BMRB Entry 34986

Name: Solution structure of the TAF3-PHD bound to a H3K4me3Q5ser histone tail peptide with a serotonylated glutamine
Published: 2025-07-08

Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR34986

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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 the TAF3-PHD bound to a H3K4me3Q5ser histone tail peptide with a serotonylated glutamine

Deposition date:

2025-03-21

Original release date:

2025-07-08

Authors:

van Ingen, H.; Gielingh, H.; Pulido-Cortes, L.; Thijssen, V.; Timmers, H.; Jongkees, S.; Honorato, R.; Bonvin, A.; Liu, M.; Yoshisada, R.; Soares, L.

Citation:

Citation: Pulido-Cortes, L.; Gielingh, H.; Thijssen, V.; Liu, M.; Yoshisada, R.; Soares, L.; Sheikh, N.; Friedrich, F.; Greschik, H.; Peng, L.; Honorato, R.; Jung, M.; Bonvin, A.; Biniossek, M.; Schule, R.; van Ingen, H.; Timmers, H.; Jongkees, S.. "Molecular determinants for recognition of serotonylated chromatin" .

Assembly members:

Assembly members:
entity_1, polymer, 75 residues, 8611.936 Da.
entity_2, polymer, 12 residues, 1351.553 Da.
entity_ZN, non-polymer, 65.409 Da.
entity_SRO, non-polymer, 176.215 Da.

Natural source:

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

Experimental source:

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

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: GSHMAMAYVIRDEWGNQIWI CPGCNKPDDGSPMIGCDDCD DWYHWPCVGIMAAPPEEMQW FCPKCANKIKKDKKH
entity_2: ARTXETARKSTG

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
13C chemical shifts	228
15N chemical shifts	75
1H chemical shifts	547

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	unit_1	1
2	unit_2	2
3	unit_3	3
4	unit_4	3
5	unit_5	4

Entities:

Entity 1, unit_1 75 residues - 8611.936 Da.

1

GLY

SER

HIS

MET

ALA

MET

ALA

TYR

VAL

ILE

2

ARG

ASP

GLU

TRP

GLY

ASN

GLN

ILE

TRP

ILE

3

CYS

PRO

GLY

CYS

ASN

LYS

PRO

ASP

GLY

4

SER

PRO

MET

ILE

GLY

CYS

ASP

CYS

ASP

5

ASP

TRP

TYR

HIS

TRP

PRO

CYS

VAL

GLY

ILE

6

MET

ALA

PRO

GLU

MET

GLN

TRP

7

PHE

CYS

PRO

LYS

CYS

ALA

ASN

LYS

ILE

LYS

8

LYS

ASP

LYS

HIS

Entity 2, unit_2 12 residues - 1351.553 Da.

1

ALA

ARG

THR

M3L

GLU

THR

ALA

ARG

LYS

SER

2

THR

GLY

Entity 3, unit_3 - Zn - 65.409 Da.

1

ZN

Entity 4, unit_5 - C10 H12 N2 O - 176.215 Da.

1

SRO

Samples:

sample_1: TAF3-PHD, [U-13C; U-15N], 0.88 mM; H3K4me3Q5ser 0.88 mM; potassium phosphate 20 mM; potassium chloride 4 mM; zinc chloride 10 uM; sodium azide 0.01 % w/v

sample_conditions_1: ionic strength: 44 mM; pH: 7.0; pressure: 1 atm; temperature: 293 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D F2-filtered NOESY	sample_1	isotropic	sample_conditions_1
2D F2-filtered TOCSY	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY aliphatic	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY aromatic	sample_1	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_1	isotropic	sample_conditions_1
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1

Software:

HADDOCK, Bonvin - refinement, structure calculation

Poky, Manthey, Tonelli, Clos II, Rahimi, Markley and Lee - chemical shift assignment, peak picking

NMR spectrometers:

Bruker AVANCE III 900 MHz

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