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- PDB-6mg1: C-terminal bZIP domain of human C/EBPbeta with 16bp Methylated Ol... -

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Basic information

Entry
Database: PDB / ID: 6mg1
TitleC-terminal bZIP domain of human C/EBPbeta with 16bp Methylated Oligonucleotide Containing Consensus Recognition Sequence-C2 Crystal Form
Components
  • 16-bp methylated oligonucleotide
  • CCAAT/enhancer-binding protein beta
KeywordsTRANSCRIPTION/DNA / bZIP Transciption Factor DNA Methylation CpA methylation PROTEIN-DNA COMPLEX / TRANSCRIPTION / 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 / 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 / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsHorton, J.R. / Cheng, X. / Yang, J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM049245-23 United States
CitationJournal: Nucleic Acids Res. / Year: 2019
Title: Structural basis for effects of CpA modifications on C/EBP beta binding of DNA.
Authors: Yang, J. / Horton, J.R. / Wang, D. / Ren, R. / Li, J. / Sun, D. / Huang, Y. / Zhang, X. / Blumenthal, R.M. / Cheng, X.
History
DepositionSep 12, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 12, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 16, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Feb 6, 2019Group: Data collection / Source and taxonomy / Category: entity_src_gen / Item: _entity_src_gen.pdbx_host_org_scientific_name
Revision 1.3May 29, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.4Aug 28, 2019Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.type
Revision 1.5Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.0Oct 26, 2022Group: Advisory / Database references ...Advisory / Database references / Derived calculations / Polymer sequence / Structure summary
Category: database_2 / entity ...database_2 / entity / entity_poly / ndb_struct_na_base_pair / ndb_struct_na_base_pair_step / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight / _entity_poly.type
Revision 2.1Oct 18, 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

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Assembly

Deposited unit
A: CCAAT/enhancer-binding protein beta
B: CCAAT/enhancer-binding protein beta
C: 16-bp methylated oligonucleotide
D: 16-bp methylated oligonucleotide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,8409
Polymers28,5004
Non-polymers3405
Water2,378132
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9500 Å2
ΔGint9 kcal/mol
Surface area14510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.110, 77.405, 99.825
Angle α, β, γ (deg.)90.00, 103.90, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein CCAAT/enhancer-binding protein beta / C/EBP beta / Liver activator protein / LAP / Liver-enriched inhibitory protein / LIP / Nuclear ...C/EBP beta / Liver activator protein / LAP / Liver-enriched inhibitory protein / LIP / Nuclear factor NF-IL6 / Transcription factor 5 / TCF-5


Mass: 9325.746 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CEBPB, TCF5, PP9092 / Production host: Escherichia Coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P17676
#2: DNA chain 16-bp methylated oligonucleotide


Mass: 4924.270 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C2H6O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 132 / 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: 3.17 Å3/Da / Density % sol: 61.14 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2 M sodium chloride, 0.1 M BIS-TRIS pH 6.5, 25% (w/v) polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: RIGAKU MICROMAX-003 / Wavelength: 1 Å
DetectorType: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Feb 4, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.63→34.542 Å / Num. obs: 35611 / % possible obs: 80.8 % / Redundancy: 10.3 % / Rmerge(I) obs: 0.08 / Rpim(I) all: 0.024 / Net I/σ(I): 25.4
Reflection shellResolution: 1.63→1.69 Å / Rmerge(I) obs: 0.519 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 842 / CC1/2: 0.787 / Rpim(I) all: 0.374

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Starting model: 2.0E+42 / Resolution: 1.75→34.542 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 32.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2496 1647 4.96 %
Rwork0.2138 --
obs0.2156 33208 92.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.75→34.542 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1731 0 22 132 1885
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051861
X-RAY DIFFRACTIONf_angle_d0.9962627
X-RAY DIFFRACTIONf_dihedral_angle_d29.056752
X-RAY DIFFRACTIONf_chiral_restr0.044290
X-RAY DIFFRACTIONf_plane_restr0.004236
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.80150.4453940.36831740X-RAY DIFFRACTION62
1.8015-1.85970.32251110.30912111X-RAY DIFFRACTION74
1.8597-1.92610.36041250.292412X-RAY DIFFRACTION86
1.9261-2.00320.2771350.29432679X-RAY DIFFRACTION94
2.0032-2.09440.30261450.29142777X-RAY DIFFRACTION99
2.0944-2.20480.33391460.25022812X-RAY DIFFRACTION99
2.2048-2.34290.26061470.23222813X-RAY DIFFRACTION100
2.3429-2.52370.26481500.23352868X-RAY DIFFRACTION100
2.5237-2.77760.23831460.2322795X-RAY DIFFRACTION100
2.7776-3.17930.27341480.21942834X-RAY DIFFRACTION99
3.1793-4.00460.23621460.17942854X-RAY DIFFRACTION100
4.0046-34.54910.21561540.19152866X-RAY DIFFRACTION99

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