[English] 日本語
Yorodumi
- PDB-1y8d: Dimeric parallel-stranded tetraplex with 3+1 5' G-tetrad interfac... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1y8d
TitleDimeric parallel-stranded tetraplex with 3+1 5' G-tetrad interface, single-residue chain reversal loops and GAG triad in the context of A(GGGG) pentad
Components5'-D(*GP*GP*GP*GP*TP*GP*GP*GP*AP*GP*GP*AP*GP*GP*GP*T)-3'
KeywordsDNA / DIMERIC PARALLEL-STRANDED QUADRUPLEX / DNA APTAMER / HIV-1 INTEGRASE INHIBITOR DESIGN / 3+1 G-TETRAD / SINGLE NUCLEOTIDE CHAIN REVERSAL LOOP / GAG TRIAD / (A)GGGG PENTAD
Function / homologyDNA / DNA (> 10)
Function and homology information
MethodSOLUTION NMR / distance geometry; simulated annealing; molecular dynamics; matrix relaxation
AuthorsPhan, A.T. / Kuryavyi, V.V. / Ma, J.-B. / Faure, A. / Andreola, M.-L. / Patel, D.J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2005
Title: An interlocked dimeric parallel-stranded DNA quadruplex: A potent inhibitor of HIV-1 integrase
Authors: Phan, A.T. / Kuryavyi, V.V. / Ma, J.-B. / Faure, A. / Andreola, M.-L. / Patel, D.J.
History
DepositionDec 11, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 1, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Experimental preparation
Category: database_2 / pdbx_nmr_exptl_sample_conditions ...database_2 / pdbx_nmr_exptl_sample_conditions / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_exptl_sample_conditions.pressure_units / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 5'-D(*GP*GP*GP*GP*TP*GP*GP*GP*AP*GP*GP*AP*GP*GP*GP*T)-3'
B: 5'-D(*GP*GP*GP*GP*TP*GP*GP*GP*AP*GP*GP*AP*GP*GP*GP*T)-3'


Theoretical massNumber of molelcules
Total (without water)10,2812
Polymers10,2812
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)10 / 100all calculated structures submitted,back calculated data agree with experimental NOESY spectrum,structures with acceptable covalent geometry,structures with favorable non-bond energy
RepresentativeModel #1fewest violations,lowest energy

-
Components

#1: DNA chain 5'-D(*GP*GP*GP*GP*TP*GP*GP*GP*AP*GP*GP*AP*GP*GP*GP*T)-3'


Mass: 5140.312 Da / Num. of mol.: 2 / Fragment: HIV INTEGRASE INHIBITOR SEQUENCE / Source method: obtained synthetically
Details: DNA aptamer obtained by SELEX of ODN inhibiting RNase H activity of HIV Reverse Transcriptase

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
2222D NOESY
1312D TOCSY
2421H-31P COSY
1511H-15N JRHMQC
1611H-13C JRHMBC
NMR detailsText: The experiments 1H-15N HMBC, 1H-13C HMBC, 1H-13C HSQC, 1H-13C sHMBC were performed for assignments

-
Sample preparation

Details
Solution-IDContentsSolvent system
1DNA 15N,13C90 MM KCL pH 7; 90%H2O,10% D2O
2DNA 15N,13C90 MM KCL pH 7; 100% D2O
Sample conditionsIonic strength: 90 mM KCl / pH: 7 / Pressure: 1 atm / Temperature: 298 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE6001
Varian UNITYVarianUNITY6002

-
Processing

NMR software
NameVersionDeveloperClassification
Felix2000Accelrysprocessing
X-PLOR3.851A.T.Brungerrefinement
VNMR6.1Variancollection
RefinementMethod: distance geometry; simulated annealing; molecular dynamics; matrix relaxation
Software ordinal: 1
Details: the structures are based on a total of 1689 restraints, 283 are NOE-derived distance constraints, 3 negative restraints, 84 dihedral angle restraints,104 distance restraints from hydrogen ...Details: the structures are based on a total of 1689 restraints, 283 are NOE-derived distance constraints, 3 negative restraints, 84 dihedral angle restraints,104 distance restraints from hydrogen bonds, 243 intensity restraints (each of five mixing times)
NMR representativeSelection criteria: fewest violations,lowest energy
NMR ensembleConformer selection criteria: all calculated structures submitted,back calculated data agree with experimental NOESY spectrum,structures with acceptable covalent geometry,structures with favorable non-bond 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