1IO4: Caat/enhancer binding protein beta

Crystal structure of runx-1/AML1/CBFALPHA runt domain-cbfbeta core domain heterodimer 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 12 Mar 2001.

Method: X-ray diffraction
Resolution: 3.0 Å
Organisms: Homo sapiens, Mus musculus
Chains: 6
Atoms: 4,197
Mol. weight: 65.66 kDa
Ligands: AU
Released: 12 Mar 2001

Explore 1IO4 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1IO4 contains 9 α-helices and 20 β-strands across 4 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	272-329	58

Chain B: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	273-333	61

Chain C: 3 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	62-64	3	1
β-strand	70-73	4	1
α-helix	74-76	3
β-strand	78-80	3	2
α-helix	83-85	3
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	124-125	2	1
β-strand	128-130	3	1
β-strand	135-136	2	4
β-strand	147-152	6	3
β-strand	158-162	5	3
β-strand	167-169	3	2
α-helix	175-177	3

Chain D: 4 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	8-14	7
α-helix	16-22	7
β-strand	25-29	5	3
α-helix	37-50	14
β-strand	52-57	6	3
β-strand	63-67	5	3
β-strand	86-87	2	3
β-strand	95-103	9	3
β-strand	107-115	9	3
β-strand	120-126	7	3
α-helix	129-138	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Csf-1R promoter	E	DNA	26
Csf-1R promoter	F	DNA	26
Caat/enhancer binding protein beta	A, B	protein	78	Homo sapiens	P17676 (AlphaFold model)
Runt-related transcription factor 1	C	protein	123	Mus musculus	Q03347 (AlphaFold model)
Core-binding factor, beta subunit	D	protein	141	Mus musculus	Q08024 (AlphaFold model)

Sequence of entity 1 (E), FASTA

>1IO4_1 CSF-1R PROMOTER (chains E)
GAAGATTTCCAAACTCTGTGGTTGCG

Sequence of entity 2 (F), FASTA

>1IO4_2 CSF-1R PROMOTER (chains F)
CCGCAACCACAGAGTTTGGAAATCTT

Sequence of entity 3 (A, B), FASTA

>1IO4_3 CAAT/ENHANCER BINDING PROTEIN BETA (chains A, B)
VKSKAKKTVDKHSDEYKIRRERNNIAVRKSRDKAKMRNLETQHKVLELTAENERLQKKVE
QLSRELSTLRNLFKQLPE

Sequence of entity 4 (C), FASTA

>1IO4_4 RUNT-RELATED TRANSCRIPTION FACTOR 1 (chains C)
GELVRTDSPNFLCSVLPTHWRCNKTLPIAFKVVALGDVPDGTLVTVMAGNDENYSAELRN
ATAAMKNQVARFNDLRFVGRSGRGKSFTLTITVFTNPPQVATYHRAIKITVDGPREPRRH
RQK

Sequence of entity 5 (D), FASTA

>1IO4_5 CORE-BINDING FACTOR, BETA SUBUNIT (chains D)
MPRVVPDQRSKFENEEFFRKLSRECEIKYTGFRDRPHEERQTRFQNACRDGRSEIAFVAT
GTNLSLQFFPASWQGEQRQTPSREYVDLEREAGKVYLKAPMILNGVCVIWKGWIDLHRLD
GMGCLEFDEERAQQEDALAQQ

Ligands and cofactors

ID	Name	Formula	Copies
AU	Gold ion	Au	3

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) 104:755-767. 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

Browse structure collections

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