5T00: Human CTCF ZnF3-7 and methylated DNA complex

Human CTCF ZnF3-7 and methylated DNA complex. Determined by X-ray diffraction at 2.19 Å resolution. Released 24 May 2017.

Method: X-ray diffraction
Resolution: 2.19 Å
Organisms: Homo sapiens, synthetic construct
Chains: 6
Atoms: 3,832
Mol. weight: 56.63 kDa
Ligands: ZN
Released: 24 May 2017

Explore 5T00 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5T00 contains 15 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: 8 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	322-323	2	1
β-strand	330-331	2	1
α-helix	334-340	7
α-helix	341-346	6
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	419-429	11
α-helix	434-436	3
β-strand	437-438	2	5
β-strand	445-446	2	5
α-helix	449-455	7
α-helix	456-460	5

Chain D: 7 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	323	1	6
β-strand	330	1	6
α-helix	334-340	7
α-helix	341-345	5
β-strand	351-352	2	7
β-strand	359-360	2	7
α-helix	363-374	12
β-strand	379-380	2	8
β-strand	387-388	2	8
α-helix	391-402	12
β-strand	407-408	2	9
β-strand	415-416	2	9
α-helix	419-425	7
α-helix	426-430	5
β-strand	437-438	2	10
β-strand	445-446	2	10
α-helix	449-459	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Transcriptional repressor CTCF	A, D	protein	150	Homo sapiens	P49711 (AlphaFold model)
DNA (5'-TAG(5CM)GCCCCCTGCTGGC-3')	B, E	DNA	17	synthetic construct
DNA (5'-GCCAGCAGGGGG(5CM)GCTA-3')	C, F	DNA	17	synthetic construct

Sequence of entity 1 (A, D), FASTA

>5T00_1 Transcriptional repressor CTCF (chains A, D)
GPLGSPHKCPDCDMAFVTSGELVRHRRYKHTHEKPFKCSMCDYASVEVSKLKRHIRSHTG
ERPFQCSLCSYASRDTYKLKRHMRTHSGEKPYECYICHARFTQSGTMKMHILQKHTENVA
KFHCPHCDTVIARKSDLGVHLRKQHSYIEQ

Sequence of entity 2 (B, E), FASTA

>5T00_2 DNA (5'-TAG(5CM)GCCCCCTGCTGGC-3') (chains B, E)
TAGCGCCCCCTGCTGGC

Sequence of entity 3 (C, F), FASTA

>5T00_3 DNA (5'-GCCAGCAGGGGG(5CM)GCTA-3') (chains C, F)
GCCAGCAGGGGGCGCTA

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	10

Primary citation

Structural Basis for the Versatile and Methylation-Dependent Binding of CTCF to DNA. Hashimoto, H., Wang, D., Horton, J.R. et al. Mol Cell (2017) 66:711-720.e3. DOI 10.1016/j.molcel.2017.05.004 · 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…
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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