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- PDB-8k8d: Crystal structure of C/EBPbeta BZIP domain bound to a high affini... -

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Basic information

Entry
Database: PDB / ID: 8k8d
TitleCrystal structure of C/EBPbeta BZIP domain bound to a high affinity DNA
Components
  • CCAAT/enhancer-binding protein beta
  • DNA (5'-D(*CP*AP*TP*TP*AP*CP*GP*TP*AP*AP*TP*G)-3')
KeywordsDNA BINDING PROTEIN/DNA / C/EBPbeta / bZIP / DNA binding / DNA BINDING PROTEIN / 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 / 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 / positive regulation of interleukin-4 production / 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 / ovarian follicle development / negative regulation of T cell proliferation / response to endoplasmic reticulum stress / liver regeneration / acute-phase response / cellular response to amino acid stimulus / RNA polymerase II transcription regulatory region sequence-specific DNA binding / neuron differentiation / chromatin DNA binding / nuclear matrix / DNA-binding transcription repressor activity, RNA polymerase II-specific / kinase binding / positive regulation of inflammatory response / Transcriptional regulation of white adipocyte differentiation / Transcriptional regulation of granulopoiesis / histone deacetylase binding / 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 / immune response / inflammatory response / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / chromatin / regulation of DNA-templated transcription / 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)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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

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(*CP*AP*TP*TP*AP*CP*GP*TP*AP*AP*TP*G)-3')
D: DNA (5'-D(*CP*AP*TP*TP*AP*CP*GP*TP*AP*AP*TP*G)-3')


Theoretical massNumber of molelcules
Total (without water)26,2014
Polymers26,2014
Non-polymers00
Water1,04558
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5130 Å2
ΔGint-40 kcal/mol
Surface area14480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.668, 46.400, 98.783
Angle α, β, γ (deg.)90.00, 108.76, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein CCAAT/enhancer-binding protein beta


Mass: 9438.920 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CEBPB / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P17676
#2: DNA chain DNA (5'-D(*CP*AP*TP*TP*AP*CP*GP*TP*AP*AP*TP*G)-3')


Mass: 3661.416 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 58 / 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: 2.64 Å3/Da / Density % sol: 53.35 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.02 M Calcium chloride dihydrate,0.1 M Sodium acetate trihydrate pH 4.6 and 20% v/v 2-Propanol

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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: 2.2→32.14 Å / Num. obs: 13958 / % possible obs: 99.9 % / Redundancy: 1.9 % / CC1/2: 0.996 / Net I/σ(I): 15.6
Reflection shellResolution: 2.2→2.27 Å / Num. unique obs: 608 / CC1/2: 0.898

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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: 2.2→30.13 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 34.28 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2918 701 5.03 %
Rwork0.2359 --
obs0.2388 13944 99.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2→30.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1143 487 0 58 1688
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081694
X-RAY DIFFRACTIONf_angle_d1.0282361
X-RAY DIFFRACTIONf_dihedral_angle_d24.845384
X-RAY DIFFRACTIONf_chiral_restr0.051261
X-RAY DIFFRACTIONf_plane_restr0.009223
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.370.32071440.27222590X-RAY DIFFRACTION99
2.37-2.610.35111370.282666X-RAY DIFFRACTION100
2.61-2.990.32021240.26572637X-RAY DIFFRACTION100
2.99-3.770.29321450.22442666X-RAY DIFFRACTION100
3.77-30.130.27131510.22192684X-RAY DIFFRACTION99
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)
10.6449-0.40530.3311.7863-2.04446.39-0.1336-0.04270.09090.1476-0.1977-0.0672-0.08570.72510.2160.41980.05480.01270.42330.00210.37570.07824.107652.2845
20.5821-0.3038-0.62981.4621.5873.3815-0.262-0.0157-0.19280.0945-0.29290.15420.0686-0.3860.44520.43010.085-0.01390.4150.01740.42380.0202-4.840251.6102
39.343-2.9932-2.3156.41163.74143.4376-0.24870.0671-0.83390.4721-0.22330.24960.0262-0.04010.45060.4120.10810.01820.30720.14740.39350.8739-0.192626.5147
47.7645-3.02171.64077.5911-2.45073.0686-0.3703-0.11590.95740.5032-0.0086-0.1946-0.2855-0.16320.35630.42990.09170.01620.3346-0.11060.3665-0.8363-0.161426.4751
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resseq 268:335)
2X-RAY DIFFRACTION2(chain B and resseq 269:333)
3X-RAY DIFFRACTION3(chain C and resseq 1:12)
4X-RAY DIFFRACTION4(chain D and resseq 1:12)

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