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- PDB-1h8a: CRYSTAL STRUCTURE OF TERNARY PROTEIN-DNA COMPLEX3 -

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Basic information

Entry
Database: PDB / ID: 1h8a
TitleCRYSTAL STRUCTURE OF TERNARY PROTEIN-DNA COMPLEX3
Components
  • CAAT/ENHANCER BINDING PROTEIN BETA
  • 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')
  • 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')
  • MYB TRANSFORMING PROTEIN
KeywordsTRANSCRIPTION/DNA / PROTEIN-DNA COMPLEX / TRANSCRIPTION REGULATION / BZIP / V-MYB / C-MYB / AMV / C/EBP / AVIAN MYELOBLASTOSIS VIRUS / TRANSFORMING PROTEIN / TRANSCRIPTION-DNA complex
Function / homology
Function and homology information


C/EBP complex / granuloma formation / regulation of odontoblast differentiation / CHOP-C/EBP complex / positive regulation of sodium-dependent phosphate transport / positive regulation of biomineral tissue development / myeloid cell development / integrated stress response signaling / T-helper 1 cell activation / Response of EIF2AK1 (HRI) to heme deficiency ...C/EBP complex / granuloma formation / regulation of odontoblast differentiation / CHOP-C/EBP complex / positive regulation of sodium-dependent phosphate transport / positive regulation of biomineral tissue development / myeloid cell development / integrated stress response signaling / T-helper 1 cell activation / Response of EIF2AK1 (HRI) to heme deficiency / hepatocyte proliferation / ATF4 activates genes in response to endoplasmic reticulum stress / regulation of osteoclast differentiation / mammary gland epithelial cell differentiation / condensed chromosome, centromeric region / regulation of dendritic cell differentiation / regulation of interleukin-6 production / mammary gland epithelial cell proliferation / histone acetyltransferase binding / positive regulation of interleukin-4 production / regulation of cell differentiation / ubiquitin-like protein ligase binding / Response of EIF2AK4 (GCN2) to amino acid deficiency / Transcriptional Regulation by VENTX / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / embryonic placenta development / positive regulation of fat cell differentiation / RNA polymerase II core promoter sequence-specific DNA binding / Nuclear events stimulated by ALK signaling in cancer / positive regulation of osteoblast differentiation / brown fat cell differentiation / negative regulation of T cell proliferation / ovarian follicle development / response to endoplasmic reticulum stress / acute-phase response / liver regeneration / RNA polymerase II transcription regulatory region sequence-specific DNA binding / cellular response to amino acid stimulus / neuron differentiation / chromatin DNA binding / kinase binding / DNA-binding transcription repressor activity, RNA polymerase II-specific / nuclear matrix / histone deacetylase binding / Transcriptional regulation of white adipocyte differentiation / positive regulation of inflammatory response / Transcriptional regulation of granulopoiesis / RNA polymerase II transcription regulator complex / sequence-specific double-stranded DNA binding / positive regulation of cold-induced thermogenesis / Senescence-Associated Secretory Phenotype (SASP) / DNA-binding transcription activator activity, RNA polymerase II-specific / negative regulation of neuron apoptotic process / transcription by RNA polymerase II / response to lipopolysaccharide / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / defense response to bacterium / inflammatory response / immune response / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / host cell nucleus / regulation of DNA-templated transcription / chromatin / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
: / : / CCAAT/enhancer-binding protein, chordates / Transcription regulator Wos2-domain / LMSTEN motif / C-myb, C-terminal / C-myb, C-terminal / Myb-like domain profile. / Basic region leucine zipper / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #170 ...: / : / CCAAT/enhancer-binding protein, chordates / Transcription regulator Wos2-domain / LMSTEN motif / C-myb, C-terminal / C-myb, C-terminal / Myb-like domain profile. / Basic region leucine zipper / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #170 / Myb-type HTH DNA-binding domain profile. / Basic-leucine zipper (bZIP) domain profile. / basic region leucin zipper / Basic-leucine zipper domain superfamily / Basic-leucine zipper domain / Myb domain / Myb-like DNA-binding domain / SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains / SANT/Myb domain / Homeodomain-like / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Homeobox-like domain superfamily / Arc Repressor Mutant, subunit A / Up-down Bundle / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / Transforming protein Myb / CCAAT/enhancer-binding protein beta
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
AVIAN MYELOBLASTOSIS VIRUS
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.23 Å
AuthorsTahirov, T.H. / Ogata, K.
Citation
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2001
Title: 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
Authors: Tahirov, T.H. / Inoue, T. / Sasaki, M. / Shiina, M. / Kimura, K. / Sato, K. / Kumasaka, T. / Yamamoto, M. / Kamiya, N. / Ogata, K.
#2: Journal: To be Published
Title: Crystal Structures of C-Myb DNA-Binding Domain in Free State: An Evidence for Binding of Na+ and Comparison with Solution Structure
Authors: Tahirov, T.H. / Morii, H. / Uedaira, H. / Sasaki, M. / Sarai, A. / Adachi, S. / Park, S.Y. / Kamiya, N. / Ogata, K.
#3: Journal: Cell(Cambridge,Mass.) / Year: 2001
Title: Structural Analyses of DNA Recognition by the Aml1/ Runx-1 Runt Domain and its Allosteric Control by Cbfbeta
Authors: 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.
History
DepositionJan 31, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 28, 2002Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2019Group: Data collection / Experimental preparation ...Data collection / Experimental preparation / Other / Source and taxonomy
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / pdbx_entity_src_syn / pdbx_seq_map_depositor_info
Item: _exptl_crystal_grow.method / _exptl_crystal_grow.temp ..._exptl_crystal_grow.method / _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval / _pdbx_seq_map_depositor_info.one_letter_code_mod
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CAAT/ENHANCER BINDING PROTEIN BETA
B: CAAT/ENHANCER BINDING PROTEIN BETA
C: MYB TRANSFORMING PROTEIN
D: 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')
E: 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')


Theoretical massNumber of molelcules
Total (without water)50,2245
Polymers50,2245
Non-polymers00
Water3,081171
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)109.860, 166.700, 39.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
DetailsOF C/EBP BETA AND MONOMER OF MYB TRANSFORMING PROTEINBOUND TO A DUPLEX DNA FRAGMENTFOR THE HETERO-ASSEMBLY DESCRIBED BY REMARK 350.

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Components

#1: Protein CAAT/ENHANCER BINDING PROTEIN BETA / C/EBP BETA / NFIL-6


Mass: 9381.868 Da / Num. of mol.: 2 / Fragment: RESIDUES 259-336
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PAR2156 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P17676
#2: Protein MYB TRANSFORMING PROTEIN / AMV V-MYB


Mass: 15483.731 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-128
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) AVIAN MYELOBLASTOSIS VIRUS / Plasmid: PAR2156 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P01104
#3: DNA chain 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')


Mass: 8028.177 Da / Num. of mol.: 1 / Fragment: FRAGMENT FROM TOM-1A PROMOTER / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#4: DNA chain 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')


Mass: 7948.129 Da / Num. of mol.: 1 / Fragment: FRAGMENT FROM TOM-1A PROMOTER / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 171 / Source method: isolated from a natural source / Formula: H2O
Compound detailsC/EBP BETA IS IMPORTANT TRANSCRIPTIONAL ACTIVATOR IN THE REGULATION OF GENES INVOLVED IN IMMUNE AND ...C/EBP BETA IS IMPORTANT TRANSCRIPTIONAL ACTIVATOR IN THE REGULATION OF GENES INVOLVED IN IMMUNE AND INFLAMMATORY RESPONSES. SPECIFICALL
Sequence detailsNUMBERING OF AMV V-MYB AMINO ACID SEQUENCE WAS CHANGED IN ORDER TO MAKE THE COMPARISON WITH ...NUMBERING OF AMV V-MYB AMINO ACID SEQUENCE WAS CHANGED IN ORDER TO MAKE THE COMPARISON WITH STRUCTURES OF MOUSE C-MYB MORE CONVENIENT

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.61 Å3/Da / Density % sol: 65 %
Description: LEUCINE ZIPPER OF C/EBP BETA AND C-MYB REPEAT 1 WERE EXCLUDED FROM STARTING MODEL.
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.04 M MAGNESIUM CHLORIDE, 20% V/V MPD, 0.05 M SODIUM CACODYLATE BUFFER PH 6.0 AT 24 DEGREES C
Crystal grow
*PLUS
Temperature: 297 K / pH: 6.8 / Method: vapor diffusion, sitting drop
Details: Tahirov, T.H., (2001) Acta Crystallogr.,Sect.D, 57, 1655.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 mMdithiothreitol1droppH6.8
210 %DNA1dropexcess
36.5-7.5 mg/mlprotein1drop
40.04 M1reservoirMgCl2
50.05 Msodium cacodylate1reservoirpH6.0
620 %(v/v)MPD1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 1.02
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Apr 29, 1999 / Details: MIRRORS
RadiationMonochromator: DIAMOND / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.02 Å / Relative weight: 1
ReflectionResolution: 2.1→20 Å / Num. obs: 42104 / % possible obs: 97.3 % / Observed criterion σ(I): 0 / Redundancy: 3.868 % / Biso Wilson estimate: 67.5 Å2 / Rsym value: 0.069 / Net I/σ(I): 23.9495
Reflection shellResolution: 2.1→2.17 Å / Redundancy: 2.56 % / Mean I/σ(I) obs: 1.784 / Rsym value: 0.389 / % possible all: 94.2
Reflection
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 20 Å / Observed criterion σ(I): 0 / Num. measured all: 162864 / Rmerge(I) obs: 0.069
Reflection shell
*PLUS
Redundancy: 2.56 %

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Processing

Software
NameVersionClassification
CNS0.9refinement
DENZOdata reduction
SCALEPACKdata scaling
CNS0.9phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1H88

1h88


Resolution: 2.23→19.85 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 2363401.12 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: BULK SOLVENT MODEL USED. ATOMS C, O, N, CA AND CB ARE HARMONICALLY RESTRAINED DURING REFINEMENT WITH HARMONIC RESTRAINT CONSTANT OF 20 TWO DATA SETS WERE COLLECTED FROM ONE CRYSTAL. FIRST ...Details: BULK SOLVENT MODEL USED. ATOMS C, O, N, CA AND CB ARE HARMONICALLY RESTRAINED DURING REFINEMENT WITH HARMONIC RESTRAINT CONSTANT OF 20 TWO DATA SETS WERE COLLECTED FROM ONE CRYSTAL. FIRST 120 IMAGES WERE OBTAINED WITH EXPOSURE TIME OF 200 SEC, OSCILLATION ANGLE OF 1 DEGREE AND CRYSTAL TO DETECTOR DISTANCE OF 240 MM. ANOTHER 60 IMAGES WERE OBTAINED WITH EXPOSURE TIME OF 30 SEC, OSCILLATION ANGLE OF 1.5 DEGREES AND CRYSTAL TO DETECTOR DISTANCE OF 420 MM.
RfactorNum. reflection% reflectionSelection details
Rfree0.288 1765 4.9 %RANDOM
Rwork0.245 ---
obs0.245 35692 97.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 39.2952 Å2 / ksol: 0.282507 e/Å3
Displacement parametersBiso mean: 64.2 Å2
Baniso -1Baniso -2Baniso -3
1--1.93 Å20 Å20 Å2
2---12.25 Å20 Å2
3---14.18 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.44 Å0.37 Å
Luzzati d res low-20 Å
Luzzati sigma a0.37 Å0.37 Å
Refinement stepCycle: LAST / Resolution: 2.23→19.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2045 1060 0 171 3276
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d17.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.19
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it6.191.5
X-RAY DIFFRACTIONc_mcangle_it7.982
X-RAY DIFFRACTIONc_scbond_it8.452
X-RAY DIFFRACTIONc_scangle_it10.512.5
LS refinement shellResolution: 2.23→2.37 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.376 275 4.8 %
Rwork0.376 5429 -
obs--96 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 20 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.07
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg17.8
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.19

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