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- PDB-1k6o: Crystal Structure of a Ternary SAP-1/SRF/c-fos SRE DNA Complex -

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Basic information

Entry
Database: PDB / ID: 1k6o
TitleCrystal Structure of a Ternary SAP-1/SRF/c-fos SRE DNA Complex
Components
  • 5'-D(*CP*AP*CP*AP*GP*GP*AP*TP*GP*TP*CP*CP*AP*TP*AP*TP*TP*AP*GP*GP*AP*CP*A)-3'
  • 5'-D(*TP*GP*TP*CP*CP*TP*AP*AP*TP*AP*TP*GP*GP*AP*CP*AP*TP*CP*CP*TP*GP*TP*G)-3'
  • ETS-domain protein ELK-4
  • Serum response factor
KeywordsTRANSCRIPTION/DNA / PROTEIN-DNA COMPLEX / TRANSCRIPTION FACTOR / COMBINATORIAL GENE REGULATION / ETS PROTEINS / MADS-BOX PROTEINS / TRANSCRIPTION-DNA COMPLEX
Function / homology
Function and homology information


serum response element binding / positive regulation of transcription by glucose / bronchus cartilage development / lung smooth muscle development / cardiac vascular smooth muscle cell differentiation / trachea cartilage development / dorsal aorta morphogenesis / morphogenesis of an epithelial sheet / regulation of smooth muscle cell differentiation / primitive streak formation ...serum response element binding / positive regulation of transcription by glucose / bronchus cartilage development / lung smooth muscle development / cardiac vascular smooth muscle cell differentiation / trachea cartilage development / dorsal aorta morphogenesis / morphogenesis of an epithelial sheet / regulation of smooth muscle cell differentiation / primitive streak formation / Regulation of NPAS4 gene transcription / tangential migration from the subventricular zone to the olfactory bulb / primary miRNA binding / epithelial cell-cell adhesion / epithelial structure maintenance / negative regulation of amyloid-beta clearance / positive regulation of smooth muscle contraction / skin morphogenesis / cardiac muscle cell myoblast differentiation / trophectodermal cell differentiation / cardiac myofibril assembly / bicellular tight junction assembly / filopodium assembly / NGF-stimulated transcription / positive thymic T cell selection / heart trabecula formation / axon extension / cell migration involved in sprouting angiogenesis / angiogenesis involved in wound healing / long-term synaptic depression / Cardiogenesis / positive regulation of filopodium assembly / platelet formation / sarcomere organization / megakaryocyte development / branching involved in blood vessel morphogenesis / muscle cell cellular homeostasis / stress fiber assembly / heart looping / erythrocyte development / lung morphogenesis / eyelid development in camera-type eye / face development / thyroid gland development / mesoderm formation / associative learning / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / hematopoietic stem cell differentiation / positive regulation of transcription initiation by RNA polymerase II / establishment of skin barrier / long-term memory / neuron development / positive regulation of DNA-binding transcription factor activity / positive regulation of axon extension / regulation of cell adhesion / response to hormone / response to cytokine / negative regulation of miRNA transcription / negative regulation of cell migration / thymus development / cell-matrix adhesion / hippocampus development / positive regulation of cell differentiation / cellular response to glucose stimulus / RHO GTPases Activate Formins / chromatin DNA binding / platelet activation / positive regulation of miRNA transcription / response to toxic substance / histone deacetylase binding / neuron migration / sequence-specific double-stranded DNA binding / cellular senescence / heart development / actin cytoskeleton organization / DNA-binding transcription activator activity, RNA polymerase II-specific / DNA-binding transcription factor binding / RNA polymerase II-specific DNA-binding transcription factor binding / transcription by RNA polymerase II / DNA-binding transcription factor activity, RNA polymerase II-specific / cell differentiation / response to hypoxia / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of cell population proliferation / chromatin binding / regulation of transcription by RNA polymerase II / chromatin / negative regulation of transcription by RNA polymerase II / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / nucleus / cytoplasm / cytosol
Similarity search - Function
MADS SRF-like / : / SRF-like / Transcription factor, MADS-box / Transcription factor, MADS-box / Transcription factor, MADS-box superfamily / SRF-type transcription factor (DNA-binding and dimerisation domain) / MADS-box domain signature. / MADS-box domain profile. / MADS ...MADS SRF-like / : / SRF-like / Transcription factor, MADS-box / Transcription factor, MADS-box / Transcription factor, MADS-box superfamily / SRF-type transcription factor (DNA-binding and dimerisation domain) / MADS-box domain signature. / MADS-box domain profile. / MADS / Ets-domain signature 1. / Ets-domain signature 2. / Ets domain / ETS family / 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 / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / Serum response factor / ETS domain-containing protein Elk-4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.19 Å
AuthorsMo, Y. / Ho, W. / Johnston, K. / Marmorstein, R.
CitationJournal: J.Mol.Biol. / Year: 2001
Title: Crystal structure of a ternary SAP-1/SRF/c-fos SRE DNA complex.
Authors: Mo, Y. / Ho, W. / Johnston, K. / Marmorstein, R.
History
DepositionOct 16, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 17, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.4Feb 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
D: 5'-D(*CP*AP*CP*AP*GP*GP*AP*TP*GP*TP*CP*CP*AP*TP*AP*TP*TP*AP*GP*GP*AP*CP*A)-3'
E: 5'-D(*TP*GP*TP*CP*CP*TP*AP*AP*TP*AP*TP*GP*GP*AP*CP*AP*TP*CP*CP*TP*GP*TP*G)-3'
A: ETS-domain protein ELK-4
B: Serum response factor
C: Serum response factor


Theoretical massNumber of molelcules
Total (without water)48,4465
Polymers48,4465
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)161.784, 161.784, 41.224
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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Components

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


Mass: 7073.600 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: c-fos SRE sequence strand 1
#2: DNA chain 5'-D(*TP*GP*TP*CP*CP*TP*AP*AP*TP*AP*TP*GP*GP*AP*CP*AP*TP*CP*CP*TP*GP*TP*G)-3'


Mass: 7046.557 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: c-fos SRE sequence strand 2
#3: Protein ETS-domain protein ELK-4 / Serum Response Factor Accessory Protein 1 / SAP-1


Mass: 11219.207 Da / Num. of mol.: 1 / Fragment: 1-93
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: Sap / Plasmid: PRSETA / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)/LysS / References: UniProt: P28324
#4: Protein Serum response factor / SRF


Mass: 11553.439 Da / Num. of mol.: 2 / Fragment: 133-235
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SRF / Plasmid: PRESTA / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)/LysS / References: UniProt: P11831

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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: 3.18 Å3/Da / Density % sol: 61.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: PEG 2000, pH 6.0, VAPOR DIFFUSION, HANGING DROP
Components of the solutionsName: PEG 2000
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
10.1 mMSAP-11drop
20.1 mMSRF dimer1drop
30.13 mMSRE DNA duplex1drop
425 mMMES1droppH6.0
58 %PEG20001drop
65 mM1dropMgCl2

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 1.0722 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 5, 1999
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0722 Å / Relative weight: 1
ReflectionResolution: 3.19→50 Å / Num. all: 10616 / Num. obs: 10302 / % possible obs: 97.1 % / Observed criterion σ(I): -1
Reflection shellResolution: 3.19→50 Å / % possible all: 97.1
Reflection
*PLUS
Highest resolution: 3.2 Å / Lowest resolution: 50 Å / Rmerge(I) obs: 0.131

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Processing

Software
NameClassification
AMoREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.19→50 Å / σ(F): 0 / Stereochemistry target values: Engh and Huber
RfactorNum. reflectionSelection details
Rfree0.2757 -10% of data
Rwork0.2204 --
all0.22 10616 -
obs0.27 10302 -
Refinement stepCycle: LAST / Resolution: 3.19→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2020 937 0 0 2957
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_d1.1746
X-RAY DIFFRACTIONc_bond_d0.007045
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 3.2 Å / Lowest resolution: 50 Å / σ(F): 0 / % reflection Rfree: 10 % / Rfactor Rwork: 0.202
Solvent computation
*PLUS
Displacement parameters
*PLUS

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