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- PDB-8k8c: Crystal structure of C/EBPalpha BZIP domain bound to a high affin... -

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Basic information

Entry
Database: PDB / ID: 8k8c
TitleCrystal structure of C/EBPalpha BZIP domain bound to a high affinity DNA
Components
  • CCAAT/enhancer-binding protein alpha
  • DNA (5'-D(*CP*AP*TP*TP*AP*CP*GP*TP*AP*AP*TP*GP*A)-3')
  • DNA (5'-D(*CP*AP*TP*TP*AP*CP*GP*TP*AP*AP*TP*GP*T)-3')
KeywordsDNA BINDING PROTEIN/DNA / C/EBPalpha / DNA binding / bZIP / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


negative regulation of hematopoietic stem cell proliferation / response to vitamin B2 / CHOP-C/EBP complex / C/EBP complex / HMG box domain binding / response to phenylpropanoid / Rb-E2F complex / RNA polymerase I transcription regulatory region sequence-specific DNA binding / integrated stress response signaling / positive regulation of DNA-templated transcription initiation ...negative regulation of hematopoietic stem cell proliferation / response to vitamin B2 / CHOP-C/EBP complex / C/EBP complex / HMG box domain binding / response to phenylpropanoid / Rb-E2F complex / RNA polymerase I transcription regulatory region sequence-specific DNA binding / integrated stress response signaling / positive regulation of DNA-templated transcription initiation / granulocyte differentiation / urea cycle / myeloid cell differentiation / positive regulation of macrophage activation / epithelial cell maturation / osteoblast development / cellular response to lithium ion / STAT family protein binding / interleukin-6-mediated signaling pathway / response to dexamethasone / hematopoietic stem cell proliferation / fat cell differentiation / lipid homeostasis / negative regulation of cell cycle / inner ear development / macrophage differentiation / white fat cell differentiation / animal organ regeneration / embryonic placenta development / positive regulation of fat cell differentiation / positive regulation of osteoblast differentiation / brown fat cell differentiation / cholesterol metabolic process / energy homeostasis / transcription by RNA polymerase I / Notch signaling pathway / lung development / acute-phase response / generation of precursor metabolites and energy / mitochondrion organization / liver development / chromatin DNA binding / Transcriptional regulation of white adipocyte differentiation / kinase binding / RNA polymerase II transcription regulator complex / memory / histone deacetylase binding / cellular response to xenobiotic stimulus / nuclear matrix / Transcriptional regulation of granulopoiesis / cytokine-mediated signaling pathway / positive regulation of inflammatory response / cellular response to tumor necrosis factor / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / glucose homeostasis / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / DNA-binding transcription activator activity, RNA polymerase II-specific / transcription regulator complex / RNA polymerase II-specific DNA-binding transcription factor binding / DNA-binding transcription factor activity, RNA polymerase II-specific / transcription cis-regulatory region binding / regulation of cell cycle / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / protein heterodimerization activity / negative regulation of cell population proliferation / negative regulation of DNA-templated transcription / intracellular membrane-bounded organelle / DNA-templated transcription / positive regulation of gene expression / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / chromatin / protein-containing complex binding / nucleolus / negative regulation of transcription by RNA polymerase II / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / identical protein binding / nucleus
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 / Basic-leucine zipper domain superfamily
Similarity search - Domain/homology
DNA / DNA (> 10) / CCAAT/enhancer-binding protein alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.06 Å
AuthorsMin, J.R. / Chen, S.Z. / Liu, K.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: J.Biol.Chem. / Year: 2024
Title: Structural basis for specific DNA sequence recognition by the transcription factor NFIL3.
Authors: Chen, S. / Lei, M. / Liu, K. / Min, J.
History
DepositionJul 29, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 6, 2024Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Database references / Category: citation / Item: _citation.journal_volume

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CCAAT/enhancer-binding protein alpha
B: CCAAT/enhancer-binding protein alpha
C: DNA (5'-D(*CP*AP*TP*TP*AP*CP*GP*TP*AP*AP*TP*GP*A)-3')
D: DNA (5'-D(*CP*AP*TP*TP*AP*CP*GP*TP*AP*AP*TP*GP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,8076
Polymers22,6234
Non-polymers1842
Water99155
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6010 Å2
ΔGint-38 kcal/mol
Surface area12670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.382, 63.366, 128.546
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein CCAAT/enhancer-binding protein alpha


Mass: 7341.220 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CEBPA / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P49715
#2: DNA chain DNA (5'-D(*CP*AP*TP*TP*AP*CP*GP*TP*AP*AP*TP*GP*A)-3')


Mass: 3974.623 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(*CP*AP*TP*TP*AP*CP*GP*TP*AP*AP*TP*GP*T)-3')


Mass: 3965.609 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 55 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.54 Å3/Da / Density % sol: 65.3 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.015 M Calcium chloride dihydrate,0.1 M Sodium acetate trihydrate pH 4.6, 30% v/v 2-Methyl-2,4-pentanediol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 9, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.06→64.27 Å / Num. obs: 20836 / % possible obs: 99.9 % / Redundancy: 12.5 % / CC1/2: 1 / Net I/σ(I): 18.9
Reflection shellResolution: 2.06→2.17 Å / Num. unique obs: 2979 / CC1/2: 0.938

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487)refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.06→19.96 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 34.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2823 1986 9.61 %
Rwork0.2255 --
obs0.2308 20673 99.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.06→19.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1004 527 12 55 1598
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081604
X-RAY DIFFRACTIONf_angle_d1.0732250
X-RAY DIFFRACTIONf_dihedral_angle_d25.259398
X-RAY DIFFRACTIONf_chiral_restr0.049248
X-RAY DIFFRACTIONf_plane_restr0.011207
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.06-2.110.50431390.4971311X-RAY DIFFRACTION100
2.11-2.160.47341400.44361305X-RAY DIFFRACTION99
2.16-2.230.42741360.40081307X-RAY DIFFRACTION99
2.23-2.30.37161410.33141314X-RAY DIFFRACTION99
2.3-2.380.35551380.31031298X-RAY DIFFRACTION100
2.38-2.480.32871440.25561358X-RAY DIFFRACTION100
2.48-2.590.26721380.24021291X-RAY DIFFRACTION100
2.59-2.720.29741410.24521322X-RAY DIFFRACTION100
2.72-2.890.30661420.24351335X-RAY DIFFRACTION100
2.89-3.120.27411400.23681334X-RAY DIFFRACTION100
3.12-3.430.23521420.20451334X-RAY DIFFRACTION99
3.43-3.920.28351450.18781355X-RAY DIFFRACTION99
3.92-4.930.21381460.1781375X-RAY DIFFRACTION100
4.93-19.960.27271540.18871448X-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)
10.19420.01220.56080.1833-0.50331.0803-0.19090.0847-0.18520.0317-0.0084-0.15510.0353-0.1833-0.0010.44440.06090.03360.32950.03870.37046.0155.620133.7934
20.15560.0629-0.37840.6074-0.90320.9392-0.11310.15720.17640.1844-0.1662-0.1538-0.27460.121-0.00060.46950.0259-0.02410.3656-0.00470.399-0.091913.595537.63
30.5465-0.27820.03551.81670.30012.0134-0.2884-0.05240.22550.0335-0.03460.19420.085-0.2185-0.00030.39120.00590.05870.42920.00080.42060.110614.690113.6178
41.1921-0.9712-0.40420.9404-0.19731.7618-0.0924-0.3242-0.18010.1185-0.04160.05760.03330.1633-0.00040.39160.00560.00380.4678-0.02640.38934.699416.980814.6827
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resseq 281:402)
2X-RAY DIFFRACTION2(chain B and resseq 283:340)
3X-RAY DIFFRACTION3(chain C and resseq 1:13)
4X-RAY DIFFRACTION4(chain D and resseq 1:13)

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