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- PDB-1k78: Pax5(1-149)+Ets-1(331-440)+DNA -

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Basic information

Entry
Database: PDB / ID: 1k78
TitlePax5(1-149)+Ets-1(331-440)+DNA
Components
  • (Pax5/Ets Binding Site on the mb-1 promoter) x 2
  • C-ets-1 Protein
  • Paired Box Protein Pax5
KeywordsTRANSCRIPTION/DNA / Paired domain / ETS domain / transcription factor / TRANSCRIPTION-DNA COMPLEX
Function / homology
Function and homology information


RUNX1 regulates transcription of genes involved in BCR signaling / Oncogene Induced Senescence / lateral ventricle development / regulation of extracellular matrix disassembly / embryonic cranial skeleton morphogenesis / histone acetyltransferase binding / immune system process / adult behavior / skeletal muscle cell differentiation / regulation of angiogenesis ...RUNX1 regulates transcription of genes involved in BCR signaling / Oncogene Induced Senescence / lateral ventricle development / regulation of extracellular matrix disassembly / embryonic cranial skeleton morphogenesis / histone acetyltransferase binding / immune system process / adult behavior / skeletal muscle cell differentiation / 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 / positive regulation of angiogenesis / sequence-specific double-stranded DNA binding / spermatogenesis / DNA-binding transcription activator activity, RNA polymerase II-specific / DNA-binding transcription factor binding / transcription regulator complex / sequence-specific DNA binding / transcription by RNA polymerase II / nucleic acid binding / DNA-binding transcription factor activity, RNA polymerase II-specific / positive regulation of cell migration / DNA-binding transcription factor activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / positive regulation of cell population proliferation / chromatin / regulation of transcription by RNA polymerase II / 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 / SYNCHROTRON / MAD / Resolution: 2.25 Å
AuthorsGarvie, C.W. / Hagman, J. / Wolberger, C.
CitationJournal: Mol.Cell / Year: 2001
Title: Structural studies of Ets-1/Pax5 complex formation on DNA.
Authors: Garvie, C.W. / Hagman, J. / Wolberger, C.
History
DepositionOct 18, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 4, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 300BIOMOLECULE: 1,2 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 9 ...BIOMOLECULE: 1,2 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 9 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). An extra molecule (chain I) was found bound to the DNA. This is believed to be a crystallographic artifact due to a pseudo-consensus sequence. It was not observed in the second biomolecule.

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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
G: Pax5/Ets Binding Site on the mb-1 promoter
H: Pax5/Ets Binding Site on the mb-1 promoter
A: Paired Box Protein Pax5
B: C-ets-1 Protein
E: Paired Box Protein Pax5
F: C-ets-1 Protein
I: Paired Box Protein Pax5


Theoretical massNumber of molelcules
Total (without water)109,1269
Polymers109,1269
Non-polymers00
Water8,719484
1
C: Pax5/Ets Binding Site on the mb-1 promoter
D: Pax5/Ets Binding Site on the mb-1 promoter
A: Paired Box Protein Pax5
B: C-ets-1 Protein
I: Paired Box Protein Pax5


Theoretical massNumber of molelcules
Total (without water)62,8905
Polymers62,8905
Non-polymers00
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
G: Pax5/Ets Binding Site on the mb-1 promoter
H: Pax5/Ets Binding Site on the mb-1 promoter
E: Paired Box Protein Pax5
F: C-ets-1 Protein


Theoretical massNumber of molelcules
Total (without water)46,2374
Polymers46,2374
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.840, 89.750, 170.740
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: DNA chain Pax5/Ets Binding Site on the mb-1 promoter


Mass: 8365.356 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: DNA chain Pax5/Ets Binding Site on the mb-1 promoter


Mass: 8232.301 Da / Num. of mol.: 2 / Source method: obtained synthetically
#3: Protein Paired Box Protein Pax5


Mass: 16653.172 Da / Num. of mol.: 3 / Fragment: Paired domain
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


Mass: 12985.833 Da / Num. of mol.: 2 / Fragment: ETS domain
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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 484 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.7 Å3/Da / Density % sol: 54.38 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 50mM magnesium acetate, 200mM ammonium sulphate, 20% PEG4000, 100mM acetate buffer, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1magnesium acetate11
2ammonium sulphate11
3PEG400011
4acetate buffer11
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
10.34 mMDNA1drop
250 mMmagnesium acetate1reservoir
3200 mMammonium sulfate1reservoir
4100 mM1reservoirpH4.6
520 %PEG40001reservoir

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 14-BM-D10.9788, 0.9790, 0.9537
SYNCHROTRONNSLS X4A20.9117
Detector
TypeIDDetectorDate
ADSC QUANTUM 41CCDJun 8, 2000
ADSC QUANTUM 42CCDSep 28, 2000
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1CARS-design Si(111) double-bounceMADMx-ray1
2Double Si(111) crystalSINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.97881
20.9791
30.95371
40.91171
ReflectionResolution: 2.25→45.94 Å / Num. all: 57710 / Num. obs: 57710 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Biso Wilson estimate: 24.8 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 21.8
Reflection shellResolution: 2.25→2.33 Å / Rmerge(I) obs: 0.198 / Mean I/σ(I) obs: 8 / % possible all: 100
Reflection
*PLUS
% possible obs: 100 %
Reflection shell
*PLUS
% possible obs: 99.8 %

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Processing

Software
NameVersionClassification
SOLVEphasing
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.25→45.94 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 3301348.53 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh and Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.26 2877 5.1 %RANDOM
Rwork0.227 ---
all0.231 56830 --
obs0.231 56830 98.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 60.0237 Å2 / ksol: 0.412224 e/Å3
Displacement parametersBiso mean: 48.1 Å2
Baniso -1Baniso -2Baniso -3
1--2.39 Å20 Å20 Å2
2--6.39 Å20 Å2
3----4 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.25 Å0.17 Å
Refinement stepCycle: LAST / Resolution: 2.25→45.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4215 2202 0 484 6901
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d19.7
X-RAY DIFFRACTIONc_improper_angle_d1.05
X-RAY DIFFRACTIONc_mcbond_it31.5
X-RAY DIFFRACTIONc_mcangle_it4.092
X-RAY DIFFRACTIONc_scbond_it4.672
X-RAY DIFFRACTIONc_scangle_it5.742.5
LS refinement shellResolution: 2.25→2.39 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.295 487 5.2 %
Rwork0.243 8945 -
obs--100 %
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
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 46.1 Å / σ(F): 0 / % reflection Rfree: 5.1 % / Rfactor obs: 0.229 / Rfactor Rfree: 0.257
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 48.1 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.12
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg19.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.05
X-RAY DIFFRACTIONc_mcbond_it31.5
X-RAY DIFFRACTIONc_scbond_it4.672
X-RAY DIFFRACTIONc_mcangle_it4.092
X-RAY DIFFRACTIONc_scangle_it5.742.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.295 / % reflection Rfree: 5.2 % / Rfactor Rwork: 0.243

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