1F2I: PDB entry 1F2I

Cocrystal structure of selected zinc finger dimer bound to DNA. Determined by X-ray diffraction at 2.35 Å resolution. Released 14 Sept 2001.

Method: X-ray diffraction
Resolution: 2.35 Å
Organism: Mus musculus
Chains: 12
Atoms: 5,329
Mol. weight: 79.17 kDa
Ligands: ZN
Released: 14 Sept 2001

Explore 1F2I in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1F2I contains 24 α-helices and 26 β-strands across 6 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 G: 3 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	1099-1101	3
β-strand	1105-1106	2	1
β-strand	1112	1	2
β-strand	1115-1116	2	1
α-helix	1119-1130	12
β-strand	1135-1136	2	3
β-strand	1143-1144	2	3
α-helix	1147-1154	8

Chain H: 5 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	2094-2096	3
α-helix	2099-2101	3
β-strand	2105-2106	2	4
β-strand	2115-2116	2	4
α-helix	2119-2130	12
β-strand	2135-2136	2	5
β-strand	2143-2144	2	5
α-helix	2147-2154	8
α-helix	2155-2157	3

Chain I: 4 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	3094-3096	3
β-strand	3105-3106	2	6
β-strand	3115-3116	2	6
α-helix	3119-3125	7
α-helix	3127-3130	4
β-strand	3135-3136	2	7
β-strand	3143-3144	2	7
α-helix	3147-3155	9

Chain J: 4 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	4094-4096	3
β-strand	4105-4106	2	8
β-strand	4115-4116	2	8
α-helix	4119-4125	7
α-helix	4127-4130	4
β-strand	4135-4136	2	9
β-strand	4143-4144	2	9
α-helix	4147-4154	8

Chain K: 4 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	5099-5101	3
β-strand	5105-5106	2	10
β-strand	5115-5116	2	10
α-helix	5119-5130	12
β-strand	5135-5136	2	11
β-strand	5143-5144	2	11
α-helix	5147-5153	7
α-helix	5154-5156	3

Chain L: 4 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	6094-6096	3
β-strand	6097	1	2
β-strand	6105-6106	2	12
β-strand	6115-6116	2	12
α-helix	6119-6125	7
α-helix	6126-6128	3
β-strand	6135-6136	2	13
β-strand	6143-6144	2	13
α-helix	6147-6151	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
5'-d(aptpgpgpgpcpgpcpgpcpcpcpapt)-3'	A, B, C, D, E, F	DNA	14
Fusion of N-terminal 17-mer peptide extension to ZIF12	G, H, I, J, K, L	protein	73	Mus musculus	P08046 (AlphaFold model)

Sequence of entity 1 (A, B, C, D, E, F), FASTA

>1F2I_1 5'-D(*AP*TP*GP*GP*GP*CP*GP*CP*GP*CP*CP*CP*AP*T)-3' (chains A, B, C, D, E, F)
ATGGGCGCGCCCAT

Sequence of entity 2 (G, H, I, J, K, L), FASTA

>1F2I_2 FUSION OF N-TERMINAL 17-MER PEPTIDE EXTENSION TO ZIF12 (chains G, H, I, J, K, L)
MEPHPMNNLLNYVVPKMRPYACPVESCDRRFSRSDELTRHIRIHTGQKPFQCRICMRNFS
RSDHLTTHIRTHT

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	12

Primary citation

Selected peptide extension contacts hydrophobic patch on neighboring zinc finger and mediates dimerization on DNA. Wang, B.S., Grant, R.A., Pabo, C.O. Nat Struct Biol (2001) 8:589-593. DOI 10.1038/89617 · 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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