BMRB Entry 25933

Name: NSD1-PHD_5-C5HCH tandem domain structure
Published: 2016-02-23

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PDB ID: 2naa
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_anomalous, AVS_full, LACS, SPARTA
BMRB Entry DOI: doi:10.13018/BMR25933
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:

NSD1-PHD_5-C5HCH tandem domain structure

Deposition date:

2015-12-22

Original release date:

2016-02-23

Authors:

Berardi, Andrea; Quilici, Giacomo; Spiliotopoulos, Dimitrios; Musco, Giovanna

Citation:

Citation: Berardi, Andrea; Quilici, Giacomo; Spiliotopoulos, Dimitrios; Corral-Rodriguez, Maria Angeles; Martin, Fernando; Degano, Massimo; Tonon, Giovanni; Musco, Giovanna. "Structural basis for PHDVC5HCHNSD1-C2HRNizp1 interaction: implications for Sotos syndrome" Nucleic Acids Res. 44, 3448-3463 (2016).
PubMed: 26896805

Assembly members:

Assembly members:
entity_1, polymer, 94 residues, 10480.064 Da.
ZINC ION, non-polymer, 65.409 Da.

Natural source:

Natural source: Common Name: house mouse Taxonomy ID: 10090 Superkingdom: Eukaryota Kingdom: Metazoa Genus/species: Mus musculus

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli Vector: pETM11

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: GAMEREDECFSCGDAGQLVS CKKPGCPKVYHADCLNLTKR PAGKWECPWHQCDVCGKEAA SFCEMCPSSFCKQHREGMLF ISKLDGRLSCTEHD

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	366
15N chemical shifts	93
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	ZINC ION_1	2
3	ZINC ION_2	2
4	ZINC ION_3	2
5	ZINC ION_4	2

Entities:

Entity 1, entity_1 94 residues - 10480.064 Da.

1

GLY

ALA

MET

GLU

ARG

GLU

ASP

GLU

CYS

PHE

2

SER

CYS

GLY

ASP

ALA

GLY

GLN

LEU

VAL

SER

3

CYS

LYS

PRO

GLY

CYS

PRO

LYS

VAL

TYR

4

HIS

ALA

ASP

CYS

LEU

ASN

LEU

THR

LYS

ARG

5

PRO

ALA

GLY

LYS

TRP

GLU

CYS

PRO

TRP

HIS

6

GLN

CYS

ASP

VAL

CYS

GLY

LYS

GLU

ALA

7

SER

PHE

CYS

GLU

MET

CYS

PRO

SER

PHE

8

CYS

LYS

GLN

HIS

ARG

GLU

GLY

MET

LEU

PHE

9

ILE

SER

LYS

LEU

ASP

GLY

ARG

LEU

SER

CYS

10

THR

GLU

HIS

ASP

Entity 2, ZINC ION_1 - 65.409 Da.

1

ZN

Samples:

sample_1: entity_1 0.3 mM; H2O 90%; D2O 10%

sample_4: entity_1, [U-99% 13C; U-99% 15N], 0.3 mM; H2O 90%; D2O 10%

sample_3: entity_1, [U-99% 15N], 0.3 mM; H2O 90%; D2O 10%

sample_2: entity_1 0.3 mM; D2O 100%

sample_5: entity_1, [U-99% 13C; U-99% 15N], 0.3 mM; D2O 100%

sample_conditions_1: ionic strength: 0.150 M; pH: 6.3; pressure: 1 atm; temperature: 295 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_3	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_5	isotropic	sample_conditions_1
2D 1H-1H TOCSY	sample_1	isotropic	sample_conditions_1
2D 1H-1H TOCSY	sample_2	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_1	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_2	isotropic	sample_conditions_1
3D CBCA(CO)NH	sample_4	isotropic	sample_conditions_1
3D C(CO)NH	sample_4	isotropic	sample_conditions_1
3D HNCO	sample_4	isotropic	sample_conditions_1
3D HNCA	sample_4	isotropic	sample_conditions_1
3D H(CCO)NH	sample_4	isotropic	sample_conditions_1
3D HCCH-TOCSY	sample_5	isotropic	sample_conditions_1
3D HNHA	sample_3	isotropic	sample_conditions_1
3D HNCACB	sample_4	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_3	isotropic	sample_conditions_1
3D 1H-13C NOESY	sample_5	isotropic	sample_conditions_1

Software:

ARIA v2.3, Linge, O'Donoghue and Nilges - structure solution

NMR spectrometers:

Bruker Avance 600 MHz
Bruker Avance 900 MHz

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