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Yorodumi- PDB-2mzn: NMR structure of the HLTF HIRAN domain in its DNA-bound conformation -
+Open data
-Basic information
Entry | Database: PDB / ID: 2mzn | ||||||
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Title | NMR structure of the HLTF HIRAN domain in its DNA-bound conformation | ||||||
Components | Helicase-like transcription factor | ||||||
Keywords | DNA BINDING PROTEIN / HIRAN / HLTF | ||||||
Function / homology | Function and homology information hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides / ATP-dependent chromatin remodeler activity / regulation of neurogenesis / ATP-dependent activity, acting on DNA / helicase activity / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / RING-type E3 ubiquitin transferase / mRNA transcription by RNA polymerase II / nuclear matrix / RNA polymerase II transcription regulator complex ...hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides / ATP-dependent chromatin remodeler activity / regulation of neurogenesis / ATP-dependent activity, acting on DNA / helicase activity / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / RING-type E3 ubiquitin transferase / mRNA transcription by RNA polymerase II / nuclear matrix / RNA polymerase II transcription regulator complex / ubiquitin protein ligase activity / E3 ubiquitin ligases ubiquitinate target proteins / protein ubiquitination / DNA repair / ubiquitin protein ligase binding / nucleolus / positive regulation of transcription by RNA polymerase II / DNA binding / RNA binding / zinc ion binding / nucleoplasm / ATP binding / membrane / nucleus / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR | ||||||
Authors | Korzhnev, D. / Eldirany, S. | ||||||
Citation | Journal: Mol.Cell / Year: 2015 Title: HLTF's Ancient HIRAN Domain Binds 3' DNA Ends to Drive Replication Fork Reversal. Authors: Kile, A.C. / Chavez, D.A. / Bacal, J. / Eldirany, S. / Korzhnev, D.M. / Bezsonova, I. / Eichman, B.F. / Cimprich, K.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2mzn.cif.gz | 744.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2mzn.ent.gz | 626.4 KB | Display | PDB format |
PDBx/mmJSON format | 2mzn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2mzn_validation.pdf.gz | 535.8 KB | Display | wwPDB validaton report |
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Full document | 2mzn_full_validation.pdf.gz | 794.7 KB | Display | |
Data in XML | 2mzn_validation.xml.gz | 59 KB | Display | |
Data in CIF | 2mzn_validation.cif.gz | 81.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mz/2mzn ftp://data.pdbj.org/pub/pdb/validation_reports/mz/2mzn | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 13532.326 Da / Num. of mol.: 1 / Fragment: UNP residues 51-171 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HLTF, HIP116A, RNF80, SMARCA3, SNF2L3, ZBU1 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / References: UniProt: Q14527 |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details | Contents: 1 mM [U-13C; U-15N] protein, 20 mM sodium phosphate, 100 mM sodium chloride, 90% H2O/10% D2O Solvent system: 90% H2O/10% D2O | ||||||||||||||||
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Sample |
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Sample conditions | Ionic strength: 0.1 / pH: 6.8 / Pressure: ambient / Temperature: 298 K |
-NMR measurement
NMR spectrometer | Type: Agilent PremiumCOMPACT / Manufacturer: Agilent / Model: PremiumCOMPACT / Field strength: 800 MHz |
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-Processing
NMR software |
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Refinement | Software ordinal: 1 Details: THE STRUCTURE OF THE 15N/13C-LABELED HIRAN DOMAIN WAS DETERMINED IN THE PRESENCE OF UNLABELED SSDNA (DTTTTTTTTTT). THE DNA STRUCTURE WAS NOT DETERMINED. DNA-BINDING SITE WAS MAPPED USING NMR ...Details: THE STRUCTURE OF THE 15N/13C-LABELED HIRAN DOMAIN WAS DETERMINED IN THE PRESENCE OF UNLABELED SSDNA (DTTTTTTTTTT). THE DNA STRUCTURE WAS NOT DETERMINED. DNA-BINDING SITE WAS MAPPED USING NMR CHEMICAL SHIFT CHANGES. THE VALUES OF DNA-BINDING INDUCED CHEMICAL SHIFT CHANGES ARE AVAILABLE AS PART OF BMRB DEPOSITION 25492. | ||||||||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 200 / Conformers submitted total number: 20 |