BMRB Entry 30177

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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_anomalous, AVS_full
BMRB Entry DOI: doi:10.13018/BMR30177
MolProbity Validation Chart

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NMR-STAR v3 text file.
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Title:
Solution NMR structure of PHF20 PHD domain in complex with a histone H3K4me2 peptide
Deposition date:
2016-09-12
Original release date:
2016-10-07
Authors:
Cui, G.; Botuyan, M.; Mer, G.
Citation:

Citation: Klein, Brianna; Wang, Xiaoyan; Cui, Gaofeng; Yuan, Chao; Botuyan, Maria Victoria; Lin, Kevin; Lu, Yue; Wang, Xiaolu; Zhao, Yue; Bruns, Christiane; Mer, Georges; Shi, Xiaobing; Kutateladze, Tatiana. "PHF20 Readers Link Methylation of Histone H3K4 and p53 with H4K16 Acetylation"  Cell Rep 17, 1158-1170 (2016).
PubMed: 27760318

Assembly members:

Assembly members:
entity_1, polymer, 57 residues, 6834.700 Da.
entity_2, polymer, 12 residues, 1276.490 Da.
entity_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

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: GHMDRYDFEVVRCICEVQEE NDFMIQCEECQCWQHGVCMG LLEENVPEKYTCYVCQD
entity_2: ARTXQTARKSTX

Data sets:
Data typeCount
13C chemical shifts289
15N chemical shifts62
1H chemical shifts454

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1entity_11
2entity_22
3ZINC ION, 13
4ZINC ION, 23

Entities:

Entity 1, entity_1 57 residues - 6834.700 Da.

1   GLYHISMETASPARGTYRASPPHEGLUVAL
2   VALARGCYSILECYSGLUVALGLNGLUGLU
3   ASNASPPHEMETILEGLNCYSGLUGLUCYS
4   GLNCYSTRPGLNHISGLYVALCYSMETGLY
5   LEULEUGLUGLUASNVALPROGLULYSTYR
6   THRCYSTYRVALCYSGLNASP

Entity 2, entity_2 12 residues - 1276.490 Da.

1   ALAARGTHRMLYGLNTHRALAARGLYSSER
2   THRNH2

Entity 3, ZINC ION, 1 - Zn - 65.409 Da.

1   ZN

Samples:

sample_1: DSS 0.3 mM; H3K4me2 peptide 6.0 mM; PHF20 PHD domain, [U-15N], 1.5 mM; sodium azide 1.5 mM; sodium phosphate 25 mM

sample_2: DSS 0.3 mM; H3K4me2 peptide 6.0 mM; PHF20 PHD domain, [U-13C; U-15N], 1.5 mM; sodium azide 1.5 mM; sodium phosphate 25 mM

sample_3: DSS 0.3 mM; H3K4me2 peptide 2 mM; sodium azide 1.5 mM; sodium phosphate 25 mM

sample_conditions_1: ionic strength: 20 mM; pH: 7.0; pressure: 101325 Pa; temperature: 298 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
3D 1H-15N NOESYsample_1isotropicsample_conditions_1
2D 1H-13C HSQCsample_2isotropicsample_conditions_1
3D HNCACBsample_2isotropicsample_conditions_1
3D CBCA(CO)NHsample_2isotropicsample_conditions_1
3D HNCOsample_2isotropicsample_conditions_1
3D NH(CA)COsample_2isotropicsample_conditions_1
3D HBHA(CO)NHsample_2isotropicsample_conditions_1
3D CCH-TOCSYsample_2isotropicsample_conditions_1
3D 1H-15N NOESYsample_2isotropicsample_conditions_1
3D 1H-13C NOESY aliphaticsample_2isotropicsample_conditions_1
3D 1H-13C NOESY aromaticsample_2isotropicsample_conditions_1
3D 13C,15N-filtered, 13C/15N-edited NOESYsample_2isotropicsample_conditions_1
2D 1H-13C HSQCsample_3isotropicsample_conditions_1
2D 1H-1H NOESYsample_3isotropicsample_conditions_1
2D 1H-1H COSYsample_3isotropicsample_conditions_1

Software:

AMBER v14, Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, and Kollman - refinement

CYANA, Guntert, Mumenthaler and Wuthrich - structure calculation

NMRDraw, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - chemical shift assignment, processing

NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - chemical shift assignment, processing

NMRView, Johnson, One Moon Scientific - chemical shift assignment, peak picking

SANE, Duggan, Legge, Dyson & Wright - chemical shift assignment

TALOS, Cornilescu, Delaglio and Bax - data analysis

TOPSPIN, Bruker Biospin - collection

NMR spectrometers:

  • Bruker AvanceIII 700 MHz

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