)pLysS AG'

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: ASQRRIRTTFTSAQLKELER VFAETHYPDIYTREELALKI DLTEARVQVWFQNRRAKFRK QER

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
13C chemical shifts	177
15N chemical shifts	57
1H chemical shifts	112

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	unit_1	1

Entities:

Entity 1, unit_1 63 residues - 7741.804 Da.

1

ALA

SER

GLN

ARG

ILE

ARG

THR

PHE

2

THR

SER

ALA

GLN

LEU

LYS

GLU

LEU

GLU

ARG

3

VAL

PHE

ALA

GLU

THR

HIS

TYR

PRO

ASP

ILE

4

TYR

THR

ARG

GLU

LEU

ALA

LEU

LYS

ILE

5

ASP

LEU

THR

GLU

ALA

ARG

VAL

GLN

VAL

TRP

6

PHE

GLN

ASN

ARG

ALA

LYS

PHE

ARG

LYS

7

GLN

GLU

ARG

Samples:

sample_1: Paired mesoderm homeobox protein 2B (Phox2B), [U-13C; U-15N], 0.1 mM

sample_conditions_1: ionic strength: 200 mM; pH: 7.4; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-13C HSQC	sample_1	isotropic	sample_conditions_1
2D 1H-15N HSQC	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 HNCO	sample_1	isotropic	sample_conditions_1
3D HNHA	sample_1	isotropic	sample_conditions_1

Software:

CARA, Keller and Wuthrich - chemical shift assignment, peak picking

Sparky, Goddard - chemical shift assignment

CS-ROSETTA, Shen, Vernon, Baker and Bax - refinement, structure calculation

NMR spectrometers:

Bruker AVANCE III HD 600 MHz

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