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- PDB-1nwq: CRYSTAL STRUCTURE OF C/EBPALPHA-DNA COMPLEX -

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Basic information

Entry
Database: PDB / ID: 1nwq
TitleCRYSTAL STRUCTURE OF C/EBPALPHA-DNA COMPLEX
Components
  • 5'-D(*AP*AP*AP*CP*TP*GP*GP*AP*TP*TP*GP*CP*GP*CP*AP*AP*TP*AP*GP*GP*A)-3'
  • 5'-D(*TP*TP*CP*CP*TP*AP*TP*TP*GP*CP*GP*CP*AP*AP*TP*CP*CP*AP*GP*TP*T)-3'
  • CCAAT/enhancer binding protein alpha
KeywordsTRANSCRIPTION/DNA / BASIC LEUCINE ZIPPER / PROTEIN-DNA COMPLEX / TRANSCRIPTION-DNA COMPLEX
Function / homology
Function and homology information


Transcriptional regulation of granulopoiesis / 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 / granulocyte differentiation ...Transcriptional regulation of granulopoiesis / 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 / 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 osteoblast differentiation / positive regulation of fat cell differentiation / brown fat cell differentiation / cholesterol metabolic process / energy homeostasis / transcription by RNA polymerase I / Notch signaling pathway / response to nutrient / lung development / acute-phase response / mitochondrion organization / liver development / chromatin DNA binding / kinase binding / RNA polymerase II transcription regulator complex / memory / histone deacetylase binding / cellular response to xenobiotic stimulus / nuclear matrix / positive regulation of inflammatory response / cellular response to tumor necrosis factor / glucose homeostasis / regulation of cell population proliferation / DNA-binding transcription activator activity, RNA polymerase II-specific / transcription regulator complex / DNA-binding transcription factor binding / sequence-specific DNA binding / RNA polymerase II-specific DNA-binding transcription factor binding / DNA-binding transcription factor activity, RNA polymerase II-specific / cell differentiation / cell population proliferation / transcription cis-regulatory region binding / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / protein heterodimerization activity / protein domain specific binding / negative regulation of cell population proliferation / negative regulation of DNA-templated transcription / DNA-templated transcription / chromatin binding / positive regulation of gene expression / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / protein-containing complex binding / nucleolus / negative regulation of transcription by RNA polymerase II / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / nucleoplasm / identical protein binding / nucleus
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 / Basic-leucine zipper domain superfamily / 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 alpha
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsMiller, M. / Shuman, J.D. / Sebastian, T. / Dauter, Z. / Johnson, P.F.
CitationJournal: J.Biol.Chem. / Year: 2003
Title: Structural Basis for DNA Recognition by the Basic Region Leucine Zipper Transcription Factor CCAAT/enhancer Binding Protein Alpha
Authors: Miller, M. / Shuman, J.D. / Sebastian, T. / Dauter, Z. / Johnson, P.F.
History
DepositionFeb 6, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 13, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)27,7414
Polymers27,7414
Non-polymers00
Water61334
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)140.892, 53.089, 67.406
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: DNA chain 5'-D(*TP*TP*CP*CP*TP*AP*TP*TP*GP*CP*GP*CP*AP*AP*TP*CP*CP*AP*GP*TP*T)-3'


Mass: 6364.120 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain 5'-D(*AP*AP*AP*CP*TP*GP*GP*AP*TP*TP*GP*CP*GP*CP*AP*AP*TP*AP*GP*GP*A)-3'


Mass: 6520.249 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Protein CCAAT/enhancer binding protein alpha / C/EBP alpha / Transcription Factor C/EBPalpha


Mass: 7428.297 Da / Num. of mol.: 2 / Fragment: BASIC REGION, LEUCINE ZIPPER DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: CEBPA / Plasmid: PT5 / Production host: Escherichia coli (E. coli) / References: UniProt: P05554
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 34 / 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: 4.72 Å3/Da / Density % sol: 73.72 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.7
Details: NACL, MGCL2, PEG 400, MES, GLYCEROL, pH 5.7, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
10.75 mMprotein1drop
20.5 mMDNA1drop
350 mM1dropNaCl
4100 mMMES1droppH5.7
5100 mMMES1reservoirpH5.7
6100 mM1reservoirNaCl
730 mM1reservoirMgCl2
818 %PEG4001reservoir
910 %glycerol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 1.07 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07 Å / Relative weight: 1
ReflectionResolution: 2.8→40 Å / Num. obs: 12416 / % possible obs: 95.6 % / Observed criterion σ(I): -3 / Redundancy: 17.8 % / Biso Wilson estimate: 78.5 Å2 / Rmerge(I) obs: 0.076 / Net I/σ(I): 19.2
Reflection shellResolution: 2.8→2.9 Å / Rmerge(I) obs: 0.415 / Mean I/σ(I) obs: 2.7 / % possible all: 91.6
Reflection
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 40 Å / Num. measured all: 222356
Reflection shell
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 2.9 Å / % possible obs: 91.6 %

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Processing

Software
NameVersionClassification
CNS1refinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1DH3

1dh3


Resolution: 2.8→38.53 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 1483361.25 / Data cutoff high rms absF: 1483361.25 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.275 630 5 %RANDOM
Rwork0.221 ---
obs0.221 12415 95.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 37.0305 Å2 / ksol: 0.25376 e/Å3
Displacement parametersBiso mean: 92 Å2
Baniso -1Baniso -2Baniso -3
1--21.1 Å20 Å20 Å2
2--43.07 Å20 Å2
3----21.97 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.62 Å0.48 Å
Luzzati d res low-5 Å
Luzzati sigma a0.83 Å0.77 Å
Refinement stepCycle: LAST / Resolution: 2.8→38.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1020 855 0 34 1909
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.019
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d20.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.25
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it3.753
X-RAY DIFFRACTIONc_mcangle_it5.724
X-RAY DIFFRACTIONc_scbond_it6.844
X-RAY DIFFRACTIONc_scangle_it10.057.5
LS refinement shellResolution: 2.8→2.93 Å / Rfactor Rfree error: 0.05 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.478 93 6.5 %
Rwork0.416 1331 -
obs--90.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
Refinement
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 40 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg20.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.25

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