1P47: Tandem Zif268 molecules complexed to DNA

Crystal Structure of tandem Zif268 molecules complexed to DNA. Determined by X-ray diffraction at 2.2 Å resolution. Released 24 Jun 2003.

Method: X-ray diffraction
Resolution: 2.2 Å
Organism: Mus musculus
Chains: 4
Atoms: 2,433
Mol. weight: 34.86 kDa
Ligands: ZN
Released: 24 Jun 2003

Explore 1P47 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1P47 contains 7 α-helices and 12 β-strands across 2 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 4 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	105-106	2	1
β-strand	115-116	2	1
α-helix	119-126	8
β-strand	135-136	2	2
β-strand	143-144	2	2
α-helix	147-158	12
β-strand	163-164	2	3
β-strand	171-172	2	3
α-helix	175-182	8
α-helix	183-186	4

Chain B: 3 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	105-106	2	4
β-strand	115-116	2	4
α-helix	119-130	12
β-strand	135-136	2	5
β-strand	143-144	2	5
α-helix	147-158	12
β-strand	164	1	6
β-strand	171	1	6
α-helix	175-182	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
5'-d(gptpgpgpcpgptpgpgpgpcpgpgpcpgptpgpgpgpcpgpt)-3'	C	DNA	22
5'-d(cpapcpgpcpcpcpapcpgpcpcpgpcpcpcpapcpgpcpcpa)-3'	D	DNA	22
Early growth response protein 1	A, B	protein	87	Mus musculus	P08046 (AlphaFold model)

Sequence of entity 1 (C), FASTA

>1P47_1 5'-D(*GP*TP*GP*GP*CP*GP*TP*GP*GP*GP*CP*GP*GP*CP*GP*TP*GP*GP*GP*CP*GP*T)-3' (chains C)
GTGGCGTGGGCGGCGTGGGCGT

Sequence of entity 2 (D), FASTA

>1P47_2 5'-D(*CP*AP*CP*GP*CP*CP*CP*AP*CP*GP*CP*CP*GP*CP*CP*CP*AP*CP*GP*CP*CP*A)-3' (chains D)
CACGCCCACGCCGCCCACGCCA

Sequence of entity 3 (A, B), FASTA

>1P47_3 Early growth response protein 1 (chains A, B)
ERPYACPVESCDRRFSRSDELTRHIRIHTGQKPFQCRICMRNFSRSDHLTTHIRTHTGEK
PFACDICGRKFARSDERKRHTKIHLRQ

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	6

Primary citation

Constraints for Zinc Finger Linker Design as Inferred from X-ray Crystal Structure of Tandem Zif268-DNA Complexes. Peisach, E., Pabo, C.O. J Mol Biol (2003) 330:1-7. DOI 10.1016/S0022-2836(03)00572-2 · PubMed

Other PDB entries of the same protein (UniProt P08046 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1LLM 1.5 Å, Crystal Structure of a Zif23-GCN4 Chimera Bound to DNA
1A1H 1.6 Å, Qgsr (ZIF268 variant) zinc finger-DNA complex (gcac site)
1A1I 1.6 Å, Radr (ZIF268 variant) zinc finger-DNA complex (gcac site)
1AAY 1.6 Å, ZIF268 zinc finger-DNA complex
1JK2 1.65 Å, Zif268 D20A mutant bound to the GCT DNA site
1A1G 1.9 Å, Dsnr (ZIF268 variant) zinc finger-DNA complex (gcgt site)
1A1K 1.9 Å, Radr (ZIF268 variant) zinc finger-DNA complex (gacc site)
1JK1 1.9 Å, Zif268 D20A Mutant Bound to WT DNA Site
1A1J 2.0 Å, Radr (ZIF268 variant) zinc finger-DNA complex (gcgt site)
1G2F 2.0 Å, Structure of a CYS2HIS2 zinc finger/tata box complex (tatazf;clone #6)
1A1F 2.1 Å, Dsnr (ZIF268 variant) zinc finger-DNA complex (gacc site)
1ZAA 2.1 Å, Zinc finger-DNA recognition: crystal structure of a ZIF268-DNA complex at 2.1 Å

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