8SSS: ZnFs 1-7 of CCCTC-binding factor

ZnFs 1-7 of CCCTC-binding factor (CTCF) Complexed with 23mer. Determined by X-ray diffraction at 2.3 Å resolution. Released 2 Aug 2023.

Method: X-ray diffraction
Resolution: 2.3 Å
Organism: Homo sapiens
Chains: 6
Atoms: 5,151
Mol. weight: 77.3 kDa
Ligands: ZN
Released: 2 Aug 2023

Explore 8SSS in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8SSS contains 18 α-helices and 28 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: 9 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	266-267	2	1
β-strand	274-275	2	1
α-helix	279-285	7
α-helix	286-288	3
β-strand	294-295	2	2
β-strand	302-303	2	2
α-helix	306-317	12
β-strand	322-323	2	3
β-strand	330-331	2	3
α-helix	334-341	8
α-helix	342-346	5
β-strand	351-352	2	4
β-strand	359-360	2	4
α-helix	363-374	12
β-strand	379-380	2	5
β-strand	387-388	2	5
α-helix	391-402	12
β-strand	407-408	2	6
β-strand	415-416	2	6
α-helix	419-430	12
β-strand	437-438	2	7
β-strand	445-446	2	7
α-helix	449-459	11

Chain D: 9 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	266-267	2	8
β-strand	274-275	2	8
α-helix	279-285	7
β-strand	294-295	2	9
β-strand	302-303	2	9
α-helix	306-317	12
β-strand	322-323	2	10
β-strand	330-331	2	10
α-helix	334-341	8
α-helix	342-346	5
β-strand	351-352	2	11
β-strand	359-360	2	11
α-helix	363-374	12
β-strand	379-380	2	12
β-strand	387-388	2	12
α-helix	391-402	12
β-strand	407-408	2	13
β-strand	415-416	2	13
α-helix	419-430	12
β-strand	437-438	2	14
α-helix	439	1
β-strand	445-446	2	14
α-helix	449-460	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Transcriptional repressor CTCF	A, D	protein	203	Homo sapiens	P49711 (AlphaFold model)
DNA Strand (23mer) I	B, E	DNA	23	Homo sapiens
DNA Strand (23mer) II	C, F	DNA	23	Homo sapiens

Sequence of entity 1 (A, D), FASTA

>8SSS_1 Transcriptional repressor CTCF (chains A, D)
KKTFQCELCSYTCPRRSNLDRHMKSHTDERPHKCHLCGRAFRTVTLLRNHLNTHTGTRPH
KCPDCDMAFVTSGELVRHRRYKHTHEKPFKCSMCDYASVEVSKLKRHIRSHTGERPFQCS
LCSYASRDTYKLKRHMRTHSGEKPYECYICHARFTQSGTMKMHILQKHTENVAKFHCPHC
DTVIARKSDLGVHLRKQHSYIEQ

Sequence of entity 2 (B, E), FASTA

>8SSS_2 DNA Strand (23mer) I (chains B, E)
CCTCACTAGCGCCCCCTGCTGGC

Sequence of entity 3 (C, F), FASTA

>8SSS_3 DNA Strand (23mer) II (chains C, F)
GCCAGCAGGGGGCGCTAGTGAGG

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	14

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

Primary citation

Structures of CTCF-DNA complexes including all 11 zinc fingers. Yang, J., Horton, J.R., Liu, B. et al. Nucleic Acids Res (2023) 51:8447-8462. DOI 10.1093/nar/gkad594 · 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…
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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