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- PDB-2e43: Crystal structure of C/EBPbeta Bzip homodimer K269A mutant bound ... -

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Basic information

Entry
Database: PDB / ID: 2.0E+43
TitleCrystal structure of C/EBPbeta Bzip homodimer K269A mutant bound to A High Affinity DNA fragment
Components
  • CCAAT/enhancer-binding protein beta
  • DNA (5'-D(P*DAP*DAP*DTP*DAP*DTP*DTP*DGP*DCP*DGP*DCP*DAP*DAP*DTP*DCP*DCP*DT)-3')
  • DNA (5'-D(P*DTP*DAP*DGP*DGP*DAP*DTP*DTP*DGP*DCP*DGP*DCP*DAP*DAP*DTP*DAP*DT)-3')
KeywordsTRANSCRIPTION/DNA / PROTEIN-DNA COMPLEX / 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 / 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 / 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 / Basic region leucine zipper / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #170 / Basic-leucine zipper (bZIP) domain profile. / basic region leucin zipper / Basic-leucine zipper domain superfamily / Basic-leucine zipper domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / CCAAT/enhancer-binding protein beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsTahirov, T.H. / Inoue-Bungo, T. / Sato, K. / Shiina, M. / Hamada, K. / Ogata, K.
CitationJournal: To be Published
Title: Structural Basis for Flexible Base Recognition by C/Ebpbeta
Authors: Tahirov, T.H. / Inoue-Bungo, T. / Sato, K. / Shiina, M. / Hamada, K. / Ogata, K.
History
DepositionDec 1, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 18, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 10, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: DNA (5'-D(P*DTP*DAP*DGP*DGP*DAP*DTP*DTP*DGP*DCP*DGP*DCP*DAP*DAP*DTP*DAP*DT)-3')
D: DNA (5'-D(P*DAP*DAP*DTP*DAP*DTP*DTP*DGP*DCP*DGP*DCP*DAP*DAP*DTP*DCP*DCP*DT)-3')
A: CCAAT/enhancer-binding protein beta
B: CCAAT/enhancer-binding protein beta


Theoretical massNumber of molelcules
Total (without water)28,4424
Polymers28,4424
Non-polymers00
Water5,963331
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)101.681, 112.731, 74.932
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: DNA chain DNA (5'-D(P*DTP*DAP*DGP*DGP*DAP*DTP*DTP*DGP*DCP*DGP*DCP*DAP*DAP*DTP*DAP*DT)-3')


Mass: 4937.228 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain DNA (5'-D(P*DAP*DAP*DTP*DAP*DTP*DTP*DGP*DCP*DGP*DCP*DAP*DAP*DTP*DCP*DCP*DT)-3')


Mass: 4857.179 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Protein CCAAT/enhancer-binding protein beta / C/EBP beta / Nuclear factor NF-IL6 / Transcription factor 5


Mass: 9323.767 Da / Num. of mol.: 2 / Fragment: residues 259-336 / Mutation: K269A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CEBPB, TCF5 / Plasmid: PAR VECTOR / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P17676
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 331 / Source method: isolated from a natural source / Formula: H2O

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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: 3.75 Å3/Da / Density % sol: 67 %
Crystal growpH: 7.5
Details: magnesium chloride, Tris-Hcl, PEG4000, PH 7.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K
Components of the solutions
IDNameCrystal-IDSol-ID
1magnesium chloride11
2Tris-Hcl11
3PEG400011
4H2O11
5magnesium chloride12
6Tris-Hcl12
7PEG400012
8H2O12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44B2 / Wavelength: 1
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 29, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 25384 / % possible obs: 99.3 % / Biso Wilson estimate: 30.3 Å2 / Rmerge(I) obs: 0.075
Reflection shellResolution: 2.1→2.18 Å / % possible all: 94.7

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
CNS1.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1GU4

1gu4


Resolution: 2.1→42.07 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 4405373.36 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.259 2508 9.9 %RANDOM
Rwork0.222 ---
obs0.222 25326 99.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 75.04 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 42.7 Å2
Baniso -1Baniso -2Baniso -3
1--3.87 Å20 Å20 Å2
2--5.9 Å20 Å2
3----2.03 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.2 Å0.17 Å
Refinement stepCycle: LAST / Resolution: 2.1→42.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1073 658 0 331 2062
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.004
X-RAY DIFFRACTIONc_angle_deg0.8
X-RAY DIFFRACTIONc_dihedral_angle_d14.6
X-RAY DIFFRACTIONc_improper_angle_d1.03
X-RAY DIFFRACTIONc_mcbond_it1.561.5
X-RAY DIFFRACTIONc_mcangle_it2.242
X-RAY DIFFRACTIONc_scbond_it2.252
X-RAY DIFFRACTIONc_scangle_it3.432.5
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.301 419 10.4 %
Rwork0.266 3626 -
obs--96.7 %
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

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