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- PDB-1pue: PU.1 ETS DOMAIN-DNA COMPLEX -

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Basic information

Entry
Database: PDB / ID: 1pue
TitlePU.1 ETS DOMAIN-DNA COMPLEX
Components
  • DNA (5'-D(*AP*AP*AP*AP*AP*GP*GP*GP*GP*AP*AP*GP*TP*GP*GP*G)-3')
  • DNA (5'-D(*TP*CP*CP*CP*AP*CP*TP*TP*CP*CP*CP*CP*TP*TP*TP*T)-3')
  • PROTEIN (TRANSCRIPTION FACTOR PU.1 (TF PU.1))
KeywordsTRANSCRIPTION/DNA / COMPLEX (TRANSCRIPTION REGULATING-DNA) / ONCOGENE / TRANSFORMING PROTEIN / DNA- BINDING / ACTIVATOR / NUCLEAR PROTEIN / TRANSCRIPTION-DNA COMPLEX
Function / homology
Function and homology information


positive regulation of myeloid dendritic cell chemotaxis / anatomical structure regression / follicular B cell differentiation / positive regulation of antifungal innate immune response / regulation of myeloid progenitor cell differentiation / pro-T cell differentiation / negative regulation of neutrophil degranulation / germinal center B cell differentiation / myeloid leukocyte differentiation / positive regulation of microglial cell mediated cytotoxicity ...positive regulation of myeloid dendritic cell chemotaxis / anatomical structure regression / follicular B cell differentiation / positive regulation of antifungal innate immune response / regulation of myeloid progenitor cell differentiation / pro-T cell differentiation / negative regulation of neutrophil degranulation / germinal center B cell differentiation / myeloid leukocyte differentiation / positive regulation of microglial cell mediated cytotoxicity / granulocyte differentiation / lymphocyte differentiation / apoptotic process involved in blood vessel morphogenesis / endothelial to hematopoietic transition / negative regulation of adipose tissue development / pericyte cell differentiation / immature B cell differentiation / negative regulation of MHC class II biosynthetic process / lymphoid progenitor cell differentiation / myeloid dendritic cell differentiation / vasculature development / regulation of DNA-binding transcription factor activity / oncogene-induced cell senescence / negative regulation of protein localization to chromatin / positive regulation of p38MAPK cascade / positive regulation of B cell differentiation / NFAT protein binding / somatic stem cell population maintenance / macrophage differentiation / cis-regulatory region sequence-specific DNA binding / lipopolysaccharide-mediated signaling pathway / transcription initiation-coupled chromatin remodeling / protein sequestering activity / erythrocyte differentiation / transforming growth factor beta receptor signaling pathway / DNA-binding transcription repressor activity, RNA polymerase II-specific / positive regulation of miRNA transcription / histone deacetylase binding / DNA-binding transcription activator activity, RNA polymerase II-specific / DNA-binding transcription factor binding / RNA polymerase II-specific DNA-binding transcription factor binding / transcription regulator complex / sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of gene expression / negative regulation of DNA-templated transcription / chromatin binding / positive regulation of gene expression / 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 / positive regulation of transcription by RNA polymerase II / DNA binding / RNA binding / nucleoplasm / nucleus
Similarity search - Function
Ets-domain signature 1. / ETS family / Ets-domain signature 2. / Ets domain / Ets-domain / Ets-domain profile. / erythroblast transformation specific domain / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily ...Ets-domain signature 1. / ETS family / Ets-domain signature 2. / Ets domain / Ets-domain / Ets-domain profile. / erythroblast transformation specific domain / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / 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) / Transcription factor PU.1
Similarity search - Component
Biological speciesMus musculus (house mouse)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.1 Å
AuthorsKodandapani, R. / Pio, F. / Ni, C.Z. / Piccialli, G. / Klemsz, M. / McKercher, S. / Maki, R.A. / Ely, K.R.
Citation
Journal: Nature / Year: 1996
Title: A new pattern for helix-turn-helix recognition revealed by the PU.1 ETS-domain-DNA complex.
Authors: Kodandapani, R. / Pio, F. / Ni, C.Z. / Piccialli, G. / Klemsz, M. / McKercher, S. / Maki, R.A. / Ely, K.R.
#1: Journal: J.Biol.Chem. / Year: 1996
Title: New Insights on DNA Recognition by ETS Proteins from the Crystal Structure of the PU.1 ETS Domain-DNA Complex
Authors: Pio, F. / Kodandapani, R. / Ni, C.Z. / Shepard, W. / Klemsz, M. / McKercher, S.R. / Maki, R.A. / Ely, K.R.
History
DepositionJul 8, 1996Processing site: NDB
Revision 1.0Feb 12, 1997Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 15, 2017Group: Source and taxonomy / Structure summary
Revision 1.4Feb 14, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA (5'-D(*AP*AP*AP*AP*AP*GP*GP*GP*GP*AP*AP*GP*TP*GP*GP*G)-3')
B: DNA (5'-D(*TP*CP*CP*CP*AP*CP*TP*TP*CP*CP*CP*CP*TP*TP*TP*T)-3')
C: DNA (5'-D(*AP*AP*AP*AP*AP*GP*GP*GP*GP*AP*AP*GP*TP*GP*GP*G)-3')
D: DNA (5'-D(*TP*CP*CP*CP*AP*CP*TP*TP*CP*CP*CP*CP*TP*TP*TP*T)-3')
E: PROTEIN (TRANSCRIPTION FACTOR PU.1 (TF PU.1))
F: PROTEIN (TRANSCRIPTION FACTOR PU.1 (TF PU.1))


Theoretical massNumber of molelcules
Total (without water)40,8106
Polymers40,8106
Non-polymers00
Water2,576143
1
A: DNA (5'-D(*AP*AP*AP*AP*AP*GP*GP*GP*GP*AP*AP*GP*TP*GP*GP*G)-3')
B: DNA (5'-D(*TP*CP*CP*CP*AP*CP*TP*TP*CP*CP*CP*CP*TP*TP*TP*T)-3')
E: PROTEIN (TRANSCRIPTION FACTOR PU.1 (TF PU.1))


Theoretical massNumber of molelcules
Total (without water)20,4053
Polymers20,4053
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: DNA (5'-D(*AP*AP*AP*AP*AP*GP*GP*GP*GP*AP*AP*GP*TP*GP*GP*G)-3')
D: DNA (5'-D(*TP*CP*CP*CP*AP*CP*TP*TP*CP*CP*CP*CP*TP*TP*TP*T)-3')
F: PROTEIN (TRANSCRIPTION FACTOR PU.1 (TF PU.1))


Theoretical massNumber of molelcules
Total (without water)20,4053
Polymers20,4053
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)89.100, 101.900, 55.600
Angle α, β, γ (deg.)90.00, 111.20, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: DNA chain DNA (5'-D(*AP*AP*AP*AP*AP*GP*GP*GP*GP*AP*AP*GP*TP*GP*GP*G)-3')


Mass: 5085.330 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: DNA chain DNA (5'-D(*TP*CP*CP*CP*AP*CP*TP*TP*CP*CP*CP*CP*TP*TP*TP*T)-3')


Mass: 4711.053 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Protein PROTEIN (TRANSCRIPTION FACTOR PU.1 (TF PU.1))


Mass: 10608.468 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) / References: UniProt: P17433
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 143 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.58 Å3/Da / Density % sol: 48 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 6.5
Details: HANGING DROP-VAPOR DIFFUSION METHOD RESERVOIR SOLUTION: 100 MM SODIUM CACODYLATE PH 6.5, 3% TO 10% PEG 600, 200 MM ZINC ACETATE HANGING DROP: 5 MICRO LITER OF 0.5MM COMPLEX(1:1 OF PROTEIN ...Details: HANGING DROP-VAPOR DIFFUSION METHOD RESERVOIR SOLUTION: 100 MM SODIUM CACODYLATE PH 6.5, 3% TO 10% PEG 600, 200 MM ZINC ACETATE HANGING DROP: 5 MICRO LITER OF 0.5MM COMPLEX(1:1 OF PROTEIN AND DNA) + 5 MICRO LITER OF RESERVOIR SOLUTION., vapor diffusion - hanging drop
Crystal grow
*PLUS
Temperature: 19 ℃ / Method: unknown / Details: Pio, F., (1995) J.Biol.Chem., 270, 24258.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
1100 mMsodium cacodylate11
23-10 %PEG60011
3200 mMzinc acetate11

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11301
21301
Diffraction source
SourceSiteBeamlineID
SYNCHROTRONLURE D41A1
2
Detector
TypeIDDetectorDate
UCSD MARK III1AREA DETECTORJan 21, 1994
SDMS2AREA DETECTORApr 4, 1994
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDRelative weight
11
21
ReflectionRedundancy: 3 % / Rmerge(I) obs: 0.033

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Processing

Software
NameVersionClassification
X-PLOR3.1refinement
MOSFLMdata reduction
RefinementResolution: 2.1→6 Å / σ(F): 2
RfactorNum. reflection
Rfree0.287 -
Rwork0.225 -
obs0.225 22022
Displacement parametersBiso mean: 31.6 Å2
Refinement stepCycle: LAST / Resolution: 2.1→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1485 1300 0 143 2928
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
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_deg1.63
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
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
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 6 Å / σ(F): 2
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 31.6 Å2

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