Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A2B1 Local Symmetry: Cyclic - C2  (3D View)
Local Stoichiometry: Homo 2-mer - A2 

Local Symmetry: Cyclic - C2  (3D View)
Local Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 53.93 kDa 
• Atom Count: 3,576 
• Modelled Residue Count: 345 
• Deposited Residue Count: 367 
• Unique protein chains: 2
• Unique nucleic acid chains: 2

 1H88

CRYSTAL STRUCTURE OF TERNARY PROTEIN-DNA COMPLEX1

• PDB DOI:  https://doi.org/10.2210/pdb1H88/pdb
• NDB: PD0288

• Classification: TRANSCRIPTION/DNA
• Organism(s): Homo sapiens, Mus musculus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2001-01-29 Released: 2002-01-28 
• Deposition Author(s): Tahirov, T.H., Ogata, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.277 
• R-Value Work: 0.222 
• R-Value Observed: 0.222 

Literature

Mechanism of C-Myb-C/Ebpbeta Cooperation from Separated Sites on a Promoter

Tahirov, T.H., Sato, K., Ichikawa-Iwata, E., Sasaki, M., Inoue-Bungo, T., Shiina, M., Kimura, K., Takata, S., Fujikawa, A., Morii, H., Kumasaka, T., Yamamoto, M., Ishii, S., Ogata, K.

(2002) Cell 108: 57

• PubMed: 11792321 
• DOI: https://doi.org/10.1016/s0092-8674(01)00636-5
• Primary Citation of Related Structures:  
  1H88, 1H89, 1H8A


• PubMed Abstract: 
  

c-Myb, but not avian myeloblastosis virus (AMV) v-Myb, cooperates with C/EBP beta to regulate transcription of myeloid-specific genes. To assess the structural basis for that difference, we determined the crystal structures of complexes comprised of the c-Myb or AMV v-Myb DNA-binding domain (DBD), the C/EBP beta DBD, and a promoter DNA fragment. Within the c-Myb complex, a DNA-bound C/EBP beta interacts with R2 of c-Myb bound to a different DNA fragment; point mutations in v-Myb R2 eliminate such interaction within the v-Myb complex. GST pull-down assays, luciferase trans-activation assays, and atomic force microscopy confirmed that the interaction of c-Myb and C/EBP beta observed in crystal mimics their long range interaction on the promoter, which is accompanied by intervening DNA looping.

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Related Citations: 

• Crystals of Ternary Protein-DNA Complexes Composed of DNA-Binding Domains C-Myb or V-Myb, C/Ebpalpha or C/Ebpbeta and Tom-1A Promoter Fragment
  Tahirov, T.H., Inoue, T., Sasaki, M., Shiina, M., Kimura, K., Sato, K., Kumasaka, T., Yamamoto, M., Kamiya, N., Ogata, K.
  (2001) Acta Crystallogr D Biol Crystallogr 57: 1655

• Crystal Structures of C-Myb DNA-Binding Domain in Free State: An Evidence for Binding of Na+ and Comparison with Solution Structure
  Tahirov, T.H., Morii, H., Uedaira, H., Sasaki, M., Sarai, A., Adachi, S., Park, S.Y., Kamiya, N., Ogata, K.
  () To be published --: --

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Organizational Affiliation: 

Kanagawa Academy of Science and Technology, 3-9 Fukuura, Kanazawa-ku, Yokohama 236-0004, Japan. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CCAAT/ENHANCER BINDING PROTEIN BETA	A, B	78	Homo sapiens	Mutation(s): 0  Gene Names: CEBPB, TCF5, PP9092
UniProt & NIH Common Fund Data Resources
Find proteins for P17676 (Homo sapiens) Explore P17676  Go to UniProtKB:  P17676
PHAROS:  P17676

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
MYB PROTO-ONCOGENE PROTEIN	C	159	Mus musculus	Mutation(s): 2  Gene Names: Myb
UniProt & NIH Common Fund Data Resources
Find proteins for P06876 (Mus musculus) Explore P06876  Go to UniProtKB:  P06876
IMPC:  MGI:97249

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA(5'-(*GP*AP*TP*GP*TP*GP*GP*CP*GP*CP*AP* AP*TP*CP*CP*TP*TP*AP*AP*CP*GP*GP*AP*CP*TP*G)-3')	D	26	Homo sapiens

Entity ID: 4
Molecule	Chains	Length	Organism	Image
DNA(5'-(*CP*CP*AP*GP*TP*CP*CP*GP*TP*TP*AP* AP*GP*GP*AP*TP*TP*GP*CP*GP*CP*CP*AP*CP*AP*T)-3')	E	26	Homo sapiens

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NH4	F [auth C]	AMMONIUM ION H4 N QGZKDVFQNNGYKY-UHFFFAOYSA-O

Binding Affinity Annotations
ID	Source	Binding Affinity
DNA	PDBBind:  1H88	Kd: 35.3 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.277 
• R-Value Work: 0.222 
• R-Value Observed: 0.222 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.735	α = 90
b = 156.966	β = 100.16
c = 55.868	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2002-01-28 
Deposition Author(s): Tahirov, T.H., Ogata, K.

Revision History  

• Version 1.0: 2002-01-28
  Type: Initial release
  
• Version 1.1: 2013-03-06
  Changes: Data collection, Database references, Derived calculations, Non-polymer description, Other, Refinement description, Source and taxonomy, Structure summary, Version format compliance
• Version 1.2: 2019-05-08
  Changes: Data collection, Experimental preparation, Other, Source and taxonomy