7UPZ: CCAAT/enhancer-binding protein beta

Structural basis for cell type specific DNA binding of C/EBPbeta: the case of cell cycle inhibitor p15INK4b promoter. Determined by X-ray diffraction at 2.49 Å resolution. Released 23 Nov 2022.

Method: X-ray diffraction
Resolution: 2.49 Å
Organism: Homo sapiens
Chains: 4
Atoms: 1,884
Mol. weight: 28.99 kDa
Released: 23 Nov 2022

Explore 7UPZ in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7UPZ contains 3 α-helices and 0 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: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	273-328	56
α-helix	329-331	3

Chain B: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	273-332	60

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
CCAAT/enhancer-binding protein beta	A, B	protein	80	Homo sapiens	P17676 (AlphaFold model)
DNA (5'-d(aptptpcptptpapapgpapapapgpapcpg)-3')	C	DNA	16	Homo sapiens
DNA (5'-d(tpcpgptpcptptptpcptptpapapgpapa)-3')	D	DNA	16	Homo sapiens

Sequence of entity 1 (A, B), FASTA

>7UPZ_1 CCAAT/enhancer-binding protein beta (chains A, B)
SQVKSKAKKTVDKHSDEYKIRRERNNIAVRKSRDKAKMRNLETQHKVLELTAENERLQKK
VEQLSRELSTLRNLFKQLPE

Sequence of entity 2 (C), FASTA

>7UPZ_2 DNA (5'-D(*AP*TP*TP*CP*TP*TP*AP*AP*GP*AP*AP*AP*GP*AP*CP*G)-3') (chains C)
ATTCTTAAGAAAGACG

Sequence of entity 3 (D), FASTA

>7UPZ_3 DNA (5'-D(*TP*CP*GP*TP*CP*TP*TP*TP*CP*TP*TP*AP*AP*GP*AP*A)-3') (chains D)
TCGTCTTTCTTAAGAA

Primary citation

Structural basis for cell type specific DNA binding of C/EBP beta : The case of cell cycle inhibitor p15INK4b promoter. Lountos, G.T., Cherry, S., Tropea, J.E. et al. J Struct Biol (2022) 214:107918-107918. DOI 10.1016/j.jsb.2022.107918 · PubMed

Other PDB entries of the same protein (UniProt P17676 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6MG1 1.75 Å, C-terminal bZIP domain of human C/EBPbeta with 16bp Methylated Oligonucleotide…
7L4V 1.75 Å, C-terminal bZIP domain of human C/EBPbeta Bound to DNA with Consensus Recognition with…
1GU4 1.8 Å, Crystal structure of C/EBPBETA BZIP homodimer bound to a high affinity DNA fragment
2E42 1.8 Å, Crystal structure of C/EBPbeta Bzip homodimer V285A mutant bound to A High Affinity DNA…
1GTW 1.85 Å, crystal structure of C/EBPbeta bZip homodimer bound to a DNA fragment from the tom-1A…
6MG2 1.93 Å, C-terminal bZIP domain of human C/EBPbeta with 16bp Methylated Oligonucleotide…
6MG3 2.05 Å, V285A Mutant of the C-terminal bZIP domain of human C/EBPbeta with 16bp Methylated…
1GU5 2.1 Å, Crystal structure of C/EBPBETA BZIP homodimer bound to a DNA fragment from the MIM-1…
2E43 2.1 Å, Crystal structure of C/EBPbeta Bzip homodimer K269A mutant bound to A High Affinity DNA…
8K8D 2.2 Å, Crystal structure of C/EBPbeta BZIP domain bound to a high affinity DNA
1H8A 2.23 Å, Crystal structure of ternary protein-DNA COMPLEX3
1H89 2.45 Å, Crystal structure of ternary protein-DNA COMPLEX2

Browse structure collections

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