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- PDB-1mdm: INHIBITED FRAGMENT OF ETS-1 AND PAIRED DOMAIN OF PAX5 BOUND TO DNA -

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Basic information

Entry
Database: PDB / ID: 1mdm
TitleINHIBITED FRAGMENT OF ETS-1 AND PAIRED DOMAIN OF PAX5 BOUND TO DNA
Components
  • (PAX5/ETS BINDING SITE ON THE MB-1 PROMOTER) x 2
  • C-ETS-1 PROTEIN
  • PAIRED BOX PROTEIN PAX-5
KeywordsTRANSCRIPTION/DNA / Transcription factor / ternary complex / autoinhibition / ETS domain / Paired domain / TRANSCRIPTION-DNA COMPLEX
Function / homology
Function and homology information


RUNX1 regulates transcription of genes involved in BCR signaling / Oncogene Induced Senescence / lateral ventricle development / sensory organ development / embryonic cranial skeleton morphogenesis / adult behavior / skeletal muscle cell differentiation / immune system process / regulation of angiogenesis / positive regulation of endothelial cell migration ...RUNX1 regulates transcription of genes involved in BCR signaling / Oncogene Induced Senescence / lateral ventricle development / sensory organ development / embryonic cranial skeleton morphogenesis / adult behavior / skeletal muscle cell differentiation / immune system process / regulation of angiogenesis / positive regulation of endothelial cell migration / positive regulation of erythrocyte differentiation / B cell differentiation / cerebral cortex development / negative regulation of inflammatory response / sequence-specific double-stranded DNA binding / nervous system development / DNA-binding transcription activator activity, RNA polymerase II-specific / spermatogenesis / transcription regulator complex / DNA-binding transcription factor binding / sequence-specific DNA binding / nucleic acid binding / transcription by RNA polymerase II / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / regulation of transcription by RNA polymerase II / chromatin / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
Paired-box protein 2 C-terminal / Paired-box protein 2 C terminal / Paired domain / Paired DNA-binding domain / PAX family / 'Paired box' domain / Paired DNA-binding domain signature. / Paired DNA-binding domain profile. / Paired Box domain / Protein C-ets-1, pointed domain ...Paired-box protein 2 C-terminal / Paired-box protein 2 C terminal / Paired domain / Paired DNA-binding domain / PAX family / 'Paired box' domain / Paired DNA-binding domain signature. / Paired DNA-binding domain profile. / Paired Box domain / Protein C-ets-1, pointed domain / Transforming protein C-ets / Ets1, N-terminal flanking region of Ets domain / Ets1 N-terminal flanking region of Ets domain / SAM / Pointed domain / Pointed domain / Sterile alpha motif (SAM)/Pointed domain / Pointed (PNT) domain profile. / Ets-domain signature 1. / Ets-domain signature 2. / Ets domain / ETS family / Ets-domain / Ets-domain profile. / erythroblast transformation specific domain / Sterile alpha motif/pointed domain superfamily / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Homeobox-like domain superfamily / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / Protein C-ets-1 / Paired box protein Pax-5
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsGarvie, C.W. / Pufall, M.A. / Graves, B.J. / Wolberger, C.
CitationJournal: J.Biol.Chem. / Year: 2002
Title: STRUCTURAL ANALYSIS OF THE AUTOINHIBITION OF ETS-1 AND ITS ROLE IN PROTEIN PARTNERSHIPS
Authors: Garvie, C.W. / Pufall, M.A. / Graves, B.J. / Wolberger, C.
History
DepositionAug 7, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 11, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: PAX5/ETS BINDING SITE ON THE MB-1 PROMOTER
D: PAX5/ETS BINDING SITE ON THE MB-1 PROMOTER
A: PAIRED BOX PROTEIN PAX-5
B: C-ETS-1 PROTEIN


Theoretical massNumber of molelcules
Total (without water)51,3114
Polymers51,3114
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.270, 171.230, 44.710
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 PAX5/ETS BINDING SITE ON THE MB-1 PROMOTER


Mass: 8036.150 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthesised by the phosphoramidite method
#2: DNA chain PAX5/ETS BINDING SITE ON THE MB-1 PROMOTER


Mass: 7943.119 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthesised by the phosphoramidite method
#3: Protein PAIRED BOX PROTEIN PAX-5 / B-cell specific transcription factor / BSAP


Mass: 16653.172 Da / Num. of mol.: 1 / Fragment: PAIRED DNA-BINDING DOMAIN, RESIDUES 1-149
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: Pax5 / Plasmid: pET11a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q02548
#4: Protein C-ETS-1 PROTEIN / p54


Mass: 18678.154 Da / Num. of mol.: 1
Fragment: INHIBITED ETS DNA-BINDING DOMAIN, RESIDUES 280-440
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ets-1 / Plasmid: pET11A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P27577

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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: 2.84 Å3/Da / Density % sol: 56.73 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 200mM Ammonium Acetate, 10% Peg4000, 100mM Acetate buffer, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
pH: 8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mMTris1droppH8.0
21 mMdithiothreitol1drop
30.32 mMprotein1drop
4200 mMammonium acetate1reservoir
5100 mMacetate1reservoirpH5.0
610 %PEG40001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Mar 13, 2001 / Details: mirrors
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.8→40 Å / Num. all: 39863 / Num. obs: 13405 / % possible obs: 87.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2.5 / Redundancy: 3.1 % / Biso Wilson estimate: 84.6 Å2 / Rsym value: 0.06 / Net I/σ(I): 9.3
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.116 / Mean I/σ(I) obs: 4 / Num. unique all: 2937 / Rsym value: 0.116 / % possible all: 58.7
Reflection
*PLUS
Lowest resolution: 35 Å / Rmerge(I) obs: 0.05
Reflection shell
*PLUS
% possible obs: 58.7 % / Rmerge(I) obs: 0.192

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
CNS1refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ID 1K78

1k78


Resolution: 2.8→32.03 Å / Rfactor Rfree error: 0.008 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: The side chains for the region 88-141 of Pax5 are included in the model despite a lack of electron density to uniquely define their location. The poor definition of the amino acid sidechains ...Details: The side chains for the region 88-141 of Pax5 are included in the model despite a lack of electron density to uniquely define their location. The poor definition of the amino acid sidechains in this region of Pax5 reflects the loss of contacts to the sugar-phosphate backbone, due to the less than optimal length of the DNA sequence used. This may explain the high B-factors obtained overall for the structure. The electron density for the side chains of residues in the region between residues 309-318 in Ets-1 was poorly defined and only the side chains for Arg309, Asp310 and Leu314 could be built.
RfactorNum. reflection% reflectionSelection details
Rfree0.31 1371 10.3 %RANDOM
Rwork0.259 ---
all0.252 14725 --
obs0.259 13354 87.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 21.8329 Å2 / ksol: 0.276781 e/Å3
Displacement parametersBiso mean: 73.2 Å2
Baniso -1Baniso -2Baniso -3
1-11.71 Å20 Å20 Å2
2---12.07 Å20 Å2
3---0.36 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.53 Å0.45 Å
Luzzati d res low-5 Å
Luzzati sigma a0.56 Å0.46 Å
Refinement stepCycle: LAST / Resolution: 2.8→32.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1994 1060 0 0 3054
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d20.2
X-RAY DIFFRACTIONc_improper_angle_d1.22
LS refinement shellResolution: 2.8→2.98 Å / Rfactor Rfree error: 0.034 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.433 164 11 %
Rwork0.431 1330 -
obs--59.4 %
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
X-RAY DIFFRACTION4ION.PARAMION.TOP
Refinement
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 35 Å / Rfactor Rfree: 0.31
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.36
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg20.2
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.22

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