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- PDB-7upz: Structural basis for cell type specific DNA binding of C/EBPbeta:... -

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Basic information

Entry
Database: PDB / ID: 7upz
TitleStructural basis for cell type specific DNA binding of C/EBPbeta: the case of cell cycle inhibitor p15INK4b promoter
Components
  • CCAAT/enhancer-binding protein beta
  • DNA (5'-D(*AP*TP*TP*CP*TP*TP*AP*AP*GP*AP*AP*AP*GP*AP*CP*G)-3')
  • DNA (5'-D(*TP*CP*GP*TP*CP*TP*TP*TP*CP*TP*TP*AP*AP*GP*AP*A)-3')
KeywordsDNA BINDING PROTEIN/DNA / C/EBPbeta-DNA interactions / DNA sequence motif / DNA BINDING PROTEIN-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 / Basic-leucine zipper (bZIP) domain profile. / basic region leucin zipper / Basic-leucine zipper domain superfamily / Basic-leucine zipper domain
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: 2.487 Å
AuthorsLountos, G.T. / Cherry, S. / Tropea, J.E. / Wlodawer, A. / Miller, M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI) United States
CitationJournal: J.Struct.Biol. / Year: 2022
Title: Structural basis for cell type specific DNA binding of C/EBP beta : The case of cell cycle inhibitor p15INK4b promoter.
Authors: Lountos, G.T. / Cherry, S. / Tropea, J.E. / Wlodawer, A. / Miller, M.
History
DepositionApr 18, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 23, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 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

Downloads & links

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Assembly

Deposited unit
A: CCAAT/enhancer-binding protein beta
B: CCAAT/enhancer-binding protein beta
C: DNA (5'-D(*AP*TP*TP*CP*TP*TP*AP*AP*GP*AP*AP*AP*GP*AP*CP*G)-3')
D: DNA (5'-D(*TP*CP*GP*TP*CP*TP*TP*TP*CP*TP*TP*AP*AP*GP*AP*A)-3')


Theoretical massNumber of molelcules
Total (without water)28,9884
Polymers28,9884
Non-polymers00
Water1,53185
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6050 Å2
ΔGint-47 kcal/mol
Surface area14860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.699, 112.758, 75.528
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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: 9597.074 Da / Num. of mol.: 2 / Fragment: UNP residues 257-336
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CEBPB, TCF5, PP9092 / Plasmid: pJT328 / Production host: Escherichia coli (E. coli) / References: UniProt: P17676
#2: DNA chain DNA (5'-D(*AP*TP*TP*CP*TP*TP*AP*AP*GP*AP*AP*AP*GP*AP*CP*G)-3')


Mass: 4930.242 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: DNA chain DNA (5'-D(*TP*CP*GP*TP*CP*TP*TP*TP*CP*TP*TP*AP*AP*GP*AP*A)-3')


Mass: 4863.177 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 85 / 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: 3.73 Å3/Da / Density % sol: 67.07 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 100 mM potassium chloride, 10 mM magnesium chloride, 50 mM MES, pH 6.0, 10% v/v PEG400, 5% v/v glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 22, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.487→50 Å / Num. obs: 15346 / % possible obs: 99.4 % / Redundancy: 6.6 % / CC1/2: 0.979 / Rmerge(I) obs: 0.056 / Rpim(I) all: 0.024 / Net I/σ(I): 28.8
Reflection shellResolution: 2.487→2.54 Å / Rmerge(I) obs: 1.16 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 769 / CC1/2: 0.72 / Rpim(I) all: 0.506

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1GTW

1gtw


Resolution: 2.487→42.181 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 26.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2641 790 5.47 %
Rwork0.2123 13662 -
obs0.2151 14452 92.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 147.25 Å2 / Biso mean: 49.0353 Å2 / Biso min: 10.52 Å2
Refinement stepCycle: final / Resolution: 2.487→42.181 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1121 650 0 85 1856
Biso mean---39.59 -
Num. residues----164
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.487-2.64270.345890.315145661
2.6427-2.84670.30881430.2778239899
2.8467-3.13310.32361510.26212418100
3.1331-3.58630.26341240.2196241398
3.5863-4.51750.23921090.1784245899
4.5175-42.180.22351740.1743251999
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)
11.783-3.0188-2.40246.38745.80764.91780.0058-0.39060.2291-0.17510.5215-0.7766-0.20610.4655-0.40120.3043-0.00830.10040.1772-0.03140.207123.27494.2122-3.5099
27.1036-2.50745.21126.1035-1.2443.891-0.796-0.78182.18211.7607-0.9802-0.2076-2.49650.04581.73851.28-0.3332-0.01520.8882-0.12771.124734.94347.2315-1.2365
30.42220.810.1836.11470.62320.52280.00620.23440.1082-0.0712-0.13290.4378-0.04530.2011-0.0570.28330.06340.1868-0.1542-0.09640.190125.64451.5762-13.141
45.7351-1.18120.81740.2448-0.22462.214-0.2850.07220.8932-0.0182-0.097-0.5914-0.00560.52450.09670.18190.10390.08120.40170.22780.455339.654529.8689-7.3059
56.5695-4.1407-0.67755.22753.36265.0407-0.3497-0.7595-0.00240.0498-0.07760.12980.776-0.14630.0510.3071-0.09480.21840.44170.03220.293924.440528.10472.6712
64.74685.0703-0.96745.72080.07725.4969-0.57080.98590.863-1.4210.26271.56480.1446-1.60910.2720.3911-0.103-0.09160.88540.09120.5727.481529.7587-2.3556
78.1697-1.03268.45161.9999-2.48779.2161-0.5973.3021-2.0841-1.8075-0.2782-1.89980.67190.27050.90520.6065-0.18370.43831.4608-0.02081.2306-0.432620.53121.6714
83.0517-0.5590.23170.98820.34310.8923-0.1728-0.26270.67470.0237-0.09220.53790.0201-0.4307-0.55080.1988-0.2482-0.00310.9576-0.05280.6773.03326.72676.7368
98.28312.1178-3.48173.2023-1.77984.85380.0873-0.27410.20750.2734-0.1589-0.12380.20770.28630.09230.48890.06420.08010.283-0.05380.134327.461629.1099-1.7336
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 269 through 332 )A269 - 332
2X-RAY DIFFRACTION2chain 'B' and (resid 268 through 272 )B268 - 272
3X-RAY DIFFRACTION3chain 'B' and (resid 273 through 335 )B273 - 335
4X-RAY DIFFRACTION4chain 'C' and (resid 1 through 5 )C1 - 5
5X-RAY DIFFRACTION5chain 'C' and (resid 6 through 10 )C6 - 10
6X-RAY DIFFRACTION6chain 'C' and (resid 11 through 15 )C11 - 15
7X-RAY DIFFRACTION7chain 'C' and (resid 16 through 16 )C16
8X-RAY DIFFRACTION8chain 'D' and (resid 1 through 5 )D1 - 5
9X-RAY DIFFRACTION9chain 'D' and (resid 6 through 16 )D6 - 16

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