5YEG: CTCF ZFs4-8-Hs5-1a complex

Crystal structure of CTCF ZFs4-8-Hs5-1a complex. Determined by X-ray diffraction at 2.0 Å resolution. Released 29 Nov 2017.

Method: X-ray diffraction
Resolution: 2.0 Å
Organisms: Homo sapiens, synthetic construct
Chains: 6
Atoms: 4,528
Mol. weight: 59.32 kDa
Ligands: ZN
Released: 29 Nov 2017

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

Secondary structure: helices and β-sheets

5YEG contains 12 α-helices and 20 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: 6 helices, 10 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
α-helix	434-436	3
β-strand	437-438	2	4
β-strand	445-446	2	4
α-helix	449-459	11
β-strand	467-468	2	5
β-strand	475-476	2	5
α-helix	479-486	8

Chain B: 6 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	351-352	2	6
β-strand	359-360	2	6
α-helix	363-374	12
β-strand	379-380	2	7
β-strand	387-388	2	7
α-helix	391-402	12
β-strand	407-408	2	8
β-strand	415-416	2	8
α-helix	419-429	11
α-helix	434-436	3
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	479-487	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Transcriptional repressor CTCF	A	protein	142	Homo sapiens	P49711 (AlphaFold model)
Transcriptional repressor CTCF	B	protein	141	Homo sapiens	P49711 (AlphaFold model)
DNA (5'-d(tpcpgpcpcpcptpcptpgpcptpgpgptptpapapapg)-3')	D, E	DNA	21	synthetic construct
DNA (5'-d(apcptptptpapapcpcpapgpcpapgpapgpgpgpcpg)-3')	C, F	DNA	20	synthetic construct

Sequence of entity 1 (A), FASTA

>5YEG_1 Transcriptional repressor CTCF (chains A)
KPFKCSMCDYASVEVSKLKRHIRSHTGERPFQCSLCSYASRDTYKLKRHMRTHSGEKPYE
CYICHARFTQSGTMKMHILQKHTENVAKFHCPHCDTVIARKSDLGVHLRKQHSYIEQGKK
CRYCDAVFHERYALIQHQKSHK

Sequence of entity 2 (B), FASTA

>5YEG_2 Transcriptional repressor CTCF (chains B)
KPFKCSMCDYASVEVSKLKRHIRSHTGERPFQCSLCSYASRDTYKLKRHMRTHSGEKPYE
CYICHARFTQSGTMKMHILQKHTENVAKFHCPHCDTVIARKSDLGVHLRKQHSYIEQGKK
CRYCDAVFHERYALIQHQKSH

Sequence of entity 3 (D, E), FASTA

>5YEG_3 DNA (5'-D(*TP*CP*GP*CP*CP*CP*TP*CP*TP*GP*CP*TP*GP*GP*TP*TP*AP*AP*AP*G)-3') (chains D, E)
TCGCCCTCTGCTGGTTAAAGT

Sequence of entity 4 (C, F), FASTA

>5YEG_4 DNA (5'-D(*AP*CP*TP*TP*TP*AP*AP*CP*CP*AP*GP*CP*AP*GP*AP*GP*GP*GP*CP*G)-3') (chains C, F)
ACTTTAACCAGCAGAGGGCG

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	10

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

Browse structure collections

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