[English] 日本語
Yorodumi
- PDB-7edu: RNA duplex containing C-Au-C base pair -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7edu
TitleRNA duplex containing C-Au-C base pair
ComponentsRNA (5'-R(*GP*GP*AP*CP*UP*CP*GP*AP*CP*UP*CP*C)-3')
KeywordsRNA / Metal-mediated base pair / Gold
Function / homology: / RNA / RNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsKondo, J. / Iwase, E.
Funding support Japan, 1items
OrganizationGrant numberCountry
Ministry of Education, Culture, Sports, Science and Technology (Japan)24245037 Japan
CitationJournal: Chembiochem / Year: 2025
Title: Gold-Mediated Base Pairs in Nucleic Acids: Selective Coordination to Natural and Thiocarbonyl-Modified Cytosines Dependent upon the Oxidation State of Gold
Authors: Kosugi, K. / Sugawara, A. / Iwase, E. / Park, H. / Fujiwara, S. / Kanazawa, H. / Ono, A. / Kondo, J.
History
DepositionMar 17, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 23, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 26, 2025Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: RNA (5'-R(*GP*GP*AP*CP*UP*CP*GP*AP*CP*UP*CP*C)-3')
B: RNA (5'-R(*GP*GP*AP*CP*UP*CP*GP*AP*CP*UP*CP*C)-3')
C: RNA (5'-R(*GP*GP*AP*CP*UP*CP*GP*AP*CP*UP*CP*C)-3')
D: RNA (5'-R(*GP*GP*AP*CP*UP*CP*GP*AP*CP*UP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,9378
Polymers15,1494
Non-polymers7884
Water27015
1
A: RNA (5'-R(*GP*GP*AP*CP*UP*CP*GP*AP*CP*UP*CP*C)-3')
B: RNA (5'-R(*GP*GP*AP*CP*UP*CP*GP*AP*CP*UP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,9694
Polymers7,5752
Non-polymers3942
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1440 Å2
ΔGint-19 kcal/mol
Surface area4320 Å2
MethodPISA
2
C: RNA (5'-R(*GP*GP*AP*CP*UP*CP*GP*AP*CP*UP*CP*C)-3')
D: RNA (5'-R(*GP*GP*AP*CP*UP*CP*GP*AP*CP*UP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,9694
Polymers7,5752
Non-polymers3942
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1440 Å2
ΔGint-19 kcal/mol
Surface area4350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)29.216, 29.216, 257.794
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61

-
Components

#1: RNA chain
RNA (5'-R(*GP*GP*AP*CP*UP*CP*GP*AP*CP*UP*CP*C)-3')


Mass: 3787.312 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical
ChemComp-AU / GOLD ION


Mass: 196.967 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Au / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 15 / 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: 2.1 Å3/Da / Density % sol: 41.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: sodium cacodylate, MPD, spermine tetrahydrochloride, ammonium chloride, gold chloride

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1.03906 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 9, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03906 Å / Relative weight: 1
ReflectionResolution: 2.3→25.18 Å / Num. obs: 10301 / % possible obs: 94.1 % / Redundancy: 2.58 % / Biso Wilson estimate: 48.631 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.057 / Rrim(I) all: 0.073 / Χ2: 3.113 / Net I/σ(I): 11.1 / Num. measured all: 26576
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.3-2.362.6380.3162.7319477897380.8850.39493.5
2.36-2.422.630.272.9122098588400.9310.33797.9
2.42-2.492.7060.2353.8219327337140.9270.29197.4
2.49-2.572.5840.1984.518637397210.950.24597.6
2.57-2.652.4860.1595.4418897907600.9570.20196.2
2.65-2.752.5980.1227.5815466125950.9720.15397.2
2.75-2.852.6160.1328.0218007056880.9550.16797.6
2.85-2.972.7080.09711.217416636430.9730.12197
2.97-3.12.6340.07513.614965925680.9840.09495.9
3.1-3.252.5820.06515.3114516195620.9860.08390.8
3.25-3.432.5790.06117.0412485244840.9850.07892.4
3.43-3.632.480.05617.3112705895120.990.07186.9
3.63-3.892.3620.05117.729594674060.9920.06686.9
3.89-4.22.3290.04718.7410344944440.990.06189.9
4.2-4.62.5790.04719.989263973590.990.0690.4
4.6-5.142.5670.04520.189243943600.9930.05791.4
5.14-5.942.5170.04420.038183543250.9950.05591.8
5.94-7.272.4680.03720.656492972630.9950.04788.6
7.27-10.282.6750.0321.955592162090.9970.03896.8
10.28-25.182.8640.0224.033151171100.9990.02494

-
Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.17.1refinement
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: RNA duplex constructed using Coot

Resolution: 2.3→25.18 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 1.47 / Phase error: 26.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2292 1037 10.08 %
Rwork0.1766 9255 -
obs0.1819 10292 93.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 59.12 Å2 / Biso mean: 35.81 Å2 / Biso min: 22.45 Å2
Refinement stepCycle: final / Resolution: 2.3→25.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1000 4 15 1019
Biso mean--45.39 32.96 -
Num. residues----48
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3-2.420.38861580.28621357151594
2.42-2.570.31521510.24451343149497
2.57-2.770.29561540.24991355150997
2.77-3.050.29831530.23211342149597
3.05-3.490.24541550.2011284143992
3.49-4.390.22351220.15261271139389
4.39-25.180.1271440.10471303144791

+
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