BMRB

Biological Magnetic Resonance Data Bank


A Repository for Data from NMR Spectroscopy on Proteins, Peptides, Nucleic Acids, and other Biomolecules
Member of WWPDB

BMRB Entry 26808

Title: Egr-1 - DNA complex   PubMed: 27288446

Authors: Iwahara, Junji

Citation: Esadze, Alexandre; Chen, Chuanying; Zandarashvili, Levani; Roy, Sourav; Pettitt, B. Montgomery; Iwahara, Junji. "Changes in conformational dynamics of basic side chains upon protein-DNA association"  Nucleic Acids Res. 44, 6961-6970 (2016).

Assembly members:
The_Egr-1_zinc-finger_protein, polymer, 90 residues, Formula weight is not available
DNA_strand_1, polymer, 12 residues, Formula weight is not available
DNA_strand_2, polymer, 12 residues, Formula weight is not available
entity_ZN, 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):
The_Egr-1_zinc-finger_protein: PERPYACPVESCDRRFSRSD ELTRHIRIHTGQKPFQCRIC MRNFSRSDHLTTHIRTHTGE KPFACDICGRKFARSDERKR HTKIHLRQKD
DNA_strand_1: AGCGTGGGCGTA
DNA_strand_2: TACGCCCACGCT

Data sets:
Data typeCount
13C chemical shifts366
15N chemical shifts109
1H chemical shifts542

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1The DNA-binding domain of the human Egr-1 protein1
2DNA strand 12
3DNA strand 23
4Zinc ion 14
5Zinc ion 24
6Zinc ion 34

Entities:

Entity 1, The DNA-binding domain of the human Egr-1 protein 90 residues - Formula weight is not available

1   PROGLUARGPROTYRALACYSPROVALGLU
2   SERCYSASPARGARGPHESERARGSERASP
3   GLULEUTHRARGHISILEARGILEHISTHR
4   GLYGLNLYSPROPHEGLNCYSARGILECYS
5   METARGASNPHESERARGSERASPHISLEU
6   THRTHRHISILEARGTHRHISTHRGLYGLU
7   LYSPROPHEALACYSASPILECYSGLYARG
8   LYSPHEALAARGSERASPGLUARGLYSARG
9   HISTHRLYSILEHISLEUARGGLNLYSASP

Entity 2, DNA strand 1 12 residues - Formula weight is not available

1   DADGDCDGDTDGDGDGDCDG
2   DTDA

Entity 3, DNA strand 2 12 residues - Formula weight is not available

1   DTDADCDGDCDCDCDADCDG
2   DCDT

Entity 4, Zinc ion 1 - Zn - 65.409 Da.

1   ZN

Samples:

sample_1: The Egr-1 zinc-finger protein, [U-99% 13C; U-99% 15N], 1 mM; Zinc ion 1 1 mM; Zinc ion 2 1 mM; Zinc ion 3 1 mM; DNA strand 1 1.5 mM; DNA strand 2 1.5 mM; potassium succinate, [U-99% 2H], 20 mM; potassium chloride 20 mM; zinc chloride 0.1 mM

sample_conditions_1: ionic strength: 0.040 M; pH: 5.8; pressure: 1 atm; temperature: 303.15 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
2D 1H-13C HSQCsample_1isotropicsample_conditions_1
3D HNCOsample_1isotropicsample_conditions_1
3D HN(CA)COsample_1isotropicsample_conditions_1
3D HNCAsample_1isotropicsample_conditions_1
3D HN(CO)CAsample_1isotropicsample_conditions_1
3D CBCA(CO)NHsample_1isotropicsample_conditions_1
3D HNCACBsample_1isotropicsample_conditions_1
3D HBHA(CO)NHsample_1isotropicsample_conditions_1
3D H(CCO)NHsample_1isotropicsample_conditions_1
3D C(CO)NHsample_1isotropicsample_conditions_1
3D 1H-15N NOESYsample_1isotropicsample_conditions_1
3D HCCH-TOCSYsample_1isotropicsample_conditions_1
3D HCCH-COSYsample_1isotropicsample_conditions_1
2D (H2C)N(CC)H-TOCSYsample_1isotropicsample_conditions_1

Software:

NMRView, Johnson, One Moon Scientific - data analysis

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

NMR spectrometers:

  • Bruker Avance 800 MHz
  • Bruker Avance 600 MHz
  • Bruker Avance 750 MHz

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