BMRB Entry 16865

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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR16865
MolProbity Validation Chart

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Title:
Solution structure of the double PHD (plant homeodomain) fingers of human transcriptional protein DPF3b bound to a histone H4 peptide containing N-terminal acetylation at serine 1
Deposition date:
2010-04-14
Original release date:
2010-09-03
Authors:
Zeng, Lei; Zhang, Qiang; Li, SiDe; Plotnikov, Alexander; Walsh, Martin; ZHOU, MING-MING
Citation:

Citation: Zeng, Lei; Zhang, Qiang; Li, SiDe; Plotnikov, Alexander; Walsh, Martin; ZHOU, MING-MING. "Mechanism and regulation of acetylated histone binding by the tandem PHD finger of DPF3b"  Nature 466, 258-262 (2010).
PubMed: 20613843

Assembly members:

Assembly members:
histone_H4_acet_serine_1, polymer, 20 residues, 1914.308 Da.
double_PHD_fingers, polymer, 114 residues, 12746.515 Da.
ACS, non-polymer, 395.452 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: chemical synthesis

Entity Sequences (FASTA):

Entity Sequences (FASTA):
histone_H4_acet_serine_1: XGRGKGGKGLGKGGAKRHRK
double_PHD_fingers: GSYCDFCLGGSNMNKKSGRP EELVSCADCGRSGHPTCLQF TLNMTEAVKTYKWQCIECKS CILCGTSENDDQLLFCDDCD RGYHMYCLNPPVAEPPEGSW SCHLCWELLKEKAS

Data sets:
Data typeCount
13C chemical shifts364
15N chemical shifts117
1H chemical shifts801

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1histone_H4_acet_serine_11
2double_PHD_fingerss2
3ACS3
4ZINC ION_14
5ZINC ION_24
6ZINC ION_34
7ZINC ION_44

Entities:

Entity 1, histone_H4_acet_serine_1 20 residues - 1914.308 Da.

1   SACGLYARGGLYLYSGLYGLYLYSGLYLEU
2   GLYLYSGLYGLYALALYSARGHISARGLYS

Entity 2, double_PHD_fingerss 114 residues - 12746.515 Da.

1   GLYSERTYRCYSASPPHECYSLEUGLYGLY
2   SERASNMETASNLYSLYSSERGLYARGPRO
3   GLUGLULEUVALSERCYSALAASPCYSGLY
4   ARGSERGLYHISPROTHRCYSLEUGLNPHE
5   THRLEUASNMETTHRGLUALAVALLYSTHR
6   TYRLYSTRPGLNCYSILEGLUCYSLYSSER
7   CYSILELEUCYSGLYTHRSERGLUASNASP
8   ASPGLNLEULEUPHECYSASPASPCYSASP
9   ARGGLYTYRHISMETTYRCYSLEUASNPRO
10   PROVALALAGLUPROPROGLUGLYSERTRP
11   SERCYSHISLEUCYSTRPGLULEULEULYS
12   GLULYSALASER

Entity 3, ACS - C13 H21 N3 O7 S2 - 395.452 Da.

1   ACS

Entity 4, ZINC ION_1 - Zn - 65.409 Da.

1   ZN

Samples:

sample_1: sodium phosphate 100 mM; DTT 2 mM; D2O 100%

sample_2: sodium phosphate 100 mM; DTT 2 mM; H2O 90%; D2O 10%

sample_conditions_1: pH: 6.5; pressure: 1 atm; temperature: 298 K

Experiments:

NameSampleSample stateSample conditions
3D HNCACBsample_2isotropicsample_conditions_1
3D HN(COCA)CBsample_2isotropicsample_conditions_1
3D 1H-15N NOESYsample_1isotropicsample_conditions_1
3D 1H-13C NOESYsample_1isotropicsample_conditions_1
3D_13C-Edited_13C/15N-filtered NOESYsample_1isotropicsample_conditions_1

Software:

ARIA v2.2, Linge, O'Donoghue and Nilges - refinement

NMRPipe v2.3, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - chemical shift calculation, processing

NMRView v5.04, Johnson, One Moon Scientific - chemical shift assignment, data analysis, peak picking

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

NMR spectrometers:

  • Bruker Avance 900 MHz
  • Bruker Avance 800 MHz
  • Bruker Avance 600 MHz
  • Bruker DRX 500 MHz

Related Database Links:

PDB
DBJ BAA19208 BAA21442 BAA85120 BAB08365 BAB09507 BAC30204
EMBL CAA17818 CAA24130 CAA24373 CAA24645 CAA24924
GB AAA20820 AAA20821 AAA28606 AAA30002 AAA30024 AAX20019 EDL02734 EGV99590 EHH28015 EHH63746
PIR D56618 S11312 S21367 S68537
PRF 0901261A 0912198A 1202262E 1314298A 1707275C
REF NP_001011609 NP_001016869 NP_001027284 NP_001027288 NP_001027293 NP_001254554 NP_001267471 XP_001140541 XP_001254780 XP_001375927
SP P02309 P04914 P04915 P08436 P09322 P58269 Q92784
TPE CBF86829 CBF88885 CEL65759 CEL73296
TPG DAA07130 DAA10515 DAA13862 DAA16108 DAA16158 DAA25179
BMRB 16858 16859 16861
AlphaFold P02309 P04914 P04915 P08436 P09322 P58269 Q92784

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