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- PDB-1dux: ELK-1/DNA STRUCTURE REVEALS HOW RESIDUES DISTAL FROM DNA-BINDING ... -

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Basic information

Entry
Database: PDB / ID: 1dux
TitleELK-1/DNA STRUCTURE REVEALS HOW RESIDUES DISTAL FROM DNA-BINDING SURFACE AFFECT DNA-RECOGNITION
Components
  • DNA (5'-D(*AP*CP*AP*CP*TP*TP*CP*CP*GP*GP*TP*CP*A)-3')
  • DNA (5'-D(*TP*GP*AP*CP*CP*GP*GP*AP*AP*GP*TP*GP*T)-3')
  • ETS-DOMAIN PROTEIN ELK-1
KeywordsTranscription/DNA / ETS-DOMAIN / DNA-BINDING DOMAIN / WINGED HELIX-TURN-HELIX / DNA-BINDING SPECIFICITY / Transcription-DNA COMPLEX
Function / homology
Function and homology information


hippocampal neuron apoptotic process / response to fibroblast growth factor / cellular response to testosterone stimulus / NGF-stimulated transcription / ERK/MAPK targets / response to light stimulus / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / axon terminus / nuclear receptor coactivator activity / liver development ...hippocampal neuron apoptotic process / response to fibroblast growth factor / cellular response to testosterone stimulus / NGF-stimulated transcription / ERK/MAPK targets / response to light stimulus / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / axon terminus / nuclear receptor coactivator activity / liver development / mitochondrial membrane / lung development / cellular response to gamma radiation / HCMV Early Events / sequence-specific double-stranded DNA binding / gene expression / DNA-binding transcription activator activity, RNA polymerase II-specific / RNA polymerase II-specific DNA-binding transcription factor binding / transcription cis-regulatory region 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 / dendrite / neuronal cell body / chromatin binding / chromatin / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / 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) / ETS domain-containing protein Elk-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.1 Å
AuthorsMo, Y. / Vaessen, B. / Johnston, K. / Marmorstein, R.
CitationJournal: Nat.Struct.Biol. / Year: 2000
Title: Structure of the elk-1-DNA complex reveals how DNA-distal residues affect ETS domain recognition of DNA.
Authors: Mo, Y. / Vaessen, B. / Johnston, K. / Marmorstein, R.
History
DepositionJan 19, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 17, 2000Provider: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA (5'-D(*TP*GP*AP*CP*CP*GP*GP*AP*AP*GP*TP*GP*T)-3')
B: DNA (5'-D(*AP*CP*AP*CP*TP*TP*CP*CP*GP*GP*TP*CP*A)-3')
D: DNA (5'-D(*TP*GP*AP*CP*CP*GP*GP*AP*AP*GP*TP*GP*T)-3')
E: DNA (5'-D(*AP*CP*AP*CP*TP*TP*CP*CP*GP*GP*TP*CP*A)-3')
C: ETS-DOMAIN PROTEIN ELK-1
F: ETS-DOMAIN PROTEIN ELK-1


Theoretical massNumber of molelcules
Total (without water)38,0226
Polymers38,0226
Non-polymers00
Water4,053225
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)33.245, 140.523, 38.620
Angle α, β, γ (deg.)90.00, 115.52, 90.00
Int Tables number4
Cell settingmonoclinic
Space group name H-MP1211

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Components

#1: DNA chain DNA (5'-D(*TP*GP*AP*CP*CP*GP*GP*AP*AP*GP*TP*GP*T)-3')


Mass: 4031.634 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: DNA chain DNA (5'-D(*AP*CP*AP*CP*TP*TP*CP*CP*GP*GP*TP*CP*A)-3')


Mass: 3911.562 Da / Num. of mol.: 2 / Source method: obtained synthetically
#3: Protein ETS-DOMAIN PROTEIN ELK-1 / TRANSFORMING PROTEIN ELK-1 / ELK1 / MEMBER OF ETS ONCOGENE FAMILY


Mass: 11067.706 Da / Num. of mol.: 2 / Fragment: RESIDUES 1-94
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PRSETA / Production host: Escherichia coli (E. coli) / References: UniProt: P19419
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 225 / 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: 2.11 Å3/Da / Density % sol: 41.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 5.6
Details: 50 mM sodium Cacodylate, 10% PEG 2000, 100 mM MgCl2, 100 mM NaCl, 3 mM ZnCl2, pH 5.6, VAPOR DIFFUSION, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1sodium Cacodylate11
2MgCl211
3NaClSodium chloride11
4ZnCl211
5PEG 200011
6PEG 200012
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
10.1 mMprotein1drop
20.13 mMDNA1drop
325 mMsodium cacodylate1drop
45 %(w/v)PEG20001drop
550 mM1dropMgCl2
650 mM1dropNaCl
71.5 mM1dropZnCl2
850 mMsodium cacodylate1reservoir
910 %(w/v)PEG20001reservoir
10100 mM1reservoirMgCl2
11100 mM1reservoirNaCl
123.0 mM1reservoirZnCl2

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11101
21101
Diffraction source
SourceSiteBeamlineIDWavelength
SYNCHROTRONNSLS X4A10.9791
SYNCHROTRONNSLS X8C20.98165
Detector
TypeIDDetectorDate
RIGAKU RAXIS IV1IMAGE PLATEFeb 15, 1998
MARRESEARCH2IMAGE PLATEJul 14, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97911
20.981651
ReflectionResolution: 2.1→50 Å / Num. all: 18614 / Num. obs: 17831 / % possible obs: 95.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Biso Wilson estimate: 28.5 Å2 / Rmerge(I) obs: 0.042 / Net I/σ(I): 27.1
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 2.01 % / Rmerge(I) obs: 0.092 / Num. unique all: 1443 / % possible all: 77.6

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Processing

Software
NameClassification
AMoREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2.1→50 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.236 1827 10.2 %random
Rwork0.202 ---
all-18614 --
obs-17831 95.8 %-
Refinement stepCycle: LAST / Resolution: 2.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1498 1054 0 225 2777
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.089
X-RAY DIFFRACTIONc_bond_d0.005
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Lowest resolution: 50 Å / σ(F): 0 / % reflection Rfree: 10.2 % / Rfactor obs: 0.202
Solvent computation
*PLUS
Displacement parameters
*PLUS

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