8SSQ: ZnFs 3-11 of CCCTC-binding factor

ZnFs 3-11 of CCCTC-binding factor (CTCF) Complexed with 35mer DNA 35-4. Determined by X-ray diffraction at 3.12 Å resolution. Released 2 Aug 2023.

Method: X-ray diffraction
Resolution: 3.12 Å
Organism: Homo sapiens
Chains: 6
Atoms: 6,941
Mol. weight: 112.34 kDa
Ligands: ZN
Released: 2 Aug 2023

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

Secondary structure: helices and β-sheets

8SSQ contains 23 α-helices and 34 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: 13 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	322-323	2	1
β-strand	330-331	2	1
α-helix	334-341	8
α-helix	342-346	5
β-strand	351-352	2	2
β-strand	359-360	2	2
α-helix	363-374	12
β-strand	379-380	2	3
β-strand	387-388	2	3
α-helix	391-397	7
α-helix	399-402	4
β-strand	407-408	2	4
β-strand	415-416	2	4
α-helix	419-429	11
β-strand	437-438	2	5
α-helix	439	1
β-strand	445-446	2	5
α-helix	449-458	10
β-strand	462-468	7	6
β-strand	475-478	4	6
α-helix	479-486	8
α-helix	487-489	3
β-strand	495-496	2	7
β-strand	503-504	2	7
α-helix	507-518	12
β-strand	523-524	2	8
β-strand	531-532	2	8
α-helix	535-545	11
β-strand	555-556	2	9
β-strand	563-564	2	9
α-helix	567-576	10

Chain D: 10 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	351-352	2	10
β-strand	359-360	2	10
α-helix	363-374	12
β-strand	379-380	2	11
β-strand	387-388	2	11
α-helix	391-402	12
β-strand	407-408	2	12
β-strand	415-416	2	12
α-helix	419-429	11
α-helix	436	1
β-strand	437-438	2	13
α-helix	439	1
β-strand	445-446	2	13
α-helix	450-459	10
β-strand	467-468	2	14
β-strand	475-476	2	14
α-helix	479-489	11
β-strand	495-496	2	15
β-strand	503-504	2	15
α-helix	507-516	10
β-strand	523-524	2	16
β-strand	531-532	2	16
α-helix	535-545	11
β-strand	555-556	2	17
β-strand	563-564	2	17
α-helix	567-575	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Transcriptional repressor CTCF	A, D	protein	288	Homo sapiens	P49711 (AlphaFold model)
DNA (35-MER) Strand I	B, E	DNA	35	Homo sapiens
DNA (35-MER) Strand 2	C, F	DNA	35	Homo sapiens

Sequence of entity 1 (A, D), FASTA

>8SSQ_1 Transcriptional repressor CTCF (chains A, D)
TRPHKCPDCDMAFVTSGELVRHRRYKHTHEKPFKCSMCDYASVEVSKLKRHIRSHTGERP
FQCSLCSYASRDTYKLKRHMRTHSGEKPYECYICHARFTQSGTMKMHILQKHTENVAKFH
CPHCDTVIARKSDLGVHLRKQHSYIEQGKKCRYCDAVFHERYALIQHQKSHKNEKRFKCD
QCDYACRQERHMIMHKRTHTGEKPYACSHCDKTFRQKQLLDMHFKRYHDPNFVPAAFVCS
KCGKTFTRRNTMARHADNCAGPDGVEGENGGETKKSKRGRKRKMRSKK

Sequence of entity 2 (B, E), FASTA

>8SSQ_2 DNA (35-MER) Strand I (chains B, E)
TTAGCGCCCCCTGCTGGTTAAATGTGGTACTGCAC

Sequence of entity 3 (C, F), FASTA

>8SSQ_3 DNA (35-MER) Strand 2 (chains C, F)
GTGCAGTACCACATTTAACCAGCAGGGGGCGCTAA

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	17

Water and common crystallization additives (NA) 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…
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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