+Open data
-Basic information
Entry | Database: PDB / ID: 2hdc | ||||||
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Title | STRUCTURE OF TRANSCRIPTION FACTOR GENESIS/DNA COMPLEX | ||||||
Components |
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Keywords | PROTEIN/DNA / DYANAMICS / GENESIS / WINGED HELIX PROTEIN / PROTEIN-DNA COMPLEX | ||||||
Function / homology | Function and homology information trophectodermal cell differentiation / embryonic placenta development / cellular response to leukemia inhibitory factor / RNA polymerase II transcription regulatory region sequence-specific DNA binding / DNA-binding transcription repressor activity, RNA polymerase II-specific / sequence-specific double-stranded DNA binding / double-stranded DNA binding / in utero embryonic development / transcription cis-regulatory region binding / DNA-binding transcription factor activity ...trophectodermal cell differentiation / embryonic placenta development / cellular response to leukemia inhibitory factor / RNA polymerase II transcription regulatory region sequence-specific DNA binding / DNA-binding transcription repressor activity, RNA polymerase II-specific / sequence-specific double-stranded DNA binding / double-stranded DNA binding / in utero embryonic development / transcription cis-regulatory region binding / DNA-binding transcription factor activity / chromatin / regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / nucleus Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | SOLUTION NMR / distance geometry | ||||||
Authors | Jin, C. / Marsden, I. / Chen, X. / Liao, X. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1999 Title: Dynamic DNA contacts observed in the NMR structure of winged helix protein-DNA complex. Authors: Jin, C. / Marsden, I. / Chen, X. / Liao, X. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2hdc.cif.gz | 1 MB | Display | PDBx/mmCIF format |
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PDB format | pdb2hdc.ent.gz | 843.6 KB | Display | PDB format |
PDBx/mmJSON format | 2hdc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hd/2hdc ftp://data.pdbj.org/pub/pdb/validation_reports/hd/2hdc | HTTPS FTP |
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-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: DNA chain | Mass: 5187.426 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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#2: DNA chain | Mass: 5222.404 Da / Num. of mol.: 1 / Source method: obtained synthetically |
#3: Protein | Mass: 11414.109 Da / Num. of mol.: 1 / Fragment: DNA BINDING DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: GENESIS / Organelle: NUCLEUSCell nucleus / References: UniProt: Q63245 |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||
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NMR experiment |
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NMR details | Text: THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR SPECTROSCOPY ON 13C, 15N (AND 2H)-LABELED SAMPLE |
-Sample preparation
Details | Contents: 90% WATER/10% D2O |
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Sample conditions | pH: 6.5 / Temperature: 303 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: distance geometry / Software ordinal: 1 | ||||||||||||
NMR ensemble | Conformer selection criteria: LEAST RESTRAINT VIOLATION / Conformers calculated total number: 200 / Conformers submitted total number: 20 |