BMRB Entry 15671

Name: Solution structure of the TAF3 PHD domain in complex with a H3K4me3 peptide
Published: 2008-08-22

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PDB ID: 2k17
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_anomalous, AVS_full
BMRB Entry DOI: doi:10.13018/BMR15671
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:

Solution structure of the TAF3 PHD domain in complex with a H3K4me3 peptide

Deposition date:

2008-02-22

Original release date:

2008-08-22

Authors:

van Ingen, Hugo; van Schaik, Frederik; Wienk, Hans; Timmers, Marc; Boelens, Rolf

Citation:

Citation: van Ingen, Hugo; van Schaik, Frederik; Wienk, Hans; Ballering, Joost; Rehmann, Holger; Deschesne, Annemarie; Kruijzer, John; Liskamp, Rob; Timmers, H. Th. Marc; Boelens, Rolf. "Structural Insight into the Recognition of the H3K4me3 Mark by the TFIID Subunit TAF3" Structure 16, 1245-1256 (2008).
PubMed: 18682226

Assembly members:

Assembly members:
TAF3_PHD, polymer, 75 residues, 8611.966 Da.
ZN, non-polymer, 65.409 Da.
H3K4me3, polymer, 13 residues, Formula weight is not available

Natural source:

Natural source: Common Name: not available Taxonomy ID: 10090 Superkingdom: Eukaryota Kingdom: Metazoa Genus/species: Mus musculus

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli Vector: 15670

Entity Sequences (FASTA):

Entity Sequences (FASTA):
TAF3_PHD: GSHMAMAYVIRDEWGNQIWI CPGCNKPDDGSPMIGCDDCD DWYHWPCVGIMAAPPEEMQW FCPKCANKIKKDKKH
H3K4me3: ARTXQTARKSTGG

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	236
15N chemical shifts	76
1H chemical shifts	577

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	TAF3_PHD	1
2	ZINC ION_1	2
3	ZINC ION_2	2
4	TAF3_PHD	3

Entities:

Entity 1, TAF3_PHD 75 residues - 8611.966 Da.

Residues 850-857 are non-native remaining from thrombin cleavage site

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, ZINC ION_1 - Zn - 65.409 Da.

1

ZN

Entity 3, TAF3_PHD 13 residues - Formula weight is not available

contains trimethylated lysine at position 4, M3L

1

ALA

ARG

THR

M3L

GLN

THR

ALA

ARG

LYS

SER

2

THR

GLY

Samples:

sample_1: TAF3_PHD, [U-13C; U-15N], 0.4 mM; H3K4me3, [U-13C; U-15N], 0.4 mM; potassium chloride 150 mM; potassium phosphate 20 mM; ZnCl2 0.01 mM

sample_conditions_1: pH: 7; pressure: 1 atm; temperature: 293 K

Experiments:

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

Software:

CNS, Brunger, Adams, Clore, Gros, Nilges and Read - refinement

CYANA, Guntert, Mumenthaler and Wuthrich - structure solution

NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

SPARKY, Goddard - data analysis

NMR spectrometers:

Bruker Avance 900 MHz
Bruker Avance 750 MHz
Bruker Avance 700 MHz
Bruker Avance 600 MHz

BMRB	15670
PDB	2K16 2K17
DBJ	BAE22792 BAE32543
EMBL	CAC34476
GB	AAH89030 AAI37618 AAI37619 AAI72366 EDL08000
REF	NP_001258271 NP_082024 NP_114129 XP_001157768 XP_002808540
SP	Q5HZG4 Q5VWG9
SWS	P68431
AlphaFold	Q5HZG4 Q5VWG9