5YEF: CTCF ZFs2-8-Hs5-1aE

Crystal structure of CTCF ZFs2-8-Hs5-1aE. Determined by X-ray diffraction at 2.81 Å resolution. Released 29 Nov 2017.

Method: X-ray diffraction
Resolution: 2.81 Å
Organisms: Homo sapiens, synthetic construct
Chains: 12
Atoms: 9,727
Mol. weight: 163.43 kDa
Ligands: ZN
Released: 29 Nov 2017

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

Secondary structure: helices and β-sheets

5YEF contains 25 α-helices and 40 β-strands across 4 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: 6 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	334-344	11
β-strand	351-352	2	1
β-strand	359-360	2	1
α-helix	363-374	12
β-strand	380	1	2
β-strand	387	1	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
β-strand	462-468	7	5
β-strand	475-478	4	5
α-helix	479-485	7

Chain B: 6 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	338-344	7
β-strand	351-352	2	6
β-strand	359-360	2	6
α-helix	363-374	12
β-strand	380	1	7
β-strand	387	1	7
α-helix	391-402	12
β-strand	407-408	2	8
β-strand	415-416	2	8
α-helix	419-429	11
β-strand	437-438	2	9
β-strand	445-446	2	9
α-helix	449-459	11
β-strand	467-468	2	10
β-strand	475-476	2	10
α-helix	479-485	7

Chain G: 7 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	335-340	6
α-helix	341-345	5
β-strand	351-352	2	11
β-strand	359-360	2	11
α-helix	363-374	12
β-strand	380	1	12
β-strand	387	1	12
α-helix	391-402	12
β-strand	407-408	2	13
β-strand	415-416	2	13
α-helix	419-429	11
β-strand	437-438	2	14
β-strand	445-446	2	14
α-helix	449-459	11
β-strand	462-468	7	15
β-strand	475-478	4	15
α-helix	479-485	7

Chain J: 6 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	338-344	7
β-strand	351-352	2	16
β-strand	359-360	2	16
α-helix	363-374	12
β-strand	380	1	17
β-strand	387	1	17
α-helix	391-402	12
β-strand	407-408	2	18
β-strand	415-416	2	18
α-helix	419-429	11
β-strand	437-438	2	19
β-strand	445-446	2	19
α-helix	449-459	11
β-strand	462-468	7	20
β-strand	475-478	4	20
α-helix	479-485	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Transcriptional repressor CTCF	A, B, G, J	protein	199	Homo sapiens	P49711 (AlphaFold model)
DNA (27-mer)	C, E, H, K	DNA	27	synthetic construct
DNA (27-mer)	D, F, I, L	DNA	28	synthetic construct

Sequence of entity 1 (A, B, G, J), FASTA

>5YEF_1 Transcriptional repressor CTCF (chains A, B, G, J)
RPHKCHLCGRAFRTVTLLRNHLNTHTGTRPHKCPDCDMAFVTSGELVRHRRYKHTHEKPF
KCSMCDYASVEVSKLKRHIRSHTGERPFQCSLCSYASRDTYKLKRHMRTHSGEKPYECYI
CHARFTQSGTMKMHILQKHTENVAKFHCPHCDTVIARKSDLGVHLRKQHSYIEQGKKCRY
CDAVFHERYALIQHQKSHK

Sequence of entity 2 (C, E, H, K), FASTA

>5YEF_2 DNA (27-MER) (chains C, E, H, K)
AGTCGACTCGCCCTCTGCTGGTTAAAG

Sequence of entity 3 (D, F, I, L), FASTA

>5YEF_3 DNA (27-MER) (chains D, F, I, L)
ACTTTAACCAGCAGAGGGCGAGTCGACT

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	24

Primary citation

Molecular mechanism of directional CTCF recognition of a diverse range of genomic sites. Yin, M., Wang, J., Wang, M. et al. Cell Res (2017) 27:1365-1377. DOI 10.1038/cr.2017.131 · 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
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

Browse structure collections

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