[English] 日本語
Yorodumi
- PDB-1gv6: Solution structure of alfa-L-LNA:DNA duplex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1gv6
TitleSolution structure of alfa-L-LNA:DNA duplex
Components
  • 5- D(*CP*(ATL)P*GP*CP*(ATL)P*(ATL)P*CP*(ATL)P* GP*C) -3
  • 5- D(*GP*CP*AP*GP*AP*AP*GP*CP*AP*G) -3
KeywordsLOCKED NUCLEIC ACID / LNA / DNA
Function / homologyDNA / DNA/RNA hybrid
Function and homology information
MethodSOLUTION NMR / simulated annealing
AuthorsNielsen, K.M.E. / Petersen, M. / Haakansson, A.E. / Wengel, J. / Jacobsen, J.P.
CitationJournal: Chemistry / Year: 2002
Title: Alfa-L-Lna (Alfa-L-Ribo Configured Locked Nucleic Acid) Recognition of DNA: An NMR Spectroscopic Study
Authors: Nielsen, K.M.E. / Petersen, M. / Haakansson, A.E. / Wengel, J. / Jacobsen, J.P.
History
DepositionFeb 6, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 5, 2002Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 15, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_conn.pdbx_leaving_atom_flag

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 5- D(*CP*(ATL)P*GP*CP*(ATL)P*(ATL)P*CP*(ATL)P* GP*C) -3
B: 5- D(*GP*CP*AP*GP*AP*AP*GP*CP*AP*G) -3


Theoretical massNumber of molelcules
Total (without water)6,2022
Polymers6,2022
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 20
RepresentativeModel #12

-
Components

#1: DNA/RNA hybrid 5- D(*CP*(ATL)P*GP*CP*(ATL)P*(ATL)P*CP*(ATL)P* GP*C) -3


Mass: 3098.997 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: ATL IS ALFA-L-LNA (ALFA-L-RIBO CONFIGURED LOCKED NUCLEIC ACID OR [ (1S, 3R, 4S, 7R)-7-HYDROXY-3-(THYMIN-1-YL)-2,5-DIOXABICYCLO[2. 2.1]HEPT-1-YL]METHYL DIHYDROGEN PHOSPHATE
#2: DNA chain 5- D(*GP*CP*AP*GP*AP*AP*GP*CP*AP*G) -3


Mass: 3103.057 Da / Num. of mol.: 1 / Source method: obtained synthetically
Sequence detailsMODRES: 1GV6 ATL A 2() ALFA-L-LNA (ALFA-L-RIBO CONFIGURED LOCKED NUCLEIC ACID OR [ (1S,3R,4S,7R)-7- ...MODRES: 1GV6 ATL A 2() ALFA-L-LNA (ALFA-L-RIBO CONFIGURED LOCKED NUCLEIC ACID OR [ (1S,3R,4S,7R)-7-HYDROXY-3-(THYMIN-1-YL)-2,5-DIOXABICYCLO [2.2.1]HEPT-1-YL]METHYL DIHYDROGEN PHOSPHATE MODRES: 1GV6 ATL A 5() ALFA-L-LNA (ALFA-L-RIBO CONFIGURED LOCKED NUCLEIC ACID OR [ (1S,3R,4S,7R)-7-HYDROXY-3-(THYMIN-1-YL)-2,5-DIOXABICYCLO [2.2.1]HEPT-1-YL]METHYL DIHYDROGEN PHOSPHATE MODRES: 1GV6 ATL A 6() ALFA-L-LNA (ALFA-L-RIBO CONFIGURED LOCKED NUCLEIC ACID OR [ (1S,3R,4S,7R)-7-HYDROXY-3-(THYMIN-1-YL)-2,5-DIOXABICYCLO [2.2.1]HEPT-1-YL]METHYL DIHYDROGEN PHOSPHATE MODRES: 1GV6 ATL A 8() ALFA-L-LNA (ALFA-L-RIBO CONFIGURED LOCKED NUCLEIC ACID OR [ (1S,3R,4S,7R)-7-HYDROXY-3-(THYMIN-1-YL)-2,5-DIOXABICYCLO [2.2.1]HEPT-1-YL]METHYL DIHYDROGEN PHOSPHATE

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111NOESY
121DQF-COSY
131TOCSY
NMR detailsText: THE STRUCTURE WAS DETERMINED USING 1H,1H- NOES FROM 100MS NOESY AND WATERGATE NOESY EXPERIMENTS. SUGAR TORSION RESTRAINTS WERE DERIVED BY ANALYSIS OF A DQF-COSY SPECTRUM

-
Sample preparation

Sample conditionsIonic strength: 0.01 M / pH: 7 / Pressure: 1 atm / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

-
NMR measurement

NMR spectrometerType: Varian UNITY / Manufacturer: Varian / Model: UNITY / Field strength: 500 MHz

-
Processing

NMR software
NameDeveloperClassification
AmberCASE, DA, KOLLMAN, PA, ET AL.refinement
Felixstructure solution
MARDIGRASstructure solution
Amberstructure solution
RefinementMethod: simulated annealing / Software ordinal: 1
Details: REFINEMENT DETAILS CAN BE FOUND IN THE JRNL CITATION ABOVE.
NMR ensembleConformers calculated total number: 20 / Conformers submitted total number: 20

+
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