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Biological Magnetic Resonance Data Bank


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BMRB Entry 19473

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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/BMR19473
MolProbity Validation Chart

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Title: 1H, 13C, and 15N Chemical Shift Assignments for Sp140 PHD finger cis conformer   PubMed: 24267382

Deposition date: 2013-08-29 Original release date: 2013-09-19

Authors: Zucchelli, Chiara; Quilici, Giacomo; Musco, Giovanna

Citation: Zucchelli, Chiara; Tamburri, Simone; Quilici, Giacomo; Palagano, Eleonora; Berardi, Andrea; Saare, Mario; Peterson, Part; Bachi, Angela; Musco, Giovanna. "Structure of human Sp140 PHD finger: an atypical fold interacting with Pin1."  FEBS J. 281, 216-231 (2014).

Assembly members:
Sp140_PHD_finger_cis_conformer, polymer, 56 residues, Formula weight is not available
ZINC ION, non-polymer, 65.409 Da.

Natural source:   Common Name: Human   Taxonomy ID: 9606   Superkingdom: Eukaryota   Kingdom: Metazoa   Genus/species: Homo sapiens

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

Entity Sequences (FASTA):
Sp140_PHD_finger_cis_conformer: GAMGMRNLDECEVCRDGGEL FCCDTCSRVFHEDCHIPPVE AERTPWNCIFCRMKES

Data sets:
Data typeCount
13C chemical shifts159
15N chemical shifts53
1H chemical shifts354

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1PHD finger1
2ZN12
3ZN22

Entities:

Entity 1, PHD finger 56 residues - Formula weight is not available

1   GLYALAMETGLYMETARGASNLEUASPGLU
2   CYSGLUVALCYSARGASPGLYGLYGLULEU
3   PHECYSCYSASPTHRCYSSERARGVALPHE
4   HISGLUASPCYSHISILEPROPROVALGLU
5   ALAGLUARGTHRPROTRPASNCYSILEPHE
6   CYSARGMETLYSGLUSER

Entity 2, ZN1 - Zn - 65.409 Da.

1   ZN

Samples:

sample_1: Sp140 PHD finger, [U-100% 13C; U-100% 15N], 1 mM; sodium phosphate buffer pH 6.3 20 mM; NaCl 150 mM; DTT 4 mM; ZnCl2 50 uM; DSS 0.3 mM; H2O 90%; D2O 10%

sample_2: Sp140 PHD finger, [U-100% 13C; U-100% 15N], 1 mM; sodium phosphate buffer pH 6.3 20 mM; NaCl 150 mM; DTT 4 mM; ZnCl2 50 uM; DSS 0.3 mM; H2O 90%; D2O 10%

sample_3: Sp140 PHD finger, [U-100% 15N], 1 mM; sodium phosphate buffer pH 6.3 20 mM; NaCl 150 mM; DTT 4 mM; ZnCl2 50 uM; DSS 0.3 mM; H2O 90%; D2O 10%

sample_4: Sp140 PHD finger 1 mM; sodium phosphate buffer pH 6.3 20 mM; NaCl 150 mM; DTT 4 mM; ZnCl2 50 uM; DSS 0.3 mM; H2O 90%; D2O 10%

sample_5: Sp140 PHD finger 1 mM; sodium phosphate buffer pH 6.3 20 mM; NaCl 150 mM; DTT 4 mM; ZnCl2 50 uM; DSS 0.3 mM; H2O 90%; D2O 10%

sample_conditions_1: pH: 6.3; temperature: 298 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
2D 1H-13C HSQCsample_1isotropicsample_conditions_1
2D 1H-1H TOCSYsample_4isotropicsample_conditions_1
2D 1H-1H TOCSYsample_5isotropicsample_conditions_1
2D 1H-1H NOESYsample_4isotropicsample_conditions_1
2D 1H-1H NOESYsample_5isotropicsample_conditions_1
3D CBCA(CO)NHsample_1isotropicsample_conditions_1
3D C(CO)NHsample_1isotropicsample_conditions_1
3D HNCOsample_1isotropicsample_conditions_1
3D HNCAsample_1isotropicsample_conditions_1
3D HNCACBsample_1isotropicsample_conditions_1
3D HNHAsample_3isotropicsample_conditions_1
3D H(CCO)NHsample_1isotropicsample_conditions_1
3D HCCH-TOCSYsample_2isotropicsample_conditions_1
3D 1H-15N NOESYsample_3isotropicsample_conditions_1
3D 1H-13C NOESY aliphaticsample_2isotropicsample_conditions_1
3D 1H-13C NOESY aromaticsample_2isotropicsample_conditions_1

Software:

TOPSPIN, Bruker Biospin - collection

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

ANALYSIS, T. Stevens, R. Fogh, W. Boucher, J. Ionides, C. Spronk - chemical shift assignment, peak picking

NMR spectrometers:

  • Bruker Avance 600 MHz
  • Bruker Avance 900 MHz

Related Database Links:

BMRB 19472
PDB
DBJ BAG62830
GB AAB18617 AAC50817 AAI05744 AAI05745 AAI05961
REF NP_001265380 NP_001265381 NP_001265382 NP_009168 XP_003274775
SP Q13342

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SPARKY: Backbone or all simulated shifts