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- PDB-1gtw: crystal structure of C/EBPbeta bZip homodimer bound to a DNA frag... -

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Basic information

Entry
Database: PDB / ID: 1gtw
Titlecrystal structure of C/EBPbeta bZip homodimer bound to a DNA fragment from the tom-1A promoter
Components
  • 5'-D(*AP*AP*TP*GP*TP*GP*GP*CP*GP*CP* AP*AP*TP*CP*CP*T)-3'
  • 5'-D(*TP*AP*GP*GP*AP*TP*TP*GP*CP*GP* CP*CP*AP*CP*AP*T)-3'
  • CAAT/ENHANCER BINDING PROTEIN BETA
KeywordsTRANSCRIPTION/DNA / PROTEIN-DNA COMPLEX / TRANSCRIPTION FACTOR / C/EBP / HYPOTHETICAL PROTEIN / 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 / Nuclear events stimulated by ALK signaling in cancer / positive regulation of osteoblast differentiation / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsTahirov, T.H. / Ogata, K.
Citation
Journal: To be Published
Title: Structural Basis for Flexible Base Recognition by C/Ebpbeta
Authors: Tahirov, T.H. / Inoue-Bungo, T. / Sato, K. / Sasaki, M. / Ogata, K.
#1: Journal: Cell (Cambridge,Mass.) / Year: 2002
Title: Mechanism of C-Myb-C/Ebpbeta Cooperation from Separated Sites on a Promoter
Authors: Tahirov, T.H. / Sato, K. / Ichikawa-Iwata, E. / Sasaki, M. / Inoue-Bungo, T. / Shiina, M. / Kimura, K. / Takata, S. / Fujikawa, A. / Morii, H. / Kumasaka, T. / Yamamoto, M. / Ishii, S. / Ogata, K.
#2: Journal: Acta Crystallogr.,Sect.D / Year: 2001
Title: Crystallization and Preliminary X-Ray Analysis of the C/Ebpbeta C-Terminal Region in Complex with DNA
Authors: Tahirov, T.H. / Inoue-Bungo, T. / Sasaki, M. / Fujikawa, A. / Kimura, K. / Sato, K. / Adachi, S. / Kamiyaogata, K.
#3: Journal: Cell (Cambridge,Mass.) / Year: 2001
Title: Structural Analyses of DNA Recognition by the Aml1/ Runx-1 Runt Domain and its Allosteric Control by Cbfbeta
Authors: Tahirov, T.H. / Inoue-Bungo, T. / Morii, H. / Fujikawa, A. / Sasaki, M. / Kimura, K. / Shiina, M. / Sato, K. / Kumasaka, T. / Yamamoto, M. / Ishii, S. / Ogata, K.
#4: Journal: Acta Crystallogr.,Sect.D / Year: 2001
Title: Crystallization and Preliminary X-Ray Analyses of Quaternary, Ternary and Binary Protein-DNA Complexes with Involvement of Aml1/Runx-1/Cbfalpha Runt Domain, Cbfbeta and the C/Ebpbeta bZIP Region
Authors: Tahirov, T.H. / Inoue, T. / Sasaki, M. / Shiina, M. / Kimura, K. / Sato, K. / Kumasaka, T. / Yamamoto, M. / Kamiya, N. / Ogata, K.
#5: Journal: Acta Crystallogr.,Sect.D / Year: 2001
Title: Crystals of Ternary Protein-DNA Complexes Composed of DNA-Binding Domains C-Myb or V-Myb, C/Ebpalpha or C/Ebpbeta and Tom-1A Promoter Fragment
Authors: Tahirov, T.H. / Inoue, T. / Sasaki, M. / Shiina, M. / Kimura, K. / Sato, K. / Kumasaka, T. / Yamamoto, M. / Kamiya, N. / Ogata, K.
History
DepositionJan 22, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 6, 2004Provider: repository / Type: Initial release
Revision 1.1Jan 22, 2014Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Other / Refinement description / Structure summary / Version format compliance
Revision 1.2Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CAAT/ENHANCER BINDING PROTEIN BETA
B: CAAT/ENHANCER BINDING PROTEIN BETA
C: 5'-D(*AP*AP*TP*GP*TP*GP*GP*CP*GP*CP* AP*AP*TP*CP*CP*T)-3'
D: 5'-D(*TP*AP*GP*GP*AP*TP*TP*GP*CP*GP* CP*CP*AP*CP*AP*T)-3'


Theoretical massNumber of molelcules
Total (without water)28,5604
Polymers28,5604
Non-polymers00
Water5,693316
1
A: CAAT/ENHANCER BINDING PROTEIN BETA
B: CAAT/ENHANCER BINDING PROTEIN BETA
C: 5'-D(*AP*AP*TP*GP*TP*GP*GP*CP*GP*CP* AP*AP*TP*CP*CP*T)-3'
D: 5'-D(*TP*AP*GP*GP*AP*TP*TP*GP*CP*GP* CP*CP*AP*CP*AP*T)-3'

A: CAAT/ENHANCER BINDING PROTEIN BETA
B: CAAT/ENHANCER BINDING PROTEIN BETA
C: 5'-D(*AP*AP*TP*GP*TP*GP*GP*CP*GP*CP* AP*AP*TP*CP*CP*T)-3'
D: 5'-D(*TP*AP*GP*GP*AP*TP*TP*GP*CP*GP* CP*CP*AP*CP*AP*T)-3'


Theoretical massNumber of molelcules
Total (without water)57,1208
Polymers57,1208
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_567x,-y+1,-z+21
Buried area13900 Å2
ΔGint-94.5 kcal/mol
Surface area27120 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6050 Å2
ΔGint-44.8 kcal/mol
Surface area14460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.938, 112.533, 74.349
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-2045-

HOH

DetailsDIMER OF TETRAMER CONTAINING TWO PROTEIN CHAINS AND TWO DNA CHAINS

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Components

#1: Protein CAAT/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: 9381.868 Da / Num. of mol.: 2 / Fragment: BZIP DOMAIN, RESIDUES 259-336
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PAR2156 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P17676
#2: DNA chain 5'-D(*AP*AP*TP*GP*TP*GP*GP*CP*GP*CP* AP*AP*TP*CP*CP*T)-3'


Mass: 4898.190 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: TOM-1A PROMOTER
#3: DNA chain 5'-D(*TP*AP*GP*GP*AP*TP*TP*GP*CP*GP* CP*CP*AP*CP*AP*T)-3'


Mass: 4898.191 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: TOM-1A PROMOTER
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 316 / 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: 3.7 Å3/Da / Density % sol: 66 %
Crystal growpH: 6.5
Details: 0.2 M POTASSIUM CHLORIDE, 0.1 M MAGNESIUM ACETATE, 10.0% W/V PEG 8000, 0.05 M SODIUM CACODYLATE CACODYLATE BUFFER PH 6.5, PROTEIN-DNA COMPLEX SOLUTION CONTAINS 0.01 M DTT AND 0.005 M NAN3, ...Details: 0.2 M POTASSIUM CHLORIDE, 0.1 M MAGNESIUM ACETATE, 10.0% W/V PEG 8000, 0.05 M SODIUM CACODYLATE CACODYLATE BUFFER PH 6.5, PROTEIN-DNA COMPLEX SOLUTION CONTAINS 0.01 M DTT AND 0.005 M NAN3, PROTEIN:DNA RATIO IS 1:1.2

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44B2 / Wavelength: 0.6
DetectorType: RIGAKU IMAGE PLATE RAXIS IV / Detector: IMAGE PLATE / Date: Dec 11, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.6 Å / Relative weight: 1
ReflectionResolution: 1.7→20 Å / Num. obs: 44759 / % possible obs: 95.8 % / Observed criterion σ(I): 0 / Redundancy: 4.008 % / Biso Wilson estimate: 34.2 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 21.0506
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 2.43 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 1.343 / % possible all: 82.9

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1H8A

1h8a


Resolution: 1.85→19.87 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 327560.56 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.271 1809 5.1 %RANDOM
Rwork0.231 ---
obs0.231 35717 98 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 25 Å2 / ksol: 0.348766 e/Å3
Displacement parametersBiso mean: 42.9 Å2
Baniso -1Baniso -2Baniso -3
1-7.95 Å20 Å20 Å2
2---5.16 Å20 Å2
3----2.79 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.27 Å
Luzzati d res low-20 Å
Luzzati sigma a0.44 Å0.39 Å
Refinement stepCycle: LAST / Resolution: 1.85→19.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1129 650 0 316 2095
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.004
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_deg1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d15.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.13
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it4.971.5
X-RAY DIFFRACTIONc_mcangle_it5.682
X-RAY DIFFRACTIONc_scbond_it6.942
X-RAY DIFFRACTIONc_scangle_it9.232.5
LS refinement shellResolution: 1.85→1.97 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.432 282 5 %
Rwork0.378 5402 -
obs--94.9 %
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

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