[English] 日本語
Yorodumi
- PDB-9oky: 16mer self-complementary duplex RNA with dG:s(2)C pair sequence 1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9oky
Title16mer self-complementary duplex RNA with dG:s(2)C pair sequence 1
ComponentsDNA/RNA (5'-R(*A)-D(P*G)-R(P*AP*GP*AP*AP*GP*AP*UP*CP*UP*UP*CP*UP*(RSP)P*U)-3')
KeywordsRNA / Deoxyribo-purine / 2-thiocytidine / RNA duplex / Origin of Life
Function / homologyDNA/RNA hybrid / DNA/RNA hybrid (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.478 Å
AuthorsFang, Z. / Szostak, J.W.
Funding support United States, 2items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)2104708 United States
Howard Hughes Medical Institute (HHMI) United States
Citation
Journal: Nucleic Acids Res. / Year: 2025
Title: Impact of 2'-deoxyribo-purine substrates on nonenzymatic RNA template-directed primer extension.
Authors: Fang, Z. / Acikgoz, O. / Jia, X. / Essex, J. / Wen, R. / Szostak, J.W.
#1: Journal: Biorxiv / Year: 2025
Title: Impact of 2'-deoxyribo-purine substrates on nonenzymatic RNA template-directed primer extension.
Authors: Fang, Z. / Acikgoz, O. / Jia, X. / Essex, J. / Wen, R. / Szostak, J.W.
History
DepositionMay 11, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 22, 2025Provider: repository / Type: Initial release
Revision 1.1Nov 26, 2025Group: Database references / Category: citation / citation_author

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DNA/RNA (5'-R(*A)-D(P*G)-R(P*AP*GP*AP*AP*GP*AP*UP*CP*UP*UP*CP*UP*(RSP)P*U)-3')
B: DNA/RNA (5'-R(*A)-D(P*G)-R(P*AP*GP*AP*AP*GP*AP*UP*CP*UP*UP*CP*UP*(RSP)P*U)-3')


Theoretical massNumber of molelcules
Total (without water)10,1662
Polymers10,1662
Non-polymers00
Water2,486138
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.422, 43.422, 256.437
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-103-

HOH

21A-115-

HOH

31A-122-

HOH

41A-136-

HOH

51A-141-

HOH

61A-145-

HOH

71A-166-

HOH

81B-105-

HOH

91B-109-

HOH

101B-138-

HOH

111B-139-

HOH

121B-140-

HOH

-
Components

#1: DNA/RNA hybrid DNA/RNA (5'-R(*A)-D(P*G)-R(P*AP*GP*AP*AP*GP*AP*UP*CP*UP*UP*CP*UP*(RSP)P*U)-3')


Mass: 5083.128 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 138 / 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: 2.28 Å3/Da / Density % sol: 46.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 0.1 M BIS-TRIS pH 5.5, 2.0 M Ammonium sulfate

-
Data collection

DiffractionMean temperature: 99 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 0.97648 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Jun 28, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97648 Å / Relative weight: 1
ReflectionResolution: 1.478→50 Å / Num. obs: 15145 / % possible obs: 93.2 % / Redundancy: 8.2 % / CC1/2: 0.989 / CC star: 0.997 / Rmerge(I) obs: 0.07 / Rpim(I) all: 0.025 / Rrim(I) all: 0.075 / Χ2: 0.942 / Net I/σ(I): 20.2
Reflection shellResolution: 1.478→1.51 Å / Redundancy: 5 % / Rmerge(I) obs: 0.506 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 756 / CC1/2: 0.866 / CC star: 0.963 / Rpim(I) all: 0.237 / Rrim(I) all: 0.562 / Χ2: 0.81 / % possible all: 93.6

-
Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.478→30.326 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.919 / SU B: 1.456 / SU ML: 0.055 / Cross valid method: THROUGHOUT / ESU R: 0.092 / ESU R Free: 0.092
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2484 818 5.439 %
Rwork0.22 14221 -
all0.222 --
obs-15039 92.377 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 12.195 Å2
Baniso -1Baniso -2Baniso -3
1--0.003 Å2-0.002 Å20 Å2
2---0.003 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.478→30.326 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 670 0 138 808
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.011748
X-RAY DIFFRACTIONr_bond_other_d0.0020.019312
X-RAY DIFFRACTIONr_angle_refined_deg2.2121.8971160
X-RAY DIFFRACTIONr_angle_other_deg0.7191.728762
X-RAY DIFFRACTIONr_dihedral_angle_other_2_deg0.074520
X-RAY DIFFRACTIONr_chiral_restr0.1090.2156
X-RAY DIFFRACTIONr_gen_planes_refined0.0220.02366
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02118
X-RAY DIFFRACTIONr_nbd_refined0.0940.277
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1850.2408
X-RAY DIFFRACTIONr_nbtor_refined0.2510.2281
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0830.2202
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1930.2101
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.160.211
X-RAY DIFFRACTIONr_nbd_other0.180.278
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1850.230
X-RAY DIFFRACTIONr_scbond_it1.5421.388748
X-RAY DIFFRACTIONr_scbond_other1.5411.388749
X-RAY DIFFRACTIONr_scangle_it2.2362.5321160
X-RAY DIFFRACTIONr_scangle_other2.2352.5321161
X-RAY DIFFRACTIONr_lrange_it4.90617.7471044
X-RAY DIFFRACTIONr_lrange_other4.66917.5811021
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.478-1.5160.351620.283971X-RAY DIFFRACTION87.3204
1.516-1.5580.286570.2531057X-RAY DIFFRACTION97.891
1.558-1.6030.239610.2231060X-RAY DIFFRACTION99.7331
1.603-1.6520.272570.2231019X-RAY DIFFRACTION99.722
1.652-1.7060.274570.211981X-RAY DIFFRACTION99.5206
1.706-1.7660.209520.193964X-RAY DIFFRACTION99.8035
1.766-1.8320.232510.192948X-RAY DIFFRACTION99.8002
1.832-1.9060.309360.234627X-RAY DIFFRACTION70.3075
1.906-1.9910.20741752X-RAY DIFFRACTION86.0087
1.991-2.0880.22440.22811X-RAY DIFFRACTION97.8261
2.088-2.20.297500.213731X-RAY DIFFRACTION93.1981
2.2-2.3330.253270.217402X-RAY DIFFRACTION54.5108
2.333-2.4930.17644713X-RAY DIFFRACTION100
2.493-2.6910.295330.194684X-RAY DIFFRACTION99.7218
2.691-2.9450.277360.222602X-RAY DIFFRACTION99.2224
2.945-3.2890.219300.213548X-RAY DIFFRACTION96.173
3.289-3.7910.3270.259395X-RAY DIFFRACTION80.2281
3.791-4.6240.23120378X-RAY DIFFRACTION85.7759
4.624-6.4650.205160.153355X-RAY DIFFRACTION100
6.465-30.3260.18317223X-RAY DIFFRACTION98.3607

+
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