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Yorodumi- PDB-1d5v: SOLUTION STRUCTURE OF THE FORKHEAD DOMAIN OF THE ADIPOCYTE-TRANSC... -
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-Basic information
Entry | Database: PDB / ID: 1d5v | ||||||
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Title | SOLUTION STRUCTURE OF THE FORKHEAD DOMAIN OF THE ADIPOCYTE-TRANSCRIPTION FACTOR FREAC-11 (S12) | ||||||
Components | S12 TRANSCRIPTION FACTOR (FKH-14) | ||||||
Keywords | GENE REGULATION / WINGED HELIX / DNA-RECOGNITION HELIX | ||||||
Function / homology | Function and homology information apoptotic process involved in outflow tract morphogenesis / negative regulation of apoptotic process involved in outflow tract morphogenesis / paraxial mesodermal cell fate commitment / glomerular endothelium development / Formation of intermediate mesoderm / embryonic viscerocranium morphogenesis / positive regulation of vascular wound healing / glomerular mesangial cell development / Formation of the ureteric bud / podocyte differentiation ...apoptotic process involved in outflow tract morphogenesis / negative regulation of apoptotic process involved in outflow tract morphogenesis / paraxial mesodermal cell fate commitment / glomerular endothelium development / Formation of intermediate mesoderm / embryonic viscerocranium morphogenesis / positive regulation of vascular wound healing / glomerular mesangial cell development / Formation of the ureteric bud / podocyte differentiation / lymphangiogenesis / neural crest cell development / regulation of organ growth / metanephros development / embryonic heart tube development / camera-type eye development / collagen fibril organization / positive regulation of cell adhesion mediated by integrin / negative regulation of cold-induced thermogenesis / ventricular cardiac muscle tissue morphogenesis / cardiac muscle cell proliferation / artery morphogenesis / ureteric bud development / DNA-binding transcription activator activity / branching involved in blood vessel morphogenesis / positive regulation of cell migration involved in sprouting angiogenesis / mesoderm development / blood vessel remodeling / anatomical structure morphogenesis / vascular endothelial growth factor receptor signaling pathway / somitogenesis / Notch signaling pathway / positive regulation of endothelial cell migration / blood vessel diameter maintenance / ossification / response to hormone / promoter-specific chromatin binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / chromatin DNA binding / sequence-specific double-stranded DNA binding / insulin receptor signaling pathway / heart development / DNA-binding transcription activator activity, RNA polymerase II-specific / sequence-specific DNA binding / cell differentiation / nuclear body / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / chromatin / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / nucleoplasm / identical protein binding / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / COMBINED DISTANCE GEOMETRY, SIMULATING ANNEALING PROCEDURE | ||||||
Authors | van Dongen, M.J.P. / Cederberg, A. / Carlsson, P. / Enerback, S. / Wikstrom, M. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2000 Title: Solution structure and dynamics of the DNA-binding domain of the adipocyte-transcription factor FREAC-11. Authors: van Dongen, M.J. / Cederberg, A. / Carlsson, P. / Enerback, S. / Wikstrom, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1d5v.cif.gz | 827.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1d5v.ent.gz | 707.4 KB | Display | PDB format |
PDBx/mmJSON format | 1d5v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1d5v_validation.pdf.gz | 356.9 KB | Display | wwPDB validaton report |
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Full document | 1d5v_full_validation.pdf.gz | 521.2 KB | Display | |
Data in XML | 1d5v_validation.xml.gz | 36.3 KB | Display | |
Data in CIF | 1d5v_validation.cif.gz | 60.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d5/1d5v ftp://data.pdbj.org/pub/pdb/validation_reports/d5/1d5v | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 11083.717 Da / Num. of mol.: 1 / Fragment: DNA-BINDING DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Tissue: ADIPOSE TISSUE / Plasmid: PET-11A / Production host: Escherichia coli (E. coli) / References: UniProt: Q99958 |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||
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NMR experiment |
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NMR details | Text: HNCA, HN(CO)CA, HNCACB, CACB(CO)NH AND HNCO EXPERIMENTS WERE USED TO OBTAIN SEQUENTIAL ASSIGNMENTS FOR THE BACKBONE. SIDE-CHAIN RESONANCES WERE ASSIGNED USING TOCSY-15N-HSQC, C(CO)NH, H(CCO)NH ...Text: HNCA, HN(CO)CA, HNCACB, CACB(CO)NH AND HNCO EXPERIMENTS WERE USED TO OBTAIN SEQUENTIAL ASSIGNMENTS FOR THE BACKBONE. SIDE-CHAIN RESONANCES WERE ASSIGNED USING TOCSY-15N-HSQC, C(CO)NH, H(CCO)NH AND HC(C)H-TOCSY EXPERIMENTS. |
-Sample preparation
Details |
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Sample conditions | Ionic strength: 15 mM / pH: 6.1 / Pressure: AMBIENT / Temperature: 300 K | ||||||
Crystal grow | *PLUS Method: other / Details: NMR |
-NMR measurement
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: COMBINED DISTANCE GEOMETRY, SIMULATING ANNEALING PROCEDURE Software ordinal: 1 Details: THE STRUCTURE WAS DETERMINED FROM 1042 DISTANCE RESTRAINTS, COMPLEMENTED WITH 145 RESTRAINTS ON DIHEDRAL ANGLES AND 36 RESTRAINTS ON HYDROGEN BOND LENGTHS. | ||||||||||||||||
NMR representative | Selection criteria: closest to the average | ||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 125 / Conformers submitted total number: 25 |