[English] 日本語
Yorodumi
- PDB-2n96: An unexpected mode of small molecule DNA binding provides the str... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2n96
TitleAn unexpected mode of small molecule DNA binding provides the structural basis for DNA cleavage by the potent antiproliferative agent (-)-lomaiviticin A
ComponentsDNA (5'-D(*GP*CP*TP*AP*TP*AP*GP*C)-3')
KeywordsDNA / diazofluorene / intercalator
Function / homologyChem-4JF / DNA
Function and homology information
Biological speciessynthetic construct (others)
MethodSOLUTION NMR / molecular dynamics
Model detailsminimized average structure, model1
Model type detailsminimized average
AuthorsWoo, C.M. / Li, Z. / Paulson, E. / Herzon, S.B.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2016
Title: Structural basis for DNA cleavage by the potent antiproliferative agent (-)-lomaiviticin A.
Authors: Woo, C.M. / Li, Z. / Paulson, E.K. / Herzon, S.B.
History
DepositionNov 7, 2015Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jun 1, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 8, 2016Group: Database references
Revision 1.2Jun 29, 2016Group: Database references
Revision 1.3Nov 3, 2021Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Experimental preparation / Refinement description / Source and taxonomy / Structure summary
Category: chem_comp / database_2 ...chem_comp / database_2 / entity / pdbx_entity_nonpoly / pdbx_entity_src_syn / pdbx_nmr_exptl_sample / pdbx_nmr_refine / pdbx_nmr_sample_details / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_site
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_nmr_exptl_sample.component / _pdbx_nmr_exptl_sample.isotopic_labeling / _pdbx_nmr_refine.software_ordinal / _pdbx_nmr_sample_details.label / _pdbx_nmr_sample_details.type / _pdbx_nmr_software.classification / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _pdbx_nmr_spectrometer.type / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
X: DNA (5'-D(*GP*CP*TP*AP*TP*AP*GP*C)-3')
Y: DNA (5'-D(*GP*CP*TP*AP*TP*AP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,2293
Polymers4,8532
Non-polymers1,3751
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)6 / 1000structures with the least restraint violations
RepresentativeModel #1minimized average structure

-
Components

#1: DNA chain DNA (5'-D(*GP*CP*TP*AP*TP*AP*GP*C)-3')


Mass: 2426.617 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-4JF / (1R,1'R,2S,2'S,3R,3'R,5aR,10aR,11a'S)-2'-[(2,6-dideoxy-3-O-methyl-alpha-L-arabino-hexopyranosyl)oxy]-2,2'-diethyl-11,11 '-dihydrazinyl-6,6',9,9'-tetrahydroxy-4,4',5,5',10,10'-hexaoxo-1,1'-bis{[2,4,6-trideoxy-4-(dimethylamino)-beta-L-arabino -hexopyranosyl]oxy}[2,2',3,3',4,4',5,5',5a,8,10,10',10a,11a'-tetradecahydro-1H,1'H-[3,3'-bibenzo[b]fluorene]]-2-yl 2,6-dideoxy-3-O-methyl-alpha-L-arabino-hexopyranoside / Lomaiviticin A


Mass: 1375.468 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C68H90N6O24

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D DQF-COSY
1212D 1H-13C HSQC
1312D 1H-1H NOESY
1412D 1H-1H NOESY
1522D 1H-1H NOESY
1622D DQF-COSY

-
Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution11.1 uM DNA (5'-D(*(DG5)P*CP*TP*AP*TP*AP*GP*(DC3)*(DG5)P*CP*TP*AP*TP*AP*GP*(DC3))-3'), 1.1 uM lomaiviticin A, 100% D2Osample_1100% D2O
solution21.1 uM DNA (5'-D(*(DG5)P*CP*TP*AP*TP*AP*GP*(DC3)*(DG5)P*CP*TP*AP*TP*AP*GP*(DC3))-3'), 1.1 uM lomaiviticin A, 90% H2O/10% D2Osample_290% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.1 uMDNA (5'-D(*(DG5)P*CP*TP*AP*TP*AP*GP*(DC3)*(DG5)P*CP*TP*AP*TP*AP*GP*(DC3))-3')natural abundance1
1.1 uMlomaiviticin Anatural abundance1
1.1 uMDNA (5'-D(*(DG5)P*CP*TP*AP*TP*AP*GP*(DC3)*(DG5)P*CP*TP*AP*TP*AP*GP*(DC3))-3')natural abundance2
1.1 uMlomaiviticin Anatural abundance2
Sample conditionsIonic strength: 24 / pH: 7.5 / Pressure: ambient / Temperature: 297 K

-
NMR measurement

NMR spectrometerType: Agilent Direct Drive / Manufacturer: Agilent / Model: Direct Drive / Field strength: 800 MHz

-
Processing

NMR software
NameVersionDeveloperClassification
Amber14Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, and Kollmanstructure calculation
Amber14Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, and Kollmanrefinement
RefinementMethod: molecular dynamics / Software ordinal: 2
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 1000 / Conformers submitted total number: 6

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more