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- PDB-1j5n: Solution Structure of the Non-Sequence-Specific HMGB protein NHP6... -
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Open data
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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 | ||||||
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![]() | DNA BINDING PROTEIN/DNA / HMG-BOX / HMGB / PROTEIN-DNA COMPLEX / ALPHA HELIX / DOUBLE HELIX / DNA BINDING PROTEIN-DNA COMPLEX | ||||||
Function / homology | ![]() maintenance of transcriptional fidelity during transcription elongation by RNA polymerase III / Apoptosis induced DNA fragmentation / Regulation of TLR by endogenous ligand / Mitochondrial transcription initiation / MutSalpha complex binding / protein-DNA complex assembly / Pyroptosis / RNA polymerase III preinitiation complex assembly / Mitochondrial protein degradation / DNA binding, bending ...maintenance of transcriptional fidelity during transcription elongation by RNA polymerase III / Apoptosis induced DNA fragmentation / Regulation of TLR by endogenous ligand / Mitochondrial transcription initiation / MutSalpha complex binding / protein-DNA complex assembly / Pyroptosis / RNA polymerase III preinitiation complex assembly / Mitochondrial protein degradation / DNA binding, bending / negative regulation of DNA binding / nucleosome binding / RNA polymerase II preinitiation complex assembly / Neutrophil degranulation / protein-DNA complex / chromatin organization / chromosome / nucleic acid binding / chromatin remodeling / DNA repair / nucleus Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
![]() | Masse, J.E. / Wong, B. / Yen, Y.-M. / Allain, F.H.-T. / Johnson, R.C. / Feigon, J. | ||||||
![]() | ![]() 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. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 974.6 KB | Display | ![]() |
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PDB format | ![]() | 804.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 371.8 KB | Display | ![]() |
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Full document | ![]() | 779.2 KB | Display | |
Data in XML | ![]() | 114.2 KB | Display | |
Data in CIF | ![]() | 148.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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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.) ![]() ![]() Production host: ![]() ![]() |
-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. |
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Sample preparation
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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 |