[English] 日本語
Yorodumi
- PDB-1hhw: Solution structure of LNA1:RNA hybrid -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1hhw
TitleSolution structure of LNA1:RNA hybrid
Components
  • 5- D(*CP*TP*GP*AP*+TLNP*AP*TP*GP*C) -3
  • 5- R(*GP*CP*AP*UP*AP*UP*CP*AP*G) -3
KeywordsANTISENSE / LOCKED NUCLEIC ACID / DNA / RNA / HYBRID / RNASE H
Function / homologyDNA/RNA hybrid / RNA
Function and homology information
MethodSOLUTION NMR / simulated annealing
AuthorsPetersen, M. / Bondensgaard, K. / Wengel, J. / Jacobsen, J.P.
Citation
Journal: J.Am.Chem.Soc. / Year: 2002
Title: Locked Nucleic Acid (Lna) Recognition of RNA: NMR Solution Structures of Lna:RNA Hybrids
Authors: Petersen, M. / Bondensgaard, K. / Wengel, J. / Jacobsen, J.P.
#1: Journal: Chemistry / Year: 2000
Title: Origin of Locked Nucleic Acid High-Affinity Recognition of RNA as Revealed by High-Resolution NMR Structures
Authors: Petersen, M. / Bondensgaard, K. / Wengel, J. / Jacobsen, J.P.
History
DepositionDec 29, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 30, 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*TP*GP*AP*+TLNP*AP*TP*GP*C) -3
B: 5- R(*GP*CP*AP*UP*AP*UP*CP*AP*G) -3


Theoretical massNumber of molelcules
Total (without water)5,6152
Polymers5,6152
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)40 / 40
RepresentativeModel #7

-
Components

#1: DNA/RNA hybrid 5- D(*CP*TP*GP*AP*+TLNP*AP*TP*GP*C) -3


Mass: 2758.821 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: RNA chain 5- R(*GP*CP*AP*UP*AP*UP*CP*AP*G) -3


Mass: 2855.767 Da / Num. of mol.: 1 / Source method: obtained synthetically
Sequence detailsCHAIN A RESIDUE 5 IS A LOCKED NUCLEIC ACID OR (1R,3R,4R,7S) -7-HYDROXY-1-HYDROXYMETHYL-3-(THYMIN-1- ...CHAIN A RESIDUE 5 IS A LOCKED NUCLEIC ACID OR (1R,3R,4R,7S) -7-HYDROXY-1-HYDROXYMETHYL-3-(THYMIN-1-YL)-2,5-DIOXABICYCL O[2.2.1]HEPTANE

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: NOESY

-
Sample preparation

Sample conditionsIonic strength: 0.1 / pH: 7 / Pressure: 1 atm / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

-
NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 750 MHz

-
Processing

NMR software
NameDeveloperClassification
AmberCASE, DA, KOLLMAN, PArefinement
MARDIGRASstructure solution
Amberstructure solution
Felixstructure solution
RefinementMethod: simulated annealing / Software ordinal: 1
Details: A TOTAL OF 284 NOE DISTANCE RESTRAINTS WERE OBTAINED FROM A FULL RELAXATION MATRIX ANALYSIS WITH THE PROGRAM RANDMARDI. 16 J-COUPLING CONSTANT RESTRAINTS WERE DERIVED FROM A J-SCALED-1H-31P- ...Details: A TOTAL OF 284 NOE DISTANCE RESTRAINTS WERE OBTAINED FROM A FULL RELAXATION MATRIX ANALYSIS WITH THE PROGRAM RANDMARDI. 16 J-COUPLING CONSTANT RESTRAINTS WERE DERIVED FROM A J-SCALED-1H-31P-HMBC SPECTRUM. 22 WATSON-CRICK BASE PAIRING RESTRAINTS.
NMR ensembleConformers calculated total number: 40 / Conformers submitted total number: 40

+
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