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Yorodumi- PDB-1j5n: Solution Structure of the Non-Sequence-Specific HMGB protein NHP6... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1j5n | ||||||
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Title | Solution Structure of the Non-Sequence-Specific HMGB protein NHP6A in complex with SRY DNA | ||||||
Components |
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Keywords | DNA BINDING PROTEIN/DNA / HMG-BOX / HMGB / PROTEIN-DNA COMPLEX / ALPHA HELIX / DOUBLE HELIX / DNA BINDING PROTEIN-DNA COMPLEX | ||||||
Function / homology | Function and homology information maintenance of transcriptional fidelity during transcription elongation by RNA polymerase III / Mitochondrial transcription initiation / MutSalpha complex binding / protein-DNA complex assembly / RNA polymerase III preinitiation complex assembly / DNA binding, bending / negative regulation of DNA binding / nucleosome binding / RNA polymerase II preinitiation complex assembly / protein-DNA complex ...maintenance of transcriptional fidelity during transcription elongation by RNA polymerase III / Mitochondrial transcription initiation / MutSalpha complex binding / protein-DNA complex assembly / RNA polymerase III preinitiation complex assembly / DNA binding, bending / negative regulation of DNA binding / nucleosome binding / RNA polymerase II preinitiation complex assembly / protein-DNA complex / chromosome / chromatin organization / nucleic acid binding / chromatin remodeling / DNA repair / nucleus Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
Authors | Masse, J.E. / Wong, B. / Yen, Y.-M. / Allain, F.H.-T. / Johnson, R.C. / Feigon, J. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2002 Title: The S. cerevisiae architectural HMGB protein NHP6A complexed with DNA: DNA and protein conformational changes upon binding Authors: Masse, J.E. / Wong, B. / Yen, Y.-M. / Allain, F.H.-T. / Johnson, R.C. / Feigon, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1j5n.cif.gz | 974.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1j5n.ent.gz | 804.2 KB | Display | PDB format |
PDBx/mmJSON format | 1j5n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j5/1j5n ftp://data.pdbj.org/pub/pdb/validation_reports/j5/1j5n | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: DNA chain | Mass: 4696.042 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: unlabeled DNA made on a commercial synthesizer, 15N,13C-labeled DNA made enzymatically in vitro with Taq polymerase |
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#2: DNA chain | Mass: 4482.940 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: unlabeled DNA made on a commercial synthesizer, 15N,13C-labeled DNA made enzymatically in vitro with Taq polymerase |
#3: Protein | Mass: 10824.364 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Production host: Escherichia coli (E. coli) / References: UniProt: P11632 |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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NMR details | Text: This structure calculated using standard 3D heteronuclear filtering and editing techniques with both labeled protein and labeled DNA. |
-Sample preparation
Details |
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Sample conditions |
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Crystal grow | *PLUS Method: other / Details: NMR |
-NMR measurement
NMR spectrometer | Type: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 600 MHz |
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-Processing
NMR software |
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Refinement | Method: simulated annealing / Software ordinal: 1 Details: The structures are based on a total of 3035 restraints. 102 are from alpha-helical hydrogen bond restraints within the protein (2/h-bond). 76 are hydrogen bond restraints for Watson-Crick ...Details: The structures are based on a total of 3035 restraints. 102 are from alpha-helical hydrogen bond restraints within the protein (2/h-bond). 76 are hydrogen bond restraints for Watson-Crick base pairs in the DNA. The rest are NOE-derived. 2197 of the NOE restraints are protein-protein restraints, 578 are DNA-DNA restraints, and 82 are protein-DNA restraints. | ||||||||||||||||
NMR representative | Selection criteria: closest to the average | ||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with acceptable covalent geometry Conformers calculated total number: 100 / Conformers submitted total number: 20 |