+Open data
-Basic information
Entry | Database: PDB / ID: 1hbx | ||||||
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Title | Ternary Complex of SAP-1 and SRF with specific SRE DNA | ||||||
Components |
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Keywords | GENE REGULATION / TRANSCRIPTION COMPLEX / SERUM RESPONSE FACTOR / TERNARY COMPLEX FACTOR | ||||||
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: 3.15 Å | ||||||
Authors | Hassler, M. / Richmond, T.J. | ||||||
Citation | Journal: Embo J. / Year: 2001 Title: The B-Box Dominates Sap-1/Srf Interactions in the Structure of the Ternary Complex Authors: Hassler, M. / Richmond, T.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1hbx.cif.gz | 182.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1hbx.ent.gz | 140.4 KB | Display | PDB format |
PDBx/mmJSON format | 1hbx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1hbx_validation.pdf.gz | 422.7 KB | Display | wwPDB validaton report |
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Full document | 1hbx_full_validation.pdf.gz | 481.3 KB | Display | |
Data in XML | 1hbx_validation.xml.gz | 22.1 KB | Display | |
Data in CIF | 1hbx_validation.cif.gz | 33.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hb/1hbx ftp://data.pdbj.org/pub/pdb/validation_reports/hb/1hbx | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Details | COMPLEX OF HOMODIMERIC SERUM RESPONSE FACTOR , THEETS-DOMAIN PROTEIN ELK-4 AND THE DOUBLE STRANDED DNA. |
-Components
#1: Protein | Mass: 10300.120 Da / Num. of mol.: 4 / Fragment: CORE RESIDUES 132-223 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Gene: SRF (132-223) / Plasmid: PET3A / Gene (production host): SRF CORE (132-223) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS / References: UniProt: P11831 #2: DNA chain | Mass: 8034.175 Da / Num. of mol.: 2 / Fragment: SRE SPECIFIC DNA / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) #3: Protein | Mass: 17973.408 Da / Num. of mol.: 2 / Fragment: RESIDUES 2-156 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Gene: SAP-1 (1-156) / Plasmid: PET3A / Gene (production host): SAP-1 (1-156) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS / References: UniProt: P28324 #4: DNA chain | Mass: 7941.145 Da / Num. of mol.: 2 / Fragment: SRE SPECIFIC DNA / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.6 Å3/Da / Density % sol: 63.8 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 6.5 / Details: PEG 1500, NH4NO3, BIS-TRIS BUFFER, DTT, pH 6.50 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: vapor diffusion, hanging drop / PH range low: 6.8 / PH range high: 6.3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 103 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.9326 |
Detector | Type: ADSC Q4 / Detector: CCD / Date: Apr 15, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9326 Å / Relative weight: 1 |
Reflection | Resolution: 3→51 Å / Num. obs: 31747 / % possible obs: 98.5 % / Observed criterion σ(I): 0 / Redundancy: 5.2 % / Biso Wilson estimate: 84.1 Å2 / Rmerge(I) obs: 0.042 / Net I/σ(I): 30.4 |
Reflection shell | Resolution: 3→3.05 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.583 / Mean I/σ(I) obs: 1.98 / % possible all: 96.7 |
Reflection shell | *PLUS % possible obs: 96.7 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1SRS, 1BC7 Resolution: 3.15→51 Å / Rfactor Rfree error: 0.005 / Isotropic thermal model: OVERALL / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER Details: REFINED ALSO WITH REFMAC BY MURSHUDOV, VAGIN, DODSON
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 44.37 Å2 / ksol: 0.25 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 83.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3.15→51 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.15→3.35 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 0.9 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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