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

ZnFs 3-11 of CCCTC-binding factor (CTCF) Complexed with 35mer DNA 35-20. Determined by X-ray diffraction at 3.14 Å resolution. Released 2 Aug 2023.

Method: X-ray diffraction
Resolution: 3.14 Å
Organism: Homo sapiens
Chains: 6
Atoms: 6,926
Mol. weight: 112.34 kDa
Ligands: ZN
Released: 2 Aug 2023

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

Secondary structure: helices and β-sheets

8SSR contains 21 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: 11 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	352	1	2
β-strand	359	1	2
α-helix	363-374	12
β-strand	379-380	2	3
β-strand	387-388	2	3
α-helix	391-402	12
β-strand	407-408	2	4
β-strand	415-416	2	4
α-helix	419-429	11
β-strand	437-438	2	5
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	567-574	8

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	363-373	11
β-strand	379-380	2	11
β-strand	387-388	2	11
α-helix	391-397	7
α-helix	399-402	4
β-strand	407-408	2	12
β-strand	415-416	2	12
α-helix	419-430	12
α-helix	434-436	3
β-strand	437-438	2	13
β-strand	445-446	2	13
α-helix	450-459	10
β-strand	462-468	7	14
β-strand	475-478	4	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	536-545	10
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 II	C, F	DNA	35	Homo sapiens

Sequence of entity 1 (A, D), FASTA

>8SSR_1 Transcriptional repressor CTCF (chains A, D)
TRPHKCPDCDMAFVTSGELVRHRRYKHTHEKPFKCSMCDYASVEVSKLKRHIRSHTGERP
FQCSLCSYASRDTYKLKRHMRTHSGEKPYECYICHARFTQSGTMKMHILQKHTENVAKFH
CPHCDTVIARKSDLGVHLRKQHSYIEQGKKCRYCDAVFHERYALIQHQKSHKNEKRFKCD
QCDYACRQERHMIMHKRTHTGEKPYACSHCDKTFRQKQLLDMHFKRYHDPNFVPAAFVCS
KCGKTFTRRNTMARHADNCAGPDGVEGENGGETKKSKRGRKRKMRSKK

Sequence of entity 2 (B, E), FASTA

>8SSR_2 DNA (35-MER) Strand I (chains B, E)
TTAGCGCCACCTGCTGGTTAAATGTGGTACTGCAC

Sequence of entity 3 (C, F), FASTA

>8SSR_3 DNA (35-MER) Strand II (chains C, F)
GTGCAGTACCACATTTAACCAGCAGGTGGCGCTAA

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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