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

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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


Estrogen-dependent nuclear events downstream of ESR-membrane signaling / ERK/MAPK targets / response to fibroblast growth factor / cellular response to testosterone stimulus / axon terminus / response to light stimulus / RNA polymerase II transcription factor binding / cellular response to gamma radiation / positive regulation of neuron death / DNA-binding transcription activator activity, RNA polymerase II-specific ...Estrogen-dependent nuclear events downstream of ESR-membrane signaling / ERK/MAPK targets / response to fibroblast growth factor / cellular response to testosterone stimulus / axon terminus / response to light stimulus / RNA polymerase II transcription factor binding / cellular response to gamma radiation / positive regulation of neuron death / DNA-binding transcription activator activity, RNA polymerase II-specific / RNA polymerase II proximal promoter sequence-specific DNA binding / cell differentiation / regulation of transcription by RNA polymerase II / DNA-binding transcription factor activity, RNA polymerase II-specific / dendrite / chromatin binding / neuronal cell body / DNA-binding transcription factor activity / positive regulation of transcription, DNA-templated / positive regulation of transcription by RNA polymerase II / mitochondrion / nucleoplasm / nucleus
Ets-domain / Ets-domain signature 1. / Ets domain / Ets-domain profile. / Winged helix-like DNA-binding domain superfamily / Winged helix DNA-binding domain superfamily / Ets-domain signature 2.
ETS domain-containing protein Elk-1
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.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jan 19, 2000 / Release: Apr 17, 2000
RevisionDateData content typeGroupProviderType
1.0Apr 17, 2000Structure modelrepositoryInitial release
1.1Apr 27, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelVersion format compliance

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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


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
γ
α
β
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/peptide 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


Mass: 18.015 Da / Num. of mol.: 225 / Source method: isolated from a natural source / Formula: H2O / Water

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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

Crystal-ID: 1

IDNameSol-ID
1sodium Cacodylate1
2MgCl21
3NaClSodium chloride1
4ZnCl21
5PEG 20001
6PEG 20002
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS

Crystal-ID: 1

IDConc.Common nameSol-IDChemical formula
10.1 mMproteindrop
20.13 mMDNAdrop
325 mMsodium cacodylatedrop
45 %(w/v)PEG2000drop
550 mMdropMgCl2
650 mMdropNaCl
71.5 mMdropZnCl2
850 mMsodium cacodylatereservoir
910 %(w/v)PEG2000reservoir
10100 mMreservoirMgCl2
11100 mMreservoirNaCl
123.0 mMreservoirZnCl2

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11101
21101
Diffraction source

Site: NSLS / Source: SYNCHROTRON

BeamlineDiffraction-IDWavelength
X4A10.9791
X8C20.98165
Detector

Detector: IMAGE PLATE

TypeDiffraction-IDDate
RIGAKU RAXIS IV1Feb 15, 1998
MARRESEARCH2Jul 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
Refinement-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

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