BMRB Entry 26808

Name: Egr-1 - DNA complex
Published: 2016-06-29

Chem Shift validation: AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR26808

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Nicholas Rego and David Koes
3Dmol.js: molecular visualization with WebGL
Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

Egr-1 - DNA complex

Deposition date:

2016-05-25

Original release date:

2016-06-29

Authors:

Iwahara, Junji

Citation:

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).
PubMed: 27288446

Assembly members:

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:

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: pET49b

Entity Sequences (FASTA):

Entity Sequences (FASTA):
The_Egr-1_zinc-finger_protein: PERPYACPVESCDRRFSRSD ELTRHIRIHTGQKPFQCRIC MRNFSRSDHLTTHIRTHTGE KPFACDICGRKFARSDERKR HTKIHLRQKD
DNA_strand_1: AGCGTGGGCGTA
DNA_strand_2: TACGCCCACGCT

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	366
15N chemical shifts	109
1H chemical shifts	542

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	The DNA-binding domain of the human Egr-1 protein	1
2	DNA strand 1	2
3	DNA strand 2	3
4	Zinc ion 1	4
5	Zinc ion 2	4
6	Zinc ion 3	4

Entities:

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

1	PRO	GLU	ARG	PRO	TYR	ALA	CYS	PRO	VAL	GLU
2	SER	CYS	ASP	ARG	ARG	PHE	SER	ARG	SER	ASP
3	GLU	LEU	THR	ARG	HIS	ILE	ARG	ILE	HIS	THR
4	GLY	GLN	LYS	PRO	PHE	GLN	CYS	ARG	ILE	CYS
5	MET	ARG	ASN	PHE	SER	ARG	SER	ASP	HIS	LEU
6	THR	THR	HIS	ILE	ARG	THR	HIS	THR	GLY	GLU
7	LYS	PRO	PHE	ALA	CYS	ASP	ILE	CYS	GLY	ARG
8	LYS	PHE	ALA	ARG	SER	ASP	GLU	ARG	LYS	ARG
9	HIS	THR	LYS	ILE	HIS	LEU	ARG	GLN	LYS	ASP

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

1

DA

DG

DC

DG

DT

DG

DC

DG

2

DT

DA

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

1

DT

DA

DC

DG

DC

DA

DC

DG

2

DC

DT

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

1

ZN

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_1	isotropic	sample_conditions_1
3D HNCO	sample_1	isotropic	sample_conditions_1
3D HN(CA)CO	sample_1	isotropic	sample_conditions_1
3D HNCA	sample_1	isotropic	sample_conditions_1
3D HN(CO)CA	sample_1	isotropic	sample_conditions_1
3D CBCA(CO)NH	sample_1	isotropic	sample_conditions_1
3D HNCACB	sample_1	isotropic	sample_conditions_1
3D HBHA(CO)NH	sample_1	isotropic	sample_conditions_1
3D H(CCO)NH	sample_1	isotropic	sample_conditions_1
3D C(CO)NH	sample_1	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_1	isotropic	sample_conditions_1
3D HCCH-TOCSY	sample_1	isotropic	sample_conditions_1
3D HCCH-COSY	sample_1	isotropic	sample_conditions_1
2D (H2C)N(CC)H-TOCSY	sample_1	isotropic	sample_conditions_1

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

BMRB Entry 26808

Additional metadata:

Assembly:

Entities:

Samples:

Experiments:

Software:

NMR spectrometers:

1	PRO	GLU	ARG	PRO	TYR	ALA	CYS	PRO	VAL	GLU
2	SER	CYS	ASP	ARG	ARG	PHE	SER	ARG	SER	ASP
3	GLU	LEU	THR	ARG	HIS	ILE	ARG	ILE	HIS	THR
4	GLY	GLN	LYS	PRO	PHE	GLN	CYS	ARG	ILE	CYS
5	MET	ARG	ASN	PHE	SER	ARG	SER	ASP	HIS	LEU
6	THR	THR	HIS	ILE	ARG	THR	HIS	THR	GLY	GLU
7	LYS	PRO	PHE	ALA	CYS	ASP	ILE	CYS	GLY	ARG
8	LYS	PHE	ALA	ARG	SER	ASP	GLU	ARG	LYS	ARG
9	HIS	THR	LYS	ILE	HIS	LEU	ARG	GLN	LYS	ASP

1	PRO	GLU	ARG	PRO	TYR	ALA	CYS	PRO	VAL	GLU
2	SER	CYS	ASP	ARG	ARG	PHE	SER	ARG	SER	ASP
3	GLU	LEU	THR	ARG	HIS	ILE	ARG	ILE	HIS	THR
4	GLY	GLN	LYS	PRO	PHE	GLN	CYS	ARG	ILE	CYS
5	MET	ARG	ASN	PHE	SER	ARG	SER	ASP	HIS	LEU
6	THR	THR	HIS	ILE	ARG	THR	HIS	THR	GLY	GLU
7	LYS	PRO	PHE	ALA	CYS	ASP	ILE	CYS	GLY	ARG
8	LYS	PHE	ALA	ARG	SER	ASP	GLU	ARG	LYS	ARG
9	HIS	THR	LYS	ILE	HIS	LEU	ARG	GLN	LYS	ASP

1	PRO	GLU	ARG	PRO	TYR	ALA	CYS	PRO	VAL	GLU
2	SER	CYS	ASP	ARG	ARG	PHE	SER	ARG	SER	ASP
3	GLU	LEU	THR	ARG	HIS	ILE	ARG	ILE	HIS	THR
4	GLY	GLN	LYS	PRO	PHE	GLN	CYS	ARG	ILE	CYS
5	MET	ARG	ASN	PHE	SER	ARG	SER	ASP	HIS	LEU
6	THR	THR	HIS	ILE	ARG	THR	HIS	THR	GLY	GLU
7	LYS	PRO	PHE	ALA	CYS	ASP	ILE	CYS	GLY	ARG
8	LYS	PHE	ALA	ARG	SER	ASP	GLU	ARG	LYS	ARG
9	HIS	THR	LYS	ILE	HIS	LEU	ARG	GLN	LYS	ASP