5T0U: CTCF ZnF2-7 and DNA complex structure

CTCF ZnF2-7 and DNA complex structure. Determined by X-ray diffraction at 3.2 Å resolution. Released 24 May 2017.

Method: X-ray diffraction
Resolution: 3.2 Å
Organisms: Homo sapiens, synthetic construct
Chains: 6
Atoms: 4,663
Mol. weight: 70.48 kDa
Ligands: ZN
Released: 24 May 2017

Explore 5T0U in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5T0U contains 15 α-helices and 24 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: 7 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	294-295	2	1
β-strand	302-303	2	1
α-helix	306-316	11
β-strand	322-323	2	2
β-strand	330-331	2	2
α-helix	334-344	11
β-strand	351-352	2	3
β-strand	359-360	2	3
α-helix	363-374	12
β-strand	379-380	2	4
β-strand	387-388	2	4
α-helix	391-397	7
α-helix	399-402	4
β-strand	407-408	2	5
β-strand	415-416	2	5
α-helix	419-430	12
β-strand	437-438	2	6
β-strand	445-446	2	6
α-helix	449-458	10

Chain D: 8 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	295	1	7
β-strand	302	1	7
α-helix	306-316	11
β-strand	322-323	2	8
β-strand	330-331	2	8
α-helix	334-340	7
α-helix	341-345	5
β-strand	351-352	2	9
β-strand	359-360	2	9
α-helix	363-374	12
β-strand	379-380	2	10
β-strand	387-388	2	10
α-helix	391-397	7
α-helix	399-402	4
β-strand	407-408	2	11
β-strand	415-416	2	11
α-helix	419-429	11
β-strand	437-438	2	12
β-strand	445-446	2	12
α-helix	449-458	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Transcriptional repressor CTCF	A, D	protein	177	Homo sapiens	P49711 (AlphaFold model)
DNA (5'-d(cpcptpcpapcptpapgpcpgpcpcpcpcpcptpgpcptpgpgp*c)-3')	B, E	DNA	23	synthetic construct
DNA (5'-d(gpcpcpapgpcpapgpgpgpgpgpcpgpcptpapgptpgpapgp*g)-3')	C, F	DNA	23	synthetic construct

Sequence of entity 1 (A, D), FASTA

>5T0U_1 Transcriptional repressor CTCF (chains A, D)
PLGSTHKCHLCGRAFRTVTLLRNHLNTHTGTRPHKCPDCDMAFVTSGELVRHRRYKHTHE
KPFKCSMCDYASVEVSKLKRHIRSHTGERPFQCSLCSYASRDTYKLKRHMRTHSGEKPYE
CYICHARFTQSGTMKMHILQKHTENVAKFHCPHCDTVIARKSDLGVHLRKQHSYIEQ

Sequence of entity 2 (B, E), FASTA

>5T0U_2 DNA (5'-D(*CP*CP*TP*CP*AP*CP*TP*AP*GP*CP*GP*CP*CP*CP*CP*CP*TP*GP*CP*TP*GP*GP*C)-3') (chains B, E)
CCTCACTAGCGCCCCCTGCTGGC

Sequence of entity 3 (C, F), FASTA

>5T0U_3 DNA (5'-D(*GP*CP*CP*AP*GP*CP*AP*GP*GP*GP*GP*GP*CP*GP*CP*TP*AP*GP*TP*GP*AP*GP*G)-3') (chains C, F)
GCCAGCAGGGGGCGCTAGTGAGG

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	12

Primary citation

Structural Basis for the Versatile and Methylation-Dependent Binding of CTCF to DNA. Hashimoto, H., Wang, D., Horton, J.R. et al. Mol Cell (2017) 66:711-720.e3. DOI 10.1016/j.molcel.2017.05.004 · PubMed

Other PDB entries of the same protein (UniProt P49711 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5KKQ 1.74 Å, Homo sapiens CCCTC-binding factor (CTCF) ZnF3-7 and DNA complex structure
5YEG 2.0 Å, Crystal structure of CTCF ZFs4-8-Hs5-1a complex
5K5I 2.19 Å, Homo sapiens CCCTC-binding factor (CTCF) ZnF5-8 and DNA complex structure in space group…
5T00 2.19 Å, Human CTCF ZnF3-7 and methylated DNA complex
8SST 2.19 Å, ZnFs 1-7 of CCCTC-binding factor (CTCF) K365T Mutant Complexed with 23mer
5K5J 2.29 Å, Homo sapiens CCCTC-binding factor (CTCF) ZnF5-8 and DNA complex structure in space group…
8SSS 2.3 Å, ZnFs 1-7 of CCCTC-binding factor (CTCF) Complexed with 23mer
5YEH 2.33 Å, Crystal structure of CTCF ZFs4-8-eCBS
5UND 2.55 Å, Crystal Structure of CTCF(ZnF 4-10) With 28-mer DNA
6QNX 2.7 Å, Structure of the SA2/SCC1/CTCF complex
5YEF 2.81 Å, Crystal structure of CTCF ZFs2-8-Hs5-1aE
8SSU 2.89 Å, ZnFs 3-11 of CCCTC-binding factor (CTCF) Complexed with 19mer DNA

Browse structure collections

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