+Open data
-Basic information
Entry | Database: PDB / ID: 1k6o | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of a Ternary SAP-1/SRF/c-fos SRE DNA Complex | ||||||
Components |
| ||||||
Keywords | TRANSCRIPTION/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 / morphogenesis of an epithelial sheet / dorsal aorta morphogenesis / regulation of smooth muscle cell differentiation / epithelial structure maintenance ...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 / morphogenesis of an epithelial sheet / dorsal aorta morphogenesis / regulation of smooth muscle cell differentiation / epithelial structure maintenance / primitive streak formation / tangential migration from the subventricular zone to the olfactory bulb / Regulation of NPAS4 gene transcription / primary miRNA binding / epithelial cell-cell adhesion / negative regulation of amyloid-beta clearance / cardiac myofibril assembly / skin morphogenesis / cardiac muscle cell myoblast differentiation / trophectodermal cell differentiation / positive regulation of smooth muscle contraction / bicellular tight junction assembly / angiogenesis involved in wound healing / NGF-stimulated transcription / filopodium assembly / heart trabecula formation / positive thymic T cell selection / axon extension / cell migration involved in sprouting angiogenesis / Cardiogenesis / long-term synaptic depression / positive regulation of filopodium assembly / platelet formation / megakaryocyte development / branching involved in blood vessel morphogenesis / muscle cell cellular homeostasis / sarcomere organization / lung morphogenesis / stress fiber assembly / heart looping / eyelid development in camera-type eye / face development / associative learning / thyroid gland development / mesoderm formation / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / hematopoietic stem cell differentiation / neuron development / positive regulation of transcription initiation by RNA polymerase II / establishment of skin barrier / positive regulation of axon extension / erythrocyte development / regulation of cell adhesion / long-term memory / negative regulation of cell migration / cell-matrix adhesion / negative regulation of miRNA transcription / thymus development / response to hormone / response to cytokine / RHO GTPases Activate Formins / hippocampus development / positive regulation of cell differentiation / cellular response to glucose stimulus / neuron migration / response to toxic substance / chromatin DNA binding / platelet activation / positive regulation of DNA-binding transcription factor activity / positive regulation of miRNA transcription / histone deacetylase binding / cellular senescence / sequence-specific double-stranded DNA binding / 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 / cell differentiation / response to hypoxia / 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 cell population proliferation / chromatin binding / chromatin / regulation of transcription by RNA polymerase II / 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 | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.19 Å | ||||||
Authors | Mo, Y. / Ho, W. / Johnston, K. / Marmorstein, R. | ||||||
Citation | Journal: 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1k6o.cif.gz | 81.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1k6o.ent.gz | 59.1 KB | Display | PDB format |
PDBx/mmJSON format | 1k6o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1k6o_validation.pdf.gz | 382.2 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1k6o_full_validation.pdf.gz | 395.5 KB | Display | |
Data in XML | 1k6o_validation.xml.gz | 8.6 KB | Display | |
Data in CIF | 1k6o_validation.cif.gz | 12.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k6/1k6o ftp://data.pdbj.org/pub/pdb/validation_reports/k6/1k6o | HTTPS FTP |
-Related structure data
Similar structure data |
---|
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: DNA chain | Mass: 7073.600 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: c-fos SRE sequence strand 1 |
---|---|
#2: DNA chain | Mass: 7046.557 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: c-fos SRE sequence strand 2 |
#3: Protein | 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 | 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 |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.18 Å3/Da / Density % sol: 61.31 % | |||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: PEG 2000, pH 6.0, VAPOR DIFFUSION, HANGING DROP | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | Name: PEG 2000 | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 110 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 1.0722 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 5, 1999 |
Radiation | Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0722 Å / Relative weight: 1 |
Reflection | Resolution: 3.19→50 Å / Num. all: 10616 / Num. obs: 10302 / % possible obs: 97.1 % / Observed criterion σ(I): -1 |
Reflection shell | Resolution: 3.19→50 Å / % possible all: 97.1 |
Reflection | *PLUS Highest resolution: 3.2 Å / Lowest resolution: 50 Å / Rmerge(I) obs: 0.131 |
-Processing
Software |
| ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.19→50 Å / σ(F): 0 / Stereochemistry target values: Engh and Huber
| ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.19→50 Å
| ||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||
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 |