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- PDB-1awc: MOUSE GABP ALPHA/BETA DOMAIN BOUND TO DNA -

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Basic information

Entry
Database: PDB / ID: 1awc
TitleMOUSE GABP ALPHA/BETA DOMAIN BOUND TO DNA
Components
  • DNA (5'-D(*AP*AP*(BRU)P*GP*AP*CP*CP*GP*GP*AP*AP*GP*TP*AP*(CBR)P*AP*CP*(CBR)P*GP*GP*A)-3')
  • DNA (5'-D(*TP*TP*CP*CP*GP*GP*(BRU)P*GP*(BRU)P*AP*CP*TP*TP*CP*CP*GP*GP*TP*CP*AP*T)-3')
  • PROTEIN (GA BINDING PROTEIN ALPHA)
  • PROTEIN (GA BINDING PROTEIN BETA 1)
KeywordsTRANSCRIPTION/DNA / COMPLEX (TRANSCRIPTION REGULATION-DNA) / DNA-BINDING / NUCLEAR PROTEIN / ETS DOMAIN / ANKYRIN REPEATS / TRANSCRIPTION FACTOR / TRANSCRIPTION-DNA COMPLEX
Function / homology
Function and homology information


Transcriptional activation of mitochondrial biogenesis / blastocyst formation / negative regulation of megakaryocyte differentiation / mitochondrion organization / cytoplasmic ribonucleoprotein granule / DNA-binding transcription activator activity, RNA polymerase II-specific / in utero embryonic development / cell differentiation / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific ...Transcriptional activation of mitochondrial biogenesis / blastocyst formation / negative regulation of megakaryocyte differentiation / mitochondrion organization / cytoplasmic ribonucleoprotein granule / DNA-binding transcription activator activity, RNA polymerase II-specific / in utero embryonic development / cell differentiation / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / chromatin binding / chromatin / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / nucleoplasm / nucleus
Similarity search - Function
Transcription factor, GA-binding, alpha subunit / GA-binding protein alpha subunit, N-terminal / GA-binding protein alpha chain / Domain of unknown function DUF3447 / SAM / Pointed domain / Pointed domain / Sterile alpha motif (SAM)/Pointed domain / Pointed (PNT) domain profile. / Ets-domain signature 1. / ETS family ...Transcription factor, GA-binding, alpha subunit / GA-binding protein alpha subunit, N-terminal / GA-binding protein alpha chain / Domain of unknown function DUF3447 / SAM / Pointed domain / Pointed domain / Sterile alpha motif (SAM)/Pointed domain / Pointed (PNT) domain profile. / Ets-domain signature 1. / ETS family / Ets-domain signature 2. / Ets domain / Ets-domain / Ets-domain profile. / erythroblast transformation specific domain / Ankyrin repeat-containing domain / Ankyrin repeats (many copies) / Sterile alpha motif/pointed domain superfamily / Ankyrin repeats (3 copies) / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Arc Repressor Mutant, subunit A / Ubiquitin-like domain superfamily / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / GA-binding protein subunit beta-1 / GA-binding protein alpha chain
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.15 Å
AuthorsBatchelor, A.H. / Wolberger, C.
CitationJournal: Science / Year: 1998
Title: The structure of GABPalpha/beta: an ETS domain- ankyrin repeat heterodimer bound to DNA.
Authors: Batchelor, A.H. / Piper, D.E. / de la Brousse, F.C. / McKnight, S.L. / Wolberger, C.
History
DepositionOct 1, 1997Deposition site: BNL / Processing site: NDB
Revision 1.0Mar 18, 1998Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: DNA (5'-D(*AP*AP*(BRU)P*GP*AP*CP*CP*GP*GP*AP*AP*GP*TP*AP*(CBR)P*AP*CP*(CBR)P*GP*GP*A)-3')
E: DNA (5'-D(*TP*TP*CP*CP*GP*GP*(BRU)P*GP*(BRU)P*AP*CP*TP*TP*CP*CP*GP*GP*TP*CP*AP*T)-3')
A: PROTEIN (GA BINDING PROTEIN ALPHA)
B: PROTEIN (GA BINDING PROTEIN BETA 1)


Theoretical massNumber of molelcules
Total (without water)43,1384
Polymers43,1384
Non-polymers00
Water82946
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)201.600, 34.550, 59.260
Angle α, β, γ (deg.)90.00, 99.83, 90.00
Int Tables number5
Cell settingmonoclinic
Space group name H-MC121

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Components

#1: DNA chain DNA (5'-D(*AP*AP*(BRU)P*GP*AP*CP*CP*GP*GP*AP*AP*GP*TP*AP*(CBR)P*AP*CP*(CBR)P*GP*GP*A)-3')


Mass: 6712.888 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain DNA (5'-D(*TP*TP*CP*CP*GP*GP*(BRU)P*GP*(BRU)P*AP*CP*TP*TP*CP*CP*GP*GP*TP*CP*AP*T)-3')


Mass: 6525.857 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Protein PROTEIN (GA BINDING PROTEIN ALPHA) / GABPALPHA / GABP-ALPHA SUBUNIT


Mass: 13065.230 Da / Num. of mol.: 1 / Fragment: ETS DOMAIN PLUS 30 C-TERMINAL RESIDUES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: GABP ALPHA / Plasmid: PALPHA8A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q00422
#4: Protein PROTEIN (GA BINDING PROTEIN BETA 1) / GABPBETA1 / GABP-BETA-1 SUBUNIT / GABPB1


Mass: 16834.010 Da / Num. of mol.: 1 / Fragment: ANKYRIN REPEAT DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: GABP BETA 1 / Plasmid: PBB-79 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q00420
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 46 / 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: 2.4 Å3/Da / Density % sol: 49 %
Crystal growpH: 9
Details: 100 MM BIS-TRIS PROPANE PH 9, 12 % PEG 1000, 5 MM COBALTIC HEXAMINE CHLORIDE, 1 MM DTT, 20 MM TRIS, 1 MM EDTA, 0.001 % SODIUM AZIDE, pH 9.0
Components of the solutions
IDNameCrystal-IDSol-ID
1BIS-TRIS PROPANE11
2PEG 100011
3[CO(NH3)6]Cl311
4DTT11
5TRIS11
6EDTA11
7SODIUM AZIDE11
8PEG 100012
Crystal
*PLUS
Density % sol: 49 %
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
14 mg/mlprotein1drop
210 mMTris1drop
30.5 mMEDTA1drop
40.5 mMdithiothreitol1drop
50.0005 %sodium azide1drop
650 mMBis-Tris propane1drop
72.5 mMcobaltic hexamine chloride1drop
84.5 %PEG10001drop
9100 mMBis-Tris propane1reservoir
105 mMcobaltic hexamine chloride1reservoir
119 %PEG10001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A
DetectorType: FUJI / Detector: IMAGE PLATE / Date: May 15, 1996 / Details: SPHERICAL RH COATED
RadiationMonochromator: SAGITALLY FOCUSED SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.15→30 Å / Num. obs: 18368 / % possible obs: 88 % / Observed criterion σ(I): 1.5 / Redundancy: 8.7 % / Rsym value: 0.072 / Net I/σ(I): 21
Reflection shellResolution: 2.15→2.23 Å / Redundancy: 7.9 % / Mean I/σ(I) obs: 5.3 / Rsym value: 0.22 / % possible all: 88
Reflection
*PLUS
Highest resolution: 2.15 Å / Lowest resolution: 30 Å / % possible obs: 88 % / Redundancy: 8.7 % / Rmerge(I) obs: 0.072
Reflection shell
*PLUS
% possible obs: 88 % / Rmerge(I) obs: 0.22 / Mean I/σ(I) obs: 5.3

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Processing

Software
NameVersionClassification
MLPHAREphasing
X-PLOR3.8refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MIR / Resolution: 2.15→6 Å / Rfactor Rfree error: 0.7 / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.282 1714 10 %RANDOM
Rwork0.211 ---
obs-17217 88 %-
Displacement parametersBiso mean: 35.3 Å2
Baniso -1Baniso -2Baniso -3
1--3.68 Å20 Å2-4.44 Å2
2---0.8 Å20 Å2
3---9.269 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.27 Å
Refinement stepCycle: LAST / Resolution: 2.15→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2063 852 5 46 2966
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.17
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d19.9
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.22
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 2.15→2.22 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.291 152 10 %
Rwork0.282 1477 -
obs--69.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2TOM_BR_RNA-DNA.PARMTOM_BR_RNA-DNA.TOP
X-RAY DIFFRACTION3PARAM19_MOD.SOLTOPH19.SOL
Software
*PLUS
Name: X-PLOR / Version: 3.8 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.15 Å / Lowest resolution: 6 Å / σ(F): 2 / % reflection Rfree: 10 % / Rfactor all: 0.222 / Rfactor obs: 0.211
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 35.3 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg1.171
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg19.92
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.217
LS refinement shell
*PLUS
% reflection Rfree: 10 %

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