5YEL: CTCF ZFs6-11-gb7CSE

Crystal structure of CTCF ZFs6-11-gb7CSE. Determined by X-ray diffraction at 2.96 Å resolution. Released 29 Nov 2017.

Method: X-ray diffraction
Resolution: 2.96 Å
Organisms: synthetic construct, Homo sapiens
Chains: 6
Atoms: 4,772
Mol. weight: 74.58 kDa
Ligands: ZN
Released: 29 Nov 2017

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

Secondary structure: helices and β-sheets

5YEL contains 19 α-helices and 18 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, 8 β-strands

Element	Residues	Length	Sheet
α-helix	419-428	10
β-strand	438	1	1
β-strand	445	1	1
α-helix	449-459	11
β-strand	462-468	7	2
α-helix	469	1
β-strand	475-478	4	2
α-helix	479-486	8
β-strand	495-496	2	3
β-strand	503-504	2	3
α-helix	507-517	11
β-strand	523-524	2	4
β-strand	531-532	2	4
α-helix	536-540	5
α-helix	541-545	5
α-helix	567-575	9

Chain B: 11 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	408	1	5
β-strand	415	1	5
α-helix	419-428	10
β-strand	438	1	6
β-strand	445	1	6
α-helix	449-458	10
α-helix	462-463	2
α-helix	466	1
β-strand	467-468	2	7
α-helix	469	1
β-strand	475-476	2	7
α-helix	479-486	8
α-helix	487-489	3
β-strand	495-496	2	8
β-strand	503-504	2	8
α-helix	507-517	11
β-strand	524	1	9
β-strand	531	1	9
α-helix	536-539	4
α-helix	540-545	6
α-helix	567-575	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
DNA (26-mer)	D, F	DNA	26	synthetic construct
Transcriptional repressor CTCF	A, B	protein	176	Homo sapiens	P49711 (AlphaFold model)
DNA (26-mer)	C, E	DNA	26	synthetic construct

Sequence of entity 1 (D, F), FASTA

>5YEL_1 DNA (26-MER) (chains D, F)
ATTGCAGTACCACATTTAACCAGCAG

Sequence of entity 2 (A, B), FASTA

>5YEL_2 Transcriptional repressor CTCF (chains A, B)
KPYECYICHARFTQSGTMKMHILQKHTENVAKFHCPHCDTVIARKSDLGVHLRKQHSYIE
QGKKCRYCDAVFHERYALIQHQKSHKNEKRFKCDQCDYASRQERHMIMHKRTHTGEKPYA
CSHCDKTFRQKQLLDMHFKRYHDPNFVPAAFVCSKCGKTFTRRNTMARHADNCAGP

Sequence of entity 3 (C, E), FASTA

>5YEL_3 DNA (26-MER) (chains C, E)
TCTGCTGGTTAAATGTGGTACTGCAA

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	12

Primary citation

Molecular mechanism of directional CTCF recognition of a diverse range of genomic sites. Yin, M., Wang, J., Wang, M. et al. Cell Res (2017) 27:1365-1377. DOI 10.1038/cr.2017.131 · 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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