BMRB Entry 17244

Title:
Structural basis for histone code recognition by BRPF2-PHD1 finger
Deposition date:
2010-10-10
Original release date:
2012-07-25
Authors:
Qin, Su; Zhang, Jiahai; Wu, Jihui; Shi, Yunyu
Citation:

Citation: Liu, Lei; Qin, Su; Zhang, Jiahai; Ji, Peng; Shi, Yunyu; Wu, Jihui. "Solution structure of an atypical PHD finger in BRPF2 and its interaction with DNA."  J. Struct. Biol. 180, 165-173 (2012).
PubMed: 22820306

Assembly members:

Assembly members:
BRPF2-PHD1, polymer, 88 residues, 8719.837 Da.
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: pET22b(+)

Entity Sequences (FASTA):

Data sets:
Data typeCount
13C chemical shifts206
15N chemical shifts82
1H chemical shifts426

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1BRPF2-PHD11
2Zinc 12
3Zinc 22

Entities:

Entity 1, BRPF2-PHD1 88 residues - 8719.837 Da.

Histone H3(1-12) fused to the N-ternimal of BRPF2-PHD1 finger, linked by GSSGSS

1   ALAARGTHRLYSGLNTHRALAARGLYSSER
2   THRGLYGLYSERSERGLYSERSERGLNSER
3   LEUILEASPGLUASPALAVALCYSSERILE
4   CYSMETASPGLYGLUSERGLNASNSERASN
5   VALILELEUPHECYSASPMETCYSASNLEU
6   ALAVALHISGLNGLUCYSTYRGLYVALPRO
7   TYRILEPROGLUGLYGLNTRPLEUCYSARG
8   HISCYSLEUGLNSERARGALAARGPROALA
9   LEUGLUHISHISHISHISHISHIS

Entity 2, Zinc 1 - Zn - 65.409 Da.

1   ZN

Samples:

sample_1: BRPF2-PHD1, [U-100% 13C; U-100% 15N], 0.8 mM; ZINC ION 1.6 mM; Bis-Tris 20 mM; sodium chloride 150 mM; H2O 90%; D2O 10%

sample_2: BRPF2-PHD1, [U-100% 13C; U-100% 15N], 0.8 mM; ZINC ION 1.6 mM; Bis-Tris 20 mM; sodium chloride 150 mM; D2O 100%

sample_conditions_1: ionic strength: 0.15 M; pH: 6.7; pressure: 1 atm; temperature: 293 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
3D CBCA(CO)NHsample_1isotropicsample_conditions_1
3D HNCACBsample_1isotropicsample_conditions_1
3D C(CO)NHsample_1isotropicsample_conditions_1
3D HBHA(CO)NHsample_1isotropicsample_conditions_1
3D H(CCO)NHsample_1isotropicsample_conditions_1
3D 1H-15N NOESYsample_1isotropicsample_conditions_1
3D 1H-13C NOESYsample_2isotropicsample_conditions_1

Software:

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

SPARKY v3, Goddard - chemical shift assignment, data analysis, peak picking

TALOS, Cornilescu, Delaglio and Bax - chemical shift calculation, data analysis

ProcheckNMR, Laskowski and MacArthur - data analysis

CNS v1.2, Brunger, Adams, Clore, Gros, Nilges and Read - refinement, structure solution

Molmol, Koradi, Billeter and Wuthrich - data analysis

NMR spectrometers:

  • Bruker DMX 500 MHz

Related Database Links:

GB NP_055392 NP_003484
BMRB 16721
PDB
REF XP_009232775 XP_009232776 XP_009232777 XP_009232778 XP_009232779

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