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- PDB-1gu5: Crystal structure of C/EBPBETA BZIP homodimer bound to a DNA frag... -

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Basic information

Entry
Database: PDB / ID: 1gu5
TitleCrystal structure of C/EBPBETA BZIP homodimer bound to a DNA fragment from the MIM-1 promoter
Components
  • 5'-D(*AP*TP*GP*AP*TP*TP*GP*GP*CP*CP* AP*AP*CP*AP*CP*A)-3'
  • 5'-D(*TP*TP*GP*TP*GP*TP*TP*GP*GP*CP* CP*AP*AP*TP*CP*A)-3'
  • CAAT/ENHANCER BINDING PROTEIN BETA
KeywordsTRANSCRIPTION/DNA / PROTEIN-DNA COMPLEX / TRANSCRIPTION FACTOR / BZIP / C/EBP / TRANSCRIPTION-DNA complex
Function / homology
Function and homology information


granuloma formation / regulation of odontoblast differentiation / positive regulation of sodium-dependent phosphate transport / CHOP-C/EBP complex / C/EBP complex / positive regulation of biomineral tissue development / myeloid cell development / integrated stress response signaling / T-helper 1 cell activation / hepatocyte proliferation ...granuloma formation / regulation of odontoblast differentiation / positive regulation of sodium-dependent phosphate transport / CHOP-C/EBP complex / C/EBP complex / positive regulation of biomineral tissue development / myeloid cell development / integrated stress response signaling / T-helper 1 cell activation / hepatocyte proliferation / Response of EIF2AK1 (HRI) to heme deficiency / 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 / Transcriptional Regulation by VENTX / Response of EIF2AK4 (GCN2) to amino acid deficiency / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / positive regulation of fat cell differentiation / embryonic placenta development / positive regulation of osteoblast differentiation / brown fat cell differentiation / RNA polymerase II core promoter sequence-specific DNA binding / Nuclear events stimulated by ALK signaling in cancer / ovarian follicle development / negative regulation of T cell proliferation / response to endoplasmic reticulum stress / liver regeneration / acute-phase response / RNA polymerase II transcription regulatory region sequence-specific DNA binding / cellular response to amino acid stimulus / chromatin DNA binding / Transcriptional regulation of white adipocyte differentiation / DNA-binding transcription repressor activity, RNA polymerase II-specific / kinase binding / histone deacetylase binding / RNA polymerase II transcription regulator complex / nuclear matrix / Transcriptional regulation of granulopoiesis / positive regulation of inflammatory response / neuron differentiation / sequence-specific double-stranded DNA binding / positive regulation of cold-induced thermogenesis / DNA-binding transcription activator activity, RNA polymerase II-specific / Senescence-Associated Secretory Phenotype (SASP) / negative regulation of neuron apoptotic process / response to lipopolysaccharide / transcription by RNA polymerase II / DNA-binding transcription factor activity, RNA polymerase II-specific / transcription cis-regulatory region binding / defense response to bacterium / immune response / inflammatory response / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / chromatin / 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 / 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 beta
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
SYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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 24, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 26, 2003Provider: repository / Type: Initial release
Revision 1.1Dec 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(*TP*TP*GP*TP*GP*TP*TP*GP*GP*CP* CP*AP*AP*TP*CP*A)-3'
D: 5'-D(*AP*TP*GP*AP*TP*TP*GP*GP*CP*CP* AP*AP*CP*AP*CP*A)-3'


Theoretical massNumber of molelcules
Total (without water)28,5594
Polymers28,5594
Non-polymers00
Water4,035224
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5940 Å2
ΔGint-48 kcal/mol
Surface area14540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.596, 113.037, 74.498
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-2047-

HOH

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Components

#1: Protein CAAT/ENHANCER BINDING PROTEIN BETA / C/EBP BETA / NUCLEAR FACTOR NF-IL6 / TRANSCRIPTION FACTOR 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(*TP*TP*GP*TP*GP*TP*TP*GP*GP*CP* CP*AP*AP*TP*CP*A)-3'


Mass: 4904.188 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)
#3: DNA chain 5'-D(*AP*TP*GP*AP*TP*TP*GP*GP*CP*CP* AP*AP*CP*AP*CP*A)-3'


Mass: 4891.206 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 224 / 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: 3.74 Å3/Da / Density % sol: 66 %
Crystal growpH: 6.5
Details: 0.08 M MAGNESIUM ACETATE, 15.0% V/V PEG 400, 0.05 M SODIUM CACODYLATE BUFFER PH 6.5, PROTEIN-DNA COMPLEX CONCENTRATION WAS 12 MG/ML WITH ADDITION OF 0.01 M DTT, PROTEIN:DNA RATIO WAS 1:1.2 ...Details: 0.08 M MAGNESIUM ACETATE, 15.0% V/V PEG 400, 0.05 M SODIUM CACODYLATE BUFFER PH 6.5, PROTEIN-DNA COMPLEX CONCENTRATION WAS 12 MG/ML WITH ADDITION OF 0.01 M DTT, PROTEIN:DNA RATIO WAS 1:1.2 FOR CRYOPROTECTION THE CONCENTRATION OF PEG 400 WAS ADJUSTED TO 36% V/V

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 1.02
DetectorType: RIGAKU RAXIS V / Detector: IMAGE PLATE / Date: Oct 12, 2001 / Details: MIRRORS
RadiationMonochromator: DIAMOND / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.02 Å / Relative weight: 1
ReflectionResolution: 2.08→30 Å / Num. obs: 25871 / % possible obs: 99.4 % / Observed criterion σ(I): 0 / Redundancy: 6.088 % / Biso Wilson estimate: 44 Å2 / Rmerge(I) obs: 0.069 / Net I/σ(I): 24.364
Reflection shellResolution: 2.08→2.12 Å / Redundancy: 4.55 % / Rmerge(I) obs: 0.468 / Mean I/σ(I) obs: 3.13 / % possible all: 97.3

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GTW

1gtw


Resolution: 2.1→29.74 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 734912.08 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.277 1228 4.9 %RANDOM
Rwork0.229 ---
obs0.229 25194 99.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 54.8637 Å2 / ksol: 0.335149 e/Å3
Displacement parametersBiso mean: 48.3 Å2
Baniso -1Baniso -2Baniso -3
1-4.88 Å20 Å20 Å2
2---3.32 Å20 Å2
3----1.57 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.29 Å
Luzzati d res low-30 Å
Luzzati sigma a0.26 Å0.21 Å
Refinement stepCycle: LAST / Resolution: 2.1→29.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1129 650 0 224 2003
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
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_deg0.9
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d14.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.05
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it5.231.5
X-RAY DIFFRACTIONc_mcangle_it6.252
X-RAY DIFFRACTIONc_scbond_it7.352
X-RAY DIFFRACTIONc_scangle_it9.732.5
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.333 214 5.3 %
Rwork0.27 3848 -
obs--97.4 %
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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