5K5L: Transcriptional repressor CTCF

Homo sapiens CCCTC-binding factor (CTCF) ZnF6-8 and H19 sequence DNA complex structure. Determined by X-ray diffraction at 3.13 Å resolution. Released 24 May 2017.

Method: X-ray diffraction
Resolution: 3.13 Å
Organisms: synthetic construct, Homo sapiens
Chains: 7
Atoms: 2,507
Mol. weight: 46.59 kDa
Ligands: ZN
Released: 24 May 2017

Explore 5K5L in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5K5L contains 11 α-helices and 12 β-strands across 3 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 E: 3 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	437-438	2	1
β-strand	445-446	2	1
α-helix	449-460	12
β-strand	467-468	2	2
β-strand	475-476	2	2
α-helix	479-487	9
α-helix	488-490	3

Chain F: 3 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	438	1	3
β-strand	445	1	3
α-helix	450-459	10
α-helix	461	1
β-strand	462-468	7	4
β-strand	475-478	4	4
α-helix	479-490	12

Chain G: 5 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	419-428	10
α-helix	431-433	3
β-strand	437-438	2	5
β-strand	445-446	2	5
α-helix	449-459	11
α-helix	461-463	3
β-strand	467-468	2	6
β-strand	475-476	2	6
α-helix	479-488	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
DNA (5'-d(gptptpgpcpcpgpcpgptp*g)-3')	A, C	DNA	11	synthetic construct
DNA (5'-d(papcpgpcpgpgpcpapapc)-3')	B, D	DNA	11	synthetic construct
Transcriptional repressor CTCF	E, F, G	protein	93	Homo sapiens	P49711 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>5K5L_1 DNA (5'-D(*GP*TP*TP*GP*CP*CP*GP*CP*GP*TP*G)-3') (chains A, C)
GTTGCCGCGTG

Sequence of entity 2 (B, D), FASTA

>5K5L_2 DNA (5'-D(P*AP*CP*GP*CP*GP*GP*CP*AP*AP*C)-3') (chains B, D)
CACGCGGCAAC

Sequence of entity 3 (E, F, G), FASTA

>5K5L_3 Transcriptional repressor CTCF (chains E, F, G)
GPLGSKPYECYICHARFTQSGTMKMHILQKHTENVAKFHCPHCDTVIARKSDLGVHLRKQ
HSYIEQGKKCRYCDAVFHERYALIQHQKSHKNE

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	7

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

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