BMRB

Biological Magnetic Resonance Data Bank


A Repository for Data from NMR Spectroscopy on Proteins, Peptides, Nucleic Acids, and other Biomolecules
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BMRB Entry 15671

Title: Solution structure of the TAF3 PHD domain in complex with a H3K4me3 peptide   PubMed: 18682226

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

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).

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

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

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

Data sets:
Data typeCount
13C chemical shifts236
15N chemical shifts76
1H chemical shifts577

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
  • Hide all

Assembly:

Entity Assembly IDEntity NameEntity ID
1TAF3_PHD1
2ZINC ION_12
3ZINC ION_22
4TAF3_PHD3

Entities:

Entity 1, TAF3_PHD 75 residues - 8611.966 Da.

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

1   GLYSERHISMETALAMETALATYRVALILE
2   ARGASPGLUTRPGLYASNGLNILETRPILE
3   CYSPROGLYCYSASNLYSPROASPASPGLY
4   SERPROMETILEGLYCYSASPASPCYSASP
5   ASPTRPTYRHISTRPPROCYSVALGLYILE
6   METALAALAPROPROGLUGLUMETGLNTRP
7   PHECYSPROLYSCYSALAASNLYSILELYS
8   LYSASPLYSLYSHIS

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   ALAARGTHRM3LGLNTHRALAARGLYSSER
2   THRGLYGLY

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:

NameSampleSample stateSample conditions
3D 1H-15N NOESYsample_1isotropicsample_conditions_1
3D 1H-13C NOESYsample_1isotropicsample_conditions_1
2D 1H-1H NOESYsample_1isotropicsample_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

Related Database Links:

BMRB 15670
PDB
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