[English] 日本語
Yorodumi
- PDB-5v1k: Structure of R-GNA dodecamer -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5v1k
TitleStructure of R-GNA dodecamer
ComponentsRNA (5'-R(*CP*GP*CP*GP*AP*AP*(5BU)P*(8RJ)P*AP*GP*CP*G)-3')
KeywordsRNA / Glycol Nucleic Acid / GNA / RGNA / RNA X-ray structure / Nuclease Stability / modified RNA
Function / homologyRNA / RNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.18 Å
AuthorsPallan, P.S. / Egli, M.
CitationJournal: J. Am. Chem. Soc. / Year: 2017
Title: Chirality Dependent Potency Enhancement and Structural Impact of Glycol Nucleic Acid Modification on siRNA.
Authors: Schlegel, M.K. / Foster, D.J. / Kel'in, A.V. / Zlatev, I. / Bisbe, A. / Jayaraman, M. / Lackey, J.G. / Rajeev, K.G. / Charisse, K. / Harp, J. / Pallan, P.S. / Maier, M.A. / Egli, M. / Manoharan, M.
History
DepositionMar 2, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 21, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 16, 2017Group: Refinement description / Category: pdbx_refine / refine
Item: _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work
Revision 1.2Jun 22, 2022Group: Data collection / Database references / Category: chem_comp / database_2
Item: _chem_comp.mon_nstd_flag / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: RNA (5'-R(*CP*GP*CP*GP*AP*AP*(5BU)P*(8RJ)P*AP*GP*CP*G)-3')
B: RNA (5'-R(*CP*GP*CP*GP*AP*AP*(5BU)P*(8RJ)P*AP*GP*CP*G)-3')


Theoretical massNumber of molelcules
Total (without water)7,7722
Polymers7,7722
Non-polymers00
Water3,063170
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2430 Å2
ΔGint9 kcal/mol
Surface area4260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)23.681, 27.680, 29.050
Angle α, β, γ (deg.)73.00, 87.17, 66.58
Int Tables number1
Space group name H-MP1

-
Components

#1: RNA chain RNA (5'-R(*CP*GP*CP*GP*AP*AP*(5BU)P*(8RJ)P*AP*GP*CP*G)-3')


Mass: 3886.247 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.: 170 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.14 Å3/Da / Density % sol: 47.96 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6
Details: Oligonucleotide (0.6 mM), sodium cacodylate (20 mM, pH 6.0), potassium chloride (40 mM), spermine tetrahydrochloride (6 mM), and 2-methyl-2,4-pentanediol (MPD; 5% (v/v)

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.916978 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 14, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.916978 Å / Relative weight: 1
ReflectionResolution: 1.18→50 Å / Num. obs: 20171 / % possible obs: 94.9 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.052 / Net I/σ(I): 37.5
Reflection shellResolution: 1.18→1.22 Å / Redundancy: 4 % / Rmerge(I) obs: 0.449 / Num. unique obs: 1914 / % possible all: 90.3

-
Processing

Software
NameVersionClassification
MAR345dtbMD-2 diffractometer software from EMBL (with LS-CAT developed extensions)data collection
HKL-2000data reduction
HKL-2000data scaling
SHELXDEphasing
SHELXLrefinement
RefinementResolution: 1.18→50 Å / Cross valid method: THROUGHOUT
Num. reflection% reflectionSelection details
obs18748 94.8 %-
Rfree--Random
Refinement stepCycle: LAST / Resolution: 1.18→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 506 0 170 676

+
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