5UND: CTCF(ZnF 4-10) With 28-mer DNA

Crystal Structure of CTCF(ZnF 4-10) With 28-mer DNA. Determined by X-ray diffraction at 2.55 Å resolution. Released 24 May 2017.

Method: X-ray diffraction
Resolution: 2.55 Å
Organism: Homo sapiens
Chains: 6
Atoms: 4,723
Mol. weight: 84.15 kDa
Ligands: ZN
Released: 24 May 2017

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

Secondary structure: helices and β-sheets

5UND contains 13 α-helices and 22 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	351-352	2	1
β-strand	359-360	2	1
α-helix	363-374	12
β-strand	379-380	2	2
β-strand	387-388	2	2
α-helix	391-402	12
β-strand	407-408	2	3
β-strand	415-416	2	3
α-helix	419-429	11
β-strand	437-438	2	4
β-strand	445-446	2	4
α-helix	449-459	11
α-helix	462-463	2
β-strand	467-468	2	5
β-strand	475-476	2	5
α-helix	479-488	10
β-strand	495	1	6
β-strand	504	1	6
α-helix	507-514	8

Chain B: 6 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	351-352	2	7
β-strand	359-360	2	7
α-helix	363-374	12
β-strand	379-380	2	8
β-strand	387-388	2	8
α-helix	391-402	12
β-strand	407-408	2	9
β-strand	415-416	2	9
α-helix	419-429	11
α-helix	434-436	3
β-strand	437-438	2	10
β-strand	445-446	2	10
α-helix	449-459	11
β-strand	467-468	2	11
β-strand	475-476	2	11
α-helix	479-488	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Transcriptional repressor CTCF	A, B	protein	202	Homo sapiens	P49711 (AlphaFold model)
DNA (26-mer)	C, E	DNA	28	Homo sapiens
DNA (26-mer)	D, F	DNA	28	Homo sapiens

Sequence of entity 1 (A, B), FASTA

>5UND_1 Transcriptional repressor CTCF (chains A, B)
GSEKPFKCSMCDYASVEVSKLKRHIRSHTGERPFQCSLCSYASRDTYKLKRHMRTHSGEK
PYECYICHARFTQSGTMKMHILQKHTENVAKFHCPHCDTVIARKSDLGVHLRKQHSYIEQ
GKKCRYCDAVFHERYALIQHQKSHKNEKRFKCDQCDYACRQERHMIMHKRTHTGEKPYAC
SHCDKTFRQKQLLDMHFKRYHD

Sequence of entity 2 (C, E), FASTA

>5UND_2 DNA (26-MER) (chains C, E)
CGCCCCCTGCTGGCCTCTGTGGGCACTG

Sequence of entity 3 (D, F), FASTA

>5UND_3 DNA (26-MER) (chains D, F)
CAGTGCCCACAGAGGCCAGCAGGGGGCG

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	12

Water and common crystallization additives (GOL, EDO) are not listed.

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
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
5YEL 2.96 Å, Crystal structure of CTCF ZFs6-11-gb7CSE

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