[English] 日本語
Yorodumi
- PDB-8znq: Solution structure of the complex of naphthyridine-azaquinolone a... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8znq
TitleSolution structure of the complex of naphthyridine-azaquinolone and an RNA with ACG/AUA motif
ComponentsRNA (30-MER)
KeywordsRNA / SMALL MOLECULE / DRUG
Function / homologyChem-NAZ / RNA / RNA (> 10)
Function and homology information
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsFujiwara, A. / Chen, Q. / Nakatani, K. / Murata, A. / Kawai, G.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Solution structure of the complex of naphthyridine-azaquinolone and an RNA with ACG/AUA motif
Authors: Chen, Q. / Fujiwara, A. / Nakatani, K. / Kawai, G. / Murata, A.
History
DepositionMay 27, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 4, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: RNA (30-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,0742
Polymers9,6151
Non-polymers4601
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: NMR Distance Restraints, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

-
Components

#1: RNA chain RNA (30-MER)


Mass: 9614.705 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#2: Chemical ChemComp-NAZ / N~3~-{3-[(7-METHYL-1,8-NAPHTHYRIDIN-2-YL)AMINO]-3-OXOPROPYL}-N~1~-[(7-OXO-7,8-DIHYDRO-1,8-NAPHTHYRIDIN-2-YL)METHYL]-BET A-ALANINAMIDE / NAPHTYRIDINE-AZAQUINOLONE


Mass: 459.500 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H25N7O3 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D NOESY
121isotropic12D HOHAHA
132isotropic12D 1H-13C HSQC

-
Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
solution10.26 mM no RNA (30-MER), 0.26 mM no N~3~-{3-[(7-METHYL-1,8-NAPHTHYRIDIN-2-YL)AMINO]-3-OXOPROPYL}-N~1~-[(7-OXO-7,8-DIHYDRO-1,8-NAPHTHYRIDIN-2-YL)METHYL]-BET A-ALANINAMIDE, 95% H2O/5% D2OComplex of an RNA and NAZsample95% H2O/5% D2O
solution20.08 mM [U-10% 13C; U-10% 15N]U23 and [U-10% 13C; U-10% 15N]A24 RNA (30-MER), 0.08 mM no N~3~-{3-[(7-METHYL-1,8-NAPHTHYRIDIN-2-YL)AMINO]-3-OXOPROPYL}-N~1~-[(7-OXO-7,8-DIHYDRO-1,8-NAPHTHYRIDIN-2-YL)METHYL]-BET A-ALANINAMIDE, 95% H2O/5% D2OComplex of an RNA with 13C/15N-label at U23 and A24 and NAZsample-U23L-A24L95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.26 mMRNA (30-MER)no1
0.26 mMN~3~-{3-[(7-METHYL-1,8-NAPHTHYRIDIN-2-YL)AMINO]-3-OXOPROPYL}-N~1~-[(7-OXO-7,8-DIHYDRO-1,8-NAPHTHYRIDIN-2-YL)METHYL]-BET A-ALANINAMIDEno1
0.08 mMRNA (30-MER)[U-10% 13C; U-10% 15N]U23 and [U-10% 13C; U-10% 15N]A242
0.08 mMN~3~-{3-[(7-METHYL-1,8-NAPHTHYRIDIN-2-YL)AMINO]-3-OXOPROPYL}-N~1~-[(7-OXO-7,8-DIHYDRO-1,8-NAPHTHYRIDIN-2-YL)METHYL]-BET A-ALANINAMIDEno2
Sample conditionsDetails: 20 mM sodium phosphate buffer (pH 6.5) with 50 mM sodium chloride and 5% D2O
Ionic strength: 50 mM / Label: condition1 / pH: 6.5 / Pressure: 1 atm / Temperature: 288 K

-
NMR measurement

NMR spectrometerType: Bruker AVANCE NEO / Manufacturer: Bruker / Model: AVANCE NEO / Field strength: 600 MHz

-
Processing

NMR software
NameVersionDeveloperClassification
Sparky3.114Goddardchemical shift assignment
CNS1.3Brunger, Adams, Clore, Gros, Nilges and Readstructure calculation
CNS1.3Brunger, Adams, Clore, Gros, Nilges and Readrefinement
Sparky3.114Goddardpeak picking
RefinementMethod: simulated annealing / Software ordinal: 2
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 10

+
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