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- PDB-8zh9: The structure of ELK1-DNA complex -

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Basic information

Entry
Database: PDB / ID: 8zh9
TitleThe structure of ELK1-DNA complex
Components
  • DNA (5'-D(*AP*AP*AP*TP*TP*TP*CP*CP*GP*GP*AP*CP*TP*GP*GP*T)-3')
  • DNA (5'-D(*AP*CP*CP*AP*GP*TP*CP*CP*GP*GP*AP*AP*AP*TP*TP*T)-3')
  • ETS transcription factor ELK1
KeywordsDNA BINDING PROTEIN/DNA / Complex / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


sequence-specific DNA binding / DNA-binding transcription factor activity / regulation of transcription by RNA polymerase II / nucleus
Similarity search - Function
Ets-domain signature 1. / Ets-domain signature 2. / Ets domain / ETS family / Ets-domain / Ets-domain profile. / erythroblast transformation specific domain / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
DNA / DNA (> 10) / ETS transcription factor ELK1
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsLiu, G. / Sun, L.T.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32271314 China
National Natural Science Foundation of China (NSFC)32102504 China
CitationJournal: To Be Published
Title: A Single-Nucleotide Polymorphism in CXCL13 Promoter Mitigates Porcine Circovirus-Associated Diseases via ELK1
Authors: Liu, G. / Sun, L.T.
History
DepositionMay 10, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0May 21, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA (5'-D(*AP*CP*CP*AP*GP*TP*CP*CP*GP*GP*AP*AP*AP*TP*TP*T)-3')
B: DNA (5'-D(*AP*AP*AP*TP*TP*TP*CP*CP*GP*GP*AP*CP*TP*GP*GP*T)-3')
C: ETS transcription factor ELK1


Theoretical massNumber of molelcules
Total (without water)20,8633
Polymers20,8633
Non-polymers00
Water64936
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry, ELK1 can be pulled down by DNA., gel filtration, There was a shift of ELK1 co-injected with DNA from the position of free ELK1 or DNA in size exclusion chromatography.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3270 Å2
ΔGint-28 kcal/mol
Surface area9500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)33.318, 62.345, 99.011
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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


Mass: 4882.192 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Sus scrofa (pig)
#2: DNA chain DNA (5'-D(*AP*AP*AP*TP*TP*TP*CP*CP*GP*GP*AP*CP*TP*GP*GP*T)-3')


Mass: 4913.202 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Sus scrofa (pig)
#3: Protein ETS transcription factor ELK1


Mass: 11067.706 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Gene: ELK1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A4X1T8E2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 36 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.46 Å3/Da / Density % sol: 50.09 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 0.05 M TRIS hydrochloride pH 8.5, 0.2 M Ammonium chloride, 0.01 M Calcium chloride dihydrate, 30% w/v Polyethylene glycol 4,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 17, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 8912 / % possible obs: 99.8 % / Redundancy: 6.3 % / Biso Wilson estimate: 39.15 Å2 / CC1/2: 0.958 / Net I/σ(I): 10.5
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 6 % / Mean I/σ(I) obs: 1.9 / Num. unique obs: 840 / CC1/2: 0.817 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
HKL-2000data reduction
HKL-2000data scaling
AutoSolphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1DUX

1dux


Resolution: 2.4→29.73 Å / SU ML: 0.2576 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 27.1333
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.245 413 4.97 %
Rwork0.1931 7901 -
obs0.1957 8314 97.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 45.32 Å2
Refinement stepCycle: LAST / Resolution: 2.4→29.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms726 650 0 36 1412
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091471
X-RAY DIFFRACTIONf_angle_d1.00562119
X-RAY DIFFRACTIONf_chiral_restr0.0499229
X-RAY DIFFRACTIONf_plane_restr0.0118156
X-RAY DIFFRACTIONf_dihedral_angle_d31.231410
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.750.28931170.24032506X-RAY DIFFRACTION94.42
2.75-3.460.2311460.2082628X-RAY DIFFRACTION98.82
3.46-29.730.2421500.17382767X-RAY DIFFRACTION98.58
Refinement TLS params.Method: refined / Origin x: 5.19009567119 Å / Origin y: -5.68901637343 Å / Origin z: 18.8724260794 Å
111213212223313233
T0.177643055417 Å20.0196055660215 Å2-0.00515664494488 Å2-0.217152824203 Å20.0800260849453 Å2--0.2417526308 Å2
L3.30944080063 °20.219563869771 °2-1.40354926244 °2-4.08087266264 °20.57177136306 °2--3.50767536354 °2
S0.0834475306294 Å °0.117953981112 Å °0.181743026049 Å °0.0961283876177 Å °0.158513238445 Å °0.0483223115185 Å °-0.221710241953 Å °0.213566262228 Å °-0.199981301012 Å °
Refinement TLS groupSelection details: all

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