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- PDB-1h89: CRYSTAL STRUCTURE OF TERNARY PROTEIN-DNA COMPLEX2 -

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Basic information

Entry
Database: PDB / ID: 1h89
TitleCRYSTAL STRUCTURE OF TERNARY PROTEIN-DNA COMPLEX2
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 PROTO-ONCOGENE PROTEIN
KeywordsTRANSCRIPTION/DNA / PROTEIN-DNA COMPLEX / TRANSCRIPTION REGULATION / BZIP / PROTO-ONCOGENE / MYB / C-MYB / C/EBP / 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 testosterone secretion / positive regulation of biomineral tissue development / myeloid cell development / positive regulation of hepatic stellate cell proliferation / integrated stress response signaling ...C/EBP complex / granuloma formation / regulation of odontoblast differentiation / CHOP-C/EBP complex / positive regulation of sodium-dependent phosphate transport / positive regulation of testosterone secretion / positive regulation of biomineral tissue development / myeloid cell development / positive regulation of hepatic stellate cell proliferation / integrated stress response signaling / T-helper 1 cell activation / Response of EIF2AK1 (HRI) to heme deficiency / hepatocyte proliferation / positive regulation of hepatic stellate cell activation / positive regulation of transforming growth factor beta production / ATF4 activates genes in response to endoplasmic reticulum stress / regulation of osteoclast differentiation / embryonic digestive tract development / stem cell division / mammary gland epithelial cell differentiation / myeloid cell differentiation / condensed chromosome, centromeric region / regulation of dendritic cell differentiation / cellular response to interleukin-6 / regulation of interleukin-6 production / mammary gland epithelial cell proliferation / WD40-repeat domain binding / 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 / homeostasis of number of cells / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / positive regulation of collagen biosynthetic process / 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 / positive regulation of glial cell proliferation / spleen development / response to endoplasmic reticulum stress / B cell differentiation / thymus development / cellular response to leukemia inhibitory factor / acute-phase response / liver regeneration / cellular response to amino acid stimulus / RNA polymerase II transcription regulatory region sequence-specific DNA binding / positive regulation of smooth muscle cell proliferation / neuron differentiation / G1/S transition of mitotic cell cycle / 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 / calcium ion transport / positive regulation of neuron apoptotic process / sequence-specific double-stranded DNA binding / positive regulation of cold-induced thermogenesis / mitotic cell cycle / Senescence-Associated Secretory Phenotype (SASP) / regulation of gene expression / DNA-binding transcription activator activity, RNA polymerase II-specific / in utero embryonic development / negative regulation of neuron apoptotic process / response to lipopolysaccharide / transcription by RNA polymerase II / 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 / chromatin / regulation of DNA-templated transcription / 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 / cytosol / cytoplasm
Similarity search - Function
: / CCAAT/enhancer-binding protein, chordates / Transcription regulator Wos2-domain / LMSTEN motif / C-myb, C-terminal / C-myb, C-terminal / 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. ...: / CCAAT/enhancer-binding protein, chordates / Transcription regulator Wos2-domain / LMSTEN motif / C-myb, C-terminal / C-myb, C-terminal / 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) / Transcriptional activator Myb / CCAAT/enhancer-binding protein beta
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MUS MUSCULUS (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 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 Runt Domain, Cbfbeta and the C/Ebpbeta bZIP Region
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 30, 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: exptl_crystal_grow / pdbx_database_proc ...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 / Derived calculations / 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 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry

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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 PROTO-ONCOGENE 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')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,8747
Polymers50,7955
Non-polymers782
Water2,216123
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)62.684, 73.383, 161.699
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsOF C/EBP BETA AND MONOMER OF MYB PROTO- ONCOGENE PROTEINBOUND TO A DUPLEX DNA FRAGMENTFOR THE HETERO-ASSEMBLY DESCRIBED BY REMARK 350 THE

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Components

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Protein , 2 types, 3 molecules ABC

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


Mass: 7823.048 Da / Num. of mol.: 2 / Fragment: RESIDUES 273-336
Source method: isolated from a genetically manipulated source
Details: BZIP DOMAIN / 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 PROTO-ONCOGENE PROTEIN / C-MYB


Mass: 19173.074 Da / Num. of mol.: 1 / Fragment: RESIDUES 35-193 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: DNA BINDING DOMAIN / Source: (gene. exp.) MUS MUSCULUS (house mouse) / Plasmid: PAR2156 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: GENP: CAA26552, UniProt: P06876*PLUS

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DNA chain , 2 types, 2 molecules DE

#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)

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Non-polymers , 2 types, 125 molecules

#5: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 123 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsCHAIN C ENGINEERED MUTATION LYS35MET, ARG36GLY C/EBP BETA IS IMPORTANT TRANSCRIPTIONAL ACTIVATOR IN ...CHAIN C ENGINEERED MUTATION LYS35MET, ARG36GLY C/EBP BETA IS IMPORTANT TRANSCRIPTIONAL ACTIVATOR IN THE REGULATION OF GENES INVOLVED IN IMMUNE AND INFLAMMATORY RESPONSES. SPECIFICALL
Sequence detailsLYS 35 WAS REPLACED BY MET AND ARG 36 WAS REPLACED BY GLY BECAUSE OF EXPRESSION IN ESCHERICHIA COLI.

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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: 3.66 Å3/Da / Density % sol: 65.5 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1 M KCL, 0.05 MGSO4, 4% V/V MPD, 6% V/V GLYCEROL, 0.05 M NA HEPES PH 7.0 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
40.1 M1reservoirKCl
50.005 M1reservoirMgSO4
60.05 Msodium HEPES1reservoirpH7.0
74 %(v/v)MPD1reservoir
86 %(v/v)glycerol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 1.04
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Nov 17, 1998 / Details: MIRRORS
RadiationMonochromator: DIAMOND / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.04 Å / Relative weight: 1
ReflectionResolution: 2.45→20 Å / Num. obs: 27451 / % possible obs: 99 % / Observed criterion σ(I): 0 / Redundancy: 7.496 % / Biso Wilson estimate: 67 Å2 / Rsym value: 0.072 / Net I/σ(I): 27.5043
Reflection shellResolution: 2.45→2.54 Å / Redundancy: 4 % / Mean I/σ(I) obs: 2.162 / Rsym value: 0.397 / % possible all: 95.5
Reflection
*PLUS
Highest resolution: 2.45 Å / Lowest resolution: 20 Å / Observed criterion σ(I): 0 / Num. measured all: 205777 / Rmerge(I) obs: 0.072

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Processing

Software
NameVersionClassification
CNS0.9refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.851phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1H88

1h88


Resolution: 2.45→19.94 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 979672.69 / 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 100
RfactorNum. reflection% reflectionSelection details
Rfree0.267 1339 4.9 %RANDOM
Rwork0.229 ---
obs0.229 27319 98.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 38.0889 Å2 / ksol: 0.292803 e/Å3
Displacement parametersBiso mean: 65.6 Å2
Baniso -1Baniso -2Baniso -3
1-12.16 Å20 Å20 Å2
2--6.54 Å20 Å2
3----18.7 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.45 Å0.38 Å
Luzzati d res low-20 Å
Luzzati sigma a0.71 Å0.6 Å
Refinement stepCycle: LAST / Resolution: 2.45→19.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2080 1060 2 123 3265
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_d18.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.14
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it6.931.5
X-RAY DIFFRACTIONc_mcangle_it9.812
X-RAY DIFFRACTIONc_scbond_it12.382
X-RAY DIFFRACTIONc_scangle_it14.782.5
LS refinement shellResolution: 2.45→2.6 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.393 213 5.4 %
Rwork0.422 3725 -
obs--85.4 %
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
X-RAY DIFFRACTION4ION.PARAMION.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_deg1.12
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg18.1
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.14

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