8K8D: C/EBPbeta BZIP domain

Crystal structure of C/EBPbeta BZIP domain bound to a high affinity DNA. Determined by X-ray diffraction at 2.2 Å resolution. Released 6 Mar 2024.

Method: X-ray diffraction
Resolution: 2.2 Å
Organisms: Homo sapiens, synthetic construct
Chains: 4
Atoms: 1,688
Mol. weight: 26.2 kDa
Released: 6 Mar 2024

Explore 8K8D in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8K8D contains 2 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: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	272-332	61

Chain B: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	272-331	60

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
CCAAT/enhancer-binding protein beta	A, B	protein	79	Homo sapiens	P17676 (AlphaFold model)
DNA (5'-d(cpaptptpapcpgptpapaptpg)-3')	C, D	DNA	12	synthetic construct

Sequence of entity 1 (A, B), FASTA

>8K8D_1 CCAAT/enhancer-binding protein beta (chains A, B)
GVKSKAKKTVDKHSDEYKIRRERNNIAVRKSRDKAKMRNLETQHKVLELTAENERLQKKV
EQLSRELSTLRNLFKQLPE

Sequence of entity 2 (C, D), FASTA

>8K8D_2 DNA (5'-D(*CP*AP*TP*TP*AP*CP*GP*TP*AP*AP*TP*G)-3') (chains C, D)
CATTACGTAATG

Primary citation

Structural basis for specific DNA sequence recognition by the transcription factor NFIL3. Chen, S., Lei, M., Liu, K. et al. J Biol Chem (2024) 300:105776-105776. DOI 10.1016/j.jbc.2024.105776 · 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…
1H8A 2.23 Å, Crystal structure of ternary protein-DNA COMPLEX3
1H89 2.45 Å, Crystal structure of ternary protein-DNA COMPLEX2
7UPZ 2.49 Å, Structural basis for cell type specific DNA binding of C/EBPbeta: the case of cell cycle…

Browse structure collections

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