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

ZnFs 3-11 of CCCTC-binding factor (CTCF) Complexed with 19mer DNA. Determined by X-ray diffraction at 2.89 Å resolution. Released 2 Aug 2023.

Method: X-ray diffraction
Resolution: 2.89 Å
Organism: Homo sapiens
Chains: 3
Atoms: 2,711
Mol. weight: 52.44 kDa
Ligands: ZN
Released: 2 Aug 2023

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

Secondary structure: helices and β-sheets

8SSU contains 16 α-helices and 16 β-strands across 1 chain. 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: 16 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	321	1
β-strand	322-323	2	1
α-helix	324	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	391-402	12
β-strand	407-408	2	4
β-strand	415-416	2	4
α-helix	419-430	12
α-helix	436	1
β-strand	437-438	2	5
α-helix	439	1
β-strand	445-446	2	5
α-helix	449-455	7
α-helix	456-460	5
α-helix	466	1
β-strand	467-468	2	6
α-helix	469	1
β-strand	475-476	2	6
α-helix	479-487	9
β-strand	495	1	7
β-strand	504	1	7
α-helix	509-516	8
β-strand	523-524	2	8
β-strand	531-532	2	8
α-helix	535-545	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Transcriptional repressor CTCF,LIM domain-binding protein 1	A	protein	345	Homo sapiens	P49711 (AlphaFold model), Q86U70 (AlphaFold model)
DNA (19-MER) Strand I	B	DNA	19	Homo sapiens
DNA (19-MER) Strand II	C	DNA	19	Homo sapiens

Sequence of entity 1 (A), FASTA

>8SSU_1 Transcriptional repressor CTCF,LIM domain-binding protein 1 (chains A)
RPHKCPDCDMAFVTSGELVRHRRYKHTHEKPFKCSMCDYASVEVSKLKRHIRSHTGERPF
QCSLCSYASRDTYKLKRHMRTHSGEKPYECYICHARFTQSGTMKMHILQKHTENVAKFHC
PHCDTVIARKSDLGVHLRKQHSYIEQGKKCRYCDAVFHERYALIQHQKSHKNEKRFKCDQ
CDYACRQERHMIMHKRTHTGEKPYACSHCDKTFRQKQLLDMHFKRYHDPNFVPAAFVCSK
CGKTFTRRNTMARHADNCAGPDGGSGGHMGSGGLVPRGSGGTRCGLSNSTLNYLRLCVIL
EPMQELMSRHKTYSLSPRDCLKTCLFQKWQRMVAPPAEPTRQQPS

Sequence of entity 2 (B), FASTA

>8SSU_2 DNA (19-MER) Strand I (chains B)
TGCGCCCCCTGCTGGTCCT

Sequence of entity 3 (C), FASTA

>8SSU_3 DNA (19-MER) Strand II (chains C)
AGGACCAGCAGGGGGCGCA

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	8

Water and common crystallization additives (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…
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
5YEL 2.96 Å, Crystal structure of CTCF ZFs6-11-gb7CSE

Browse structure collections

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