[English] 日本語
Yorodumi
- PDB-9v88: Crystal structure of d(CGTTAACG)2 with a four-carbon linker conta... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9v88
TitleCrystal structure of d(CGTTAACG)2 with a four-carbon linker containing quinoxaline-acridine asymmetric intercalator compound
ComponentsDNA (5'-D(P*CP*GP*TP*TP*AP*AP*CP*G)-3')
KeywordsDNA / Ligand-DNA complex / Asymmetric intercalator / Bis-intercalation / Quinoxaline / Acridine
Function / homologyACETATE ION / : / DNA
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.92 Å
AuthorsWang, S.C. / Hou, M.H.
Funding support Taiwan, 2items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, Taiwan)109-2628-M- 005-001-MY4 Taiwan
Ministry of Science and Technology (MoST, Taiwan)109-2311-B-005-007-MY3 Taiwan
CitationJournal: Nucleic Acids Res. / Year: 2026
Title: Structural basis for asymmetric bis-intercalator targeting of DNA triplex junctions enabling dual inhibition of topoisomerase I and oncogene transcription.
Authors: Wang, S.C. / Hsieh, C.C. / Yuan, T.C. / Lin, S.M. / Chen, C.W. / Chang, C.C. / Huang, S.C. / Wang, E.C. / Huang, Y.J. / Chiang, M.H. / Horng, Y.C. / Hou, M.H.
History
DepositionMay 29, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 3, 2026Provider: repository / Type: Initial release
Revision 1.1Jun 10, 2026Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DNA (5'-D(P*CP*GP*TP*TP*AP*AP*CP*G)-3')
B: DNA (5'-D(P*CP*GP*TP*TP*AP*AP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,4336
Polymers4,8532
Non-polymers5804
Water36020
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1080 Å2
ΔGint-12 kcal/mol
Surface area4140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)23.817, 40.150, 24.318
Angle α, β, γ (deg.)90.00, 98.88, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

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


Mass: 2426.617 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-XAU / N-[4-(acridin-9-ylamino)butyl]quinoxaline-2-carboxamide


Mass: 421.494 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H23N5O / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 20 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.37 Å3/Da / Density % sol: 48.07 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.6mM Oligonucleotide, 0.6mM QA4, 100mM Sodium cacodylate pH 6.5, 200mM Calcium acetate hydrate, 18% v/v PEG 8000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 07A / Wavelength: 0.97626 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 2, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97626 Å / Relative weight: 1
ReflectionResolution: 1.92→30 Å / Num. obs: 3366 / % possible obs: 95.7 % / Redundancy: 3 % / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.041 / Rpim(I) all: 0.03 / Rrim(I) all: 0.052 / Χ2: 1.049 / Net I/σ(I): 22.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
1.93-23.20.1383490.980.9950.0920.1661.06996.7
2-2.083.30.1133130.9830.9960.0760.1371.04895.7
2.08-2.173.20.0933520.9930.9980.0630.1131.07397.2
2.17-2.293.20.0833280.9880.9970.0540.0991.09497.3
2.29-2.433.10.0643580.9930.9980.0450.0781.0497.8
2.43-2.622.80.0543440.9940.9990.0380.0661.0898
2.62-2.882.90.0483280.9950.9990.0350.0591.01696.5
2.88-3.32.70.0453320.9960.9990.0350.0571.00495.7
3.3-4.152.60.0383290.9960.9990.0280.0481.02291.9
4.15-302.60.0333330.9960.9990.0240.0411.01490.2

-
Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
HKL-2000data scaling
HKL-2000data reduction
PHENIX(1.20.1_4487)phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.92→15.41 Å / SU ML: 0.28 / Cross valid method: NONE / σ(F): 1.46 / Phase error: 32.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2643 342 10.2 %
Rwork0.2266 --
obs0.2303 3352 95.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.92→15.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 328 41 20 389
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009408
X-RAY DIFFRACTIONf_angle_d2.019615
X-RAY DIFFRACTIONf_dihedral_angle_d34.375160
X-RAY DIFFRACTIONf_chiral_restr0.23164
X-RAY DIFFRACTIONf_plane_restr0.00621
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.92-20.33431720.27981517X-RAY DIFFRACTION97
2.42-15.410.24611700.21281493X-RAY DIFFRACTION95

+
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