1IO4

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

PDB DOI: https://doi.org/10.2210/pdb1IO4/pdb
NAKB: 1IO4

Classification: TRANSCRIPTION/DNA
Organism(s): Homo sapiens, Mus musculus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2001-01-10 Released: 2001-03-12
Deposition Author(s): Tahirov, T.H., Ogata, K.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å
R-Value Free: 0.299
R-Value Work: 0.247

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

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., Fujikawa, A., Sasaki, M., Kimura, K., Shiina, M., Sato, K., Kumasaka, T., Yamamoto, M., Ishii, S., Ogata, K.

(2001) Cell 104: 755-767

PubMed: 11257229 Search on PubMed
DOI: https://doi.org/10.1016/s0092-8674(01)00271-9
Primary Citation of Related Structures:
1HJB, 1HJC, 1IO4

PubMed Abstract:
The core binding factor (CBF) heterodimeric transcription factors comprised of AML/CBFA/PEBP2alpha/Runx and CBFbeta/PEBP2beta subunits are essential for differentiation of hematopoietic and bone cells, and their mutation is intimately related to the development of acute leukemias and cleidocranial dysplasia. Here, we present the crystal structures of the AML1/Runx-1/CBFalpha(Runt domain)-CBFbeta(core domain)-C/EBPbeta(bZip)-DNA, AML1/Runx-1/CBFalpha(Runt domain)-C/EBPbeta(bZip)-DNA, and AML1/Runx-1/CBFalpha(Runt domain)-DNA complexes. The hydrogen bonding network formed among CBFalpha(Runt domain) and CBFbeta, and CBFalpha(Runt domain) and DNA revealed the allosteric regulation mechanism of CBFalpha(Runt domain)-DNA binding by CBFbeta. The point mutations of CBFalpha related to the aforementioned diseases were also mapped and their effect on DNA binding is discussed.

Organizational Affiliation

Kanagawa Academy of Science and Technology (KAST), Yokohama City University School of Medicine, 3-9 Fukuura, Yokohama 236-0004, Kanazawa-ku, Japan. tahir@med.yokohama-cu.ac.jp

Macromolecule Content

Total Structure Weight: 65.66 kDa
Atom Count: 4,197
Modelled Residue Count: 433
Deposited Residue Count: 472
Unique protein chains: 3
Unique nucleic acid chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
CAAT/ENHANCER BINDING PROTEIN BETA	C [auth A], D [auth B]	78	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P17676 (Homo sapiens) Explore P17676 Go to UniProtKB: P17676
PHAROS: P17676 GTEx: ENSG00000172216
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P17676
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
RUNT-RELATED TRANSCRIPTION FACTOR 1	E [auth C]	123	Mus musculus	Mutation(s): 0
UniProt
Find proteins for Q03347 (Mus musculus) Explore Q03347 Go to UniProtKB: Q03347
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q03347
Sequence Annotations Expand
Reference Sequence

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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
CORE-BINDING FACTOR, BETA SUBUNIT	F [auth D]	141	Mus musculus	Mutation(s): 0
UniProt
Find proteins for Q08024 (Mus musculus) Explore Q08024 Go to UniProtKB: Q08024
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q08024
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Length	Organism	Image
CSF-1R PROMOTER	A [auth E]	26	N/A
Sequence Annotations Expand
Reference Sequence

Find similar nucleic acids by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Length	Organism	Image
CSF-1R PROMOTER	B [auth F]	26	N/A
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AU Query on AU Download Ideal Coordinates CCD File SDF format, chain G [auth C] SDF format, chain H [auth D] SDF format, chain I [auth D] MOL2 format, chain G [auth C] MOL2 format, chain H [auth D] MOL2 format, chain I [auth D]	G [auth C], H [auth D], I [auth D]	GOLD ION Au ZBKIUFWVEIBQRT-UHFFFAOYSA-N		Interactions Focus chain G [auth C] Focus chain H [auth D] Focus chain I [auth D] Interactions & Density Focus chain G [auth C] Focus chain H [auth D] Focus chain I [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å
R-Value Free: 0.299
R-Value Work: 0.247
Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 121.108	α = 90
b = 163.6	β = 90
c = 109.326	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
CNS	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2001-03-12

Deposition Author(s):

Tahirov, T.H.

Ogata, K.

Revision History (Full details and data files)

Version 1.0: 2001-03-12
Type: Initial release
Version 1.1: 2008-04-27
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2023-12-27
Changes: Data collection, Database references, Derived calculations