BMRB Entry 52576

Name: 15N relaxation rates of PHDvC5HCH tandem domain of NSD2
Published: 2024-10-25

Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR52576

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Nicholas Rego and David Koes
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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

15N relaxation rates of PHDvC5HCH tandem domain of NSD2

Deposition date:

2024-08-05

Original release date:

2024-10-25

Authors:

Berardi, Andrea; Quilici, Giacomo; Musco, Giovanna

Citation:

Citation: Berardi, Andrea; Leonie Kaestner, Charlotte; Ghitti, Michela; Quilici, Giacomo; Cocomazzi, Paolo; Li, Jianping; Ballabio, Federico; Zucchelli, Chiara; Knapp, Stefan; Licht, Jonathan; Musco, Giovanna. "The C-terminal PHDVC5HCH tandem domain of NSD2 is a combinatorial reader of unmodified H3K4 and tri-methylated H3K27 that regulates transcription of cell adhesion genes in multiple myeloma" Nucleic Acids Res. 53, gkae1121-gkae1121 (2025).
PubMed: 39656918

Assembly members:

Assembly members:
entity_1, polymer, 105 residues, Formula weight is not available
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: into pETM11-SUMO3

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: SRRAKGEGKRQSEDECFRCG DGGQLVLCDRKFCTKAYHLS CLGLGKRPFGKWECPWHHCD VCGKPSTSFCHLCPNSFCKE HQDGTAFSCTPDGRSYCSEH DLGAA

Data sets:

heteronucl_NOEs
- heteronucl_NOEs_1
heteronucl_T1_relaxation
- heteronucl_T1_relaxation_1
heteronucl_T2_relaxation
- heteronucl_T2_relaxation_1

Data type	Count
T1 relaxation values	90
T2 relaxation values	90
heteronuclear NOE values	94

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	PHDC5HCH domain of NSD2	1
2	ZINC ION, 1	2
3	ZINC ION, 2	2
4	ZINC ION, 3	2
5	ZINC ION, 4	2

Entities:

Entity 1, PHDC5HCH domain of NSD2 105 residues - Formula weight is not available

C198 of NSD2 (C1324) (a non-Zn binding Cysteine) was mutated into Serine (i.e. C98S, C1324S NSD2) to improve solubility

1

SER

ARG

ALA

LYS

GLY

GLU

GLY

LYS

ARG

2

GLN

SER

GLU

ASP

GLU

CYS

PHE

ARG

CYS

GLY

3

ASP

GLY

GLN

LEU

VAL

LEU

CYS

ASP

ARG

4

LYS

PHE

CYS

THR

LYS

ALA

TYR

HIS

LEU

SER

5

CYS

LEU

GLY

LEU

GLY

LYS

ARG

PRO

PHE

GLY

6

LYS

TRP

GLU

CYS

PRO

TRP

HIS

CYS

ASP

7

VAL

CYS

GLY

LYS

PRO

SER

THR

SER

PHE

CYS

8

HIS

LEU

CYS

PRO

ASN

SER

PHE

CYS

LYS

GLU

9

HIS

GLN

ASP

GLY

THR

ALA

PHE

SER

CYS

THR

10

PRO

ASP

GLY

ARG

SER

TYR

CYS

SER

GLU

HIS

11

ASP

LEU

GLY

ALA

Entity 2, ZINC ION, 1 - Zn - 65.409 Da.

1

ZN

Samples:

sample_1: PHDvC5HCH of NSD2, [U-99% 15N], 0.3 mM; ZnCl2 10 mM; NaH2PO4/Na2HPO4 20 mM; NaCl 150 mM; TCEP 1 mM

sample_conditions_1: ionic strength: 170 mM; pH: 6.3; pressure: 1 atm; temperature: 295 K

Experiments:

Name	Sample	Sample state	Sample conditions
1H-15N heteronoe	sample_1	isotropic	sample_conditions_1
T1/R1 relaxation	sample_1	isotropic	sample_conditions_1
T2/R2 relaxation	sample_1	isotropic	sample_conditions_1

Software:

CcpNMR v2.5 - data analysis

NMR spectrometers:

Bruker AVANCE III 600 MHz