1HJB: Ccaat/enhancer binding protein beta

Crystal structure of runx-1/AML1/CBFALPHA runt domain and c/ebpbeta bzip homodimer bound to a DNA fragment from the csf-1R promoter. Determined by X-ray diffraction at 3.0 Å resolution. Released 9 Mar 2001.

Method: X-ray diffraction
Resolution: 3.0 Å
Organisms: HOMO SAPIENS, MUS MUSCULUS
Chains: 10
Atoms: 6,270
Mol. weight: 100.38 kDa
Released: 9 Mar 2001

Explore 1HJB in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1HJB contains 6 α-helices and 26 β-strands across 6 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

Chains B, D and E: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	272-333	62

Chain C: 1 helix, 12 β-strands

Element	Residues	Length	Sheet
β-strand	62-64	3	1
β-strand	70-73	4	1
β-strand	78-80	3	2
β-strand	90-93	4	1
β-strand	102-108	7	3
β-strand	117-118	2	4
β-strand	121-123	3	3
β-strand	128-130	3	1
β-strand	135-136	2	4
β-strand	146-152	7	3
β-strand	158-166	9	3
β-strand	167-169	3	2
α-helix	175-177	3

Chain F: 1 helix, 14 β-strands

Element	Residues	Length	Sheet
β-strand	62-64	3	5
β-strand	70-73	4	5
β-strand	78-80	3	6
β-strand	89-93	5	5
β-strand	102-108	7	7
β-strand	115	1	7
β-strand	117-118	2	8
β-strand	121-123	3	7
β-strand	125	1	5
β-strand	128-131	4	5
β-strand	135-136	2	8
β-strand	147-152	6	7
β-strand	158-162	5	7
β-strand	167-169	3	6
α-helix	175-177	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ccaat/enhancer binding protein beta	A, B, D, E	protein	87	HOMO SAPIENS	P17676 (AlphaFold model)
Runt-related transcription factor 1	C, F	protein	123	MUS MUSCULUS	Q03347 (AlphaFold model)
DNA (5'-(gpapapgpaptptptpcpcp* apapapcptpcptpgptpgpgptptpgpcp*g)-3')	G, I	DNA	26	HOMO SAPIENS
DNA (5'-(cpcpgpcpapapcpcpapcp* apgpapgptptptpgpgpapapaptpcptp*t)-3')	H, J	DNA	26	HOMO SAPIENS

Sequence of entity 1 (A, B, D, E), FASTA

>1HJB_1 CCAAT/ENHANCER BINDING PROTEIN BETA (chains A, B, D, E)
VKSKAKKTVDKHSDEYKIRRERNNIAVRKSRDKAKMRNLETQHKVLELTAENERLQKKVE
QLSRELSTLRNLFKQLPEPLLASSGHC

Sequence of entity 2 (C, F), FASTA

>1HJB_2 RUNT-RELATED TRANSCRIPTION FACTOR 1 (chains C, F)
GELVRTDSPNFLCSVLPTHWRCNKTLPIAFKVVALGDVPDGTLVTVMAGNDENYSAELRN
ATAAMKNQVARFNDLRFVGRSGRGKSFTLTITVFTNPPQVATYHRAIKITVDGPREPRRH
RQK

Sequence of entity 3 (G, I), FASTA

>1HJB_3 DNA (5'-(*GP*AP*AP*GP*AP*TP*TP*TP*CP*CP* AP*AP*AP*CP*TP*CP*TP*GP*TP*GP*GP*TP*TP*GP*CP*G)-3') (chains G, I)
GAAGATTTCCAAACTCTGTGGTTGCG

Sequence of entity 4 (H, J), FASTA

>1HJB_4 DNA (5'-(*CP*CP*GP*CP*AP*AP*CP*CP*AP*CP* AP*GP*AP*GP*TP*TP*TP*GP*GP*AP*AP*AP*TP*CP*TP*T)-3') (chains H, J)
CCGCAACCACAGAGTTTGGAAATCTT

Primary citation

Structural Analyses of DNA Recognition by the Aml1/Runx-1 Runt Domain and its Allosteric Control by Cbfbeta. Tahirov, T.H., Inoue-Bungo, T., Morii, H. et al. Cell (2001) 104:755. DOI 10.1016/S0092-8674(01)00271-9 · 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

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