BMRB Entry 17130

Name: Zif 268 with 12bp DNA
Published: 2010-09-24

Chem Shift validation: AVS_anomalous, AVS_full
BMRB Entry DOI: doi:10.13018/BMR17130

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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:

Zif 268 with 12bp DNA

Deposition date:

2010-08-16

Original release date:

2010-09-24

Authors:

Takayama, Yuki; Sahu, Debashish

Citation:

Citation: Takayama, Yuki; Sahu, Debashish; Iwahara, Junji. "NMR studies of translocation of the Zif268 protein between its target DNA Sites." Biochemistry 49, 7998-8005 (2010).
PubMed: 20718505

Assembly members:

Assembly members:
zif268, polymer, 90 residues, Formula weight is not available
12bp_DNA, polymer, 24 residues, Formula weight is not available
ZN, non-polymer, 65.409 Da.

Natural source:

Natural source: Common Name: house mouse Taxonomy ID: 10090 Superkingdom: Eukaryota Kingdom: Metazoa Genus/species: Mus musculus

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli Vector: pET49b+zif268

Entity Sequences (FASTA):

Entity Sequences (FASTA):
zif268: PERPYACPVESCDRRFSRSD ELTRHIRIHTGQKPFQCRIC MRNFSRSDHLTTHIRTHTGE KPFACDICGRKFARSDERKR HTKIHLRQKD
12bp_DNA: AGCGTGGGCGTATACGCCCA CGCA

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	175
15N chemical shifts	82
1H chemical shifts	82

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
Hide all

Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	zif268	1
2	zinc1	3
3	zinc2	3
4	zinc3	3
5	12bp DNA	2

Entities:

Entity 1, zif268 90 residues - Formula weight is not available

zinc finger domains, amino acids 333-421 from the egr1 sequence (uniprot ID: P08046)

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 3, zinc1 - Zn - 65.409 Da.

1

ZN

Entity 2, 12bp DNA 24 residues - Formula weight is not available

1

DA

DG

DC

DG

DT

DG

DC

DG

2

DT

DA

DT

DA

DC

DG

DC

DA

3

DC

DG

DC

DA

Samples:

sample_1: TRIS 10 mM; potassium chloride 20 mM; zif268, [U-13C; U-15N], 1 mM; 12bp DNA 1.2 mM; H2O 93%; D2O 7%

sample_conditions_1: ionic strength: 20 mM; pH: 6.8; pressure: 1 atm; temperature: 273 K

Experiments:

Name	Sample	Sample state	Sample conditions
3D HNCACO	sample_1	isotropic	sample_conditions_1
3D HNCO	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 C(CO)NH	sample_1	isotropic	sample_conditions_1
3D H(CACO)NH	sample_1	isotropic	sample_conditions_1
15N Edited NOESY-HSQC	sample_1	isotropic	sample_conditions_1

Software:

NMRView, Johnson, One Moon Scientific - chemical shift assignment

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

NMR spectrometers:

Varian INOVA 600 MHz
Varian Uniform NMR System 800 MHz

PDB	1A1I 1A1J 1A1K 1A1L 1AAY 1JK1 1JK2 1P47 1ZAA 4R2A 4R2C 4R2D 4X9J
DBJ	BAC29885 BAC30748 BAE21758 BAE26289 BAE27077
EMBL	CAA36777 CAB46678 CAB60137 CAG31294 CDQ66955
GB	AAA35815 AAA37544 AAA39382 AAA40416 AAA60740
REF	NP_001039340 NP_001074426 NP_001083862 NP_001084566 NP_001090830
SP	A4II20 O73691 O73692 O73693 P08046
TPG	DAA27412
AlphaFold	A4II20 O73691 O73692 O73693 P08046

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