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- PDB-6mg3: V285A Mutant of the C-terminal bZIP domain of human C/EBPbeta wit... -

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Basic information

Entry
Database: PDB / ID: 6mg3
TitleV285A Mutant of the C-terminal bZIP domain of human C/EBPbeta with 16bp Methylated Oligonucleotide Containing Consensus Recognition Sequence
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 / positive regulation of osteoblast differentiation / Nuclear events stimulated by ALK signaling in cancer / 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: 2.05 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 1.1Dec 19, 2018Group: Data collection / Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen ...pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _pdbx_struct_assembly_gen.assembly_id / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_gen.oper_expression
Revision 1.2Jan 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 1.3Jan 30, 2019Group: Data collection / Derived calculations
Category: pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _pdbx_struct_assembly_prop.value
Revision 1.4Aug 28, 2019Group: Data collection / Database references / Category: citation / diffrn_detector
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _diffrn_detector.type
Revision 1.5Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)28,5065
Polymers28,4444
Non-polymers621
Water4,504250
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9320 Å2
ΔGint-9 kcal/mol
Surface area13550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.430, 114.042, 75.444
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: 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: 9297.693 Da / Num. of mol.: 2 / Mutation: V285A
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.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 250 / 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: 3.84 Å3/Da / Density % sol: 67.93 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1 M sodium acetate trihydrate pH 7.0, 12% (w/v) polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SEALED TUBE / Type: RIGAKU MICROMAX-003 / Wavelength: 1.54218 Å
DetectorType: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Jul 26, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54218 Å / Relative weight: 1
ReflectionResolution: 2.05→26.734 Å / Num. obs: 28807 / % possible obs: 100 % / Redundancy: 8.2 % / Rmerge(I) obs: 0.172 / Rpim(I) all: 0.064 / Net I/σ(I): 9.5
Reflection shellResolution: 2.05→2.12 Å / Redundancy: 7.7 % / Mean I/σ(I) obs: 1 / Num. unique obs: 2741 / Rpim(I) all: 0.677 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
CrysalisProdata reduction
CrysalisProdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Starting model: 2.0E+42 / Resolution: 2.05→26.734 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.61
RfactorNum. reflection% reflection
Rfree0.249 1238 4.46 %
Rwork0.2216 --
obs0.2229 27768 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.05→26.734 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1089 654 4 250 1997
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031947
X-RAY DIFFRACTIONf_angle_d0.6512769
X-RAY DIFFRACTIONf_dihedral_angle_d24.4081064
X-RAY DIFFRACTIONf_chiral_restr0.027301
X-RAY DIFFRACTIONf_plane_restr0.002236
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.13210.31411340.32052914X-RAY DIFFRACTION100
2.1321-2.22910.32811360.29452913X-RAY DIFFRACTION100
2.2291-2.34650.28651360.27272901X-RAY DIFFRACTION100
2.3465-2.49340.24681370.24722932X-RAY DIFFRACTION100
2.4934-2.68580.30821370.23712931X-RAY DIFFRACTION100
2.6858-2.95570.24171360.24222926X-RAY DIFFRACTION100
2.9557-3.38270.26921380.23122949X-RAY DIFFRACTION99
3.3827-4.25910.23711390.19382981X-RAY DIFFRACTION100
4.2591-26.73660.19751450.17813083X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.7031-1.65781.08788.3859-4.87972.9286-0.1697-0.1995-0.07890.34810.52350.4591-0.1436-0.2491-0.40920.22610.02480.02530.2558-0.00450.207727.040353.708533.4318
20.53241.21410.01047.916-0.53580.57360.10750.0179-0.02660.1968-0.1536-0.0089-0.0295-0.03440.08370.25090.01270.01510.2617-0.01240.210124.649653.253425.0134
31.06060.74881.11782.46630.04872.2588-0.14990.4582-0.3916-0.02870.1246-0.10660.20160.46460.04490.230.05310.02910.3563-0.05190.245928.537428.399435.9437
47.91852.66943.3951.56070.77943.4885-0.30380.4195-0.0551-0.10760.2564-0.14710.26340.360.06180.2832-0.00020.04920.3569-0.00610.210927.892328.666736.9895
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 269 through 332 )
2X-RAY DIFFRACTION2chain 'B' and (resid 269 through 336 )
3X-RAY DIFFRACTION3chain 'C' and (resid 1 through 16 )
4X-RAY DIFFRACTION4chain 'D' and (resid 101 through 116 )

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