[English] 日本語
Yorodumi
- PDB-7qdu: Twist-corrected RNA origami 5-helix Tile A -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7qdu
TitleTwist-corrected RNA origami 5-helix Tile A
ComponentsChains: Q
KeywordsRNA / Origami / nanostructure
Function / homologyRNA / RNA (> 10) / RNA (> 100)
Function and homology information
Biological speciessynthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 5.14 Å
AuthorsMcRae, E.K.S. / Andersen, E.S.
Funding support Denmark, 1items
OrganizationGrant numberCountry
Danish Council for Independent Research31789 Denmark
CitationJournal: Nat Nanotechnol / Year: 2023
Title: Structure, folding and flexibility of co-transcriptional RNA origami.
Authors: Ewan K S McRae / Helena Østergaard Rasmussen / Jianfang Liu / Andreas Bøggild / Michael T A Nguyen / Nestor Sampedro Vallina / Thomas Boesen / Jan Skov Pedersen / Gang Ren / Cody Geary / ...Authors: Ewan K S McRae / Helena Østergaard Rasmussen / Jianfang Liu / Andreas Bøggild / Michael T A Nguyen / Nestor Sampedro Vallina / Thomas Boesen / Jan Skov Pedersen / Gang Ren / Cody Geary / Ebbe Sloth Andersen /
Abstract: RNA origami is a method for designing RNA nanostructures that can self-assemble through co-transcriptional folding with applications in nanomedicine and synthetic biology. However, to advance the ...RNA origami is a method for designing RNA nanostructures that can self-assemble through co-transcriptional folding with applications in nanomedicine and synthetic biology. However, to advance the method further, an improved understanding of RNA structural properties and folding principles is required. Here we use cryogenic electron microscopy to study RNA origami sheets and bundles at sub-nanometre resolution revealing structural parameters of kissing-loop and crossover motifs, which are used to improve designs. In RNA bundle designs, we discover a kinetic folding trap that forms during folding and is only released after 10 h. Exploration of the conformational landscape of several RNA designs reveal the flexibility of helices and structural motifs. Finally, sheets and bundles are combined to construct a multidomain satellite shape, which is characterized by individual-particle cryo-electron tomography to reveal the domain flexibility. Together, the study provides a structural basis for future improvements to the design cycle of genetically encoded RNA nanodevices.
History
DepositionNov 30, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 14, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 29, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Aug 2, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Dec 13, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
Q: Chains: Q


Theoretical massNumber of molelcules
Total (without water)177,7201
Polymers177,7201
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area87490 Å2

-
Components

#1: RNA chain Chains: Q


Mass: 177720.031 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: In vitro transcribed RNA / Source: (synth.) synthetic construct (others)

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: Twist-corrected 5-helix tile A. / Type: COMPLEX / Details: In vitro transcribed RNA purified by SEC. / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.175 MDa / Experimental value: NO
Source (natural)Organism: synthetic construct (others)
Source (recombinant)Organism: synthetic construct (others)
Buffer solutionpH: 8
Details: Freshly prepared and filtered through 0.22 micron filter prior to use.
Buffer component
IDConc.NameFormulaBuffer-ID
125 mMHEPES1
25 mMMgCl21
3100 mMKCl1
SpecimenConc.: 3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: Sample was purified by size exclusion chromatography and concentrated in an Amicon spin concentrator.
Specimen supportDetails: 15mA current on a glocube. / Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: UltrAuFoil R1.2/1.3
VitrificationInstrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 99 % / Chamber temperature: 294 K
Details: 3 microlitre droplet, 4 second delay before blotting, 6 second blot, 0 second delay before plunging.

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 130000 X / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 1.5 sec. / Electron dose: 60 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 6122 / Details: Images were collected as 56 frame movies.
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV

-
Processing

Software
NameVersionClassification
phenix.real_space_refine1.19.2_4158refinement
PHENIX1.19.2_4158refinement
EM software
IDNameVersionCategoryDetails
1cryoSPARC3.2.0particle selection
2EPUimage acquisitionAFIS data collection
4cryoSPARC3.2.0CTF correction
7UCSF ChimeraX1.2model fitting
8ISOLDE1.2model fitting
10PHENIX1.19.2-4158-000model refinement
11cryoSPARC3.2.0initial Euler assignment
12cryoSPARC3.2.0final Euler assignment
13cryoSPARC3.2.0classification
14cryoSPARC3.2.03D reconstruction
CTF correctionDetails: Patch CTF estimation (multi) from cryoSPARC. / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 605848
Details: Particle picking was performed using the template picker from cryoSPARC with templates generated from an ab initio model from the same dataset.
3D reconstructionResolution: 5.14 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 166751 / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL / Target criteria: Correlation Coefficient
RefinementCor.coef. Fo:Fc: 0.975 / WRfactor Rwork: 0.562 / SU B: 3.157 / SU ML: 0.055 / Average fsc overall: 0.0971 / Average fsc work: 0.0971 / Cross valid method: NONE / ESU R: 0.304
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rwork0.5618 299730 -
all0.562 --
Rfree--0 %
obs--99.162 %
Solvent computationSolvent model: BABINET MODEL
Displacement parametersBiso mean: 219.884 Å2
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0070.01213133
ELECTRON MICROSCOPYr_bond_other_d0.010.0195388
ELECTRON MICROSCOPYr_angle_refined_deg2.2091.79220466
ELECTRON MICROSCOPYr_angle_other_deg0.6241.65913116
ELECTRON MICROSCOPYr_chiral_restr0.1610.22759
ELECTRON MICROSCOPYr_gen_planes_refined0.0170.026520
ELECTRON MICROSCOPYr_gen_planes_other0.0030.022076
ELECTRON MICROSCOPYr_nbd_refined0.1790.210294
ELECTRON MICROSCOPYr_symmetry_nbd_other0.2410.213492
ELECTRON MICROSCOPYr_nbtor_refined0.2440.29004
ELECTRON MICROSCOPYr_symmetry_nbtor_other0.0880.26984
ELECTRON MICROSCOPYr_xyhbond_nbd_refined0.110.2398
ELECTRON MICROSCOPYr_scbond_it10.39723.42613133
ELECTRON MICROSCOPYr_scbond_other10.38923.42513133
ELECTRON MICROSCOPYr_scangle_it17.07735.12920466
ELECTRON MICROSCOPYr_scangle_other17.07635.1320467
ELECTRON MICROSCOPYr_lrange_it24.117248.20520308
ELECTRON MICROSCOPYr_lrange_other24.12248.21820309
LS refinement shell

Refine-ID: ELECTRON MICROSCOPY / Num. reflection Rfree: 0 / Total num. of bins used: 20

Resolution (Å)Rfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc work% reflection obs (%)WRfactor Rwork
2.5-2.5650.941201940.941222410.00590.79630.941
2.565-2.6350.959213860.959218730.00397.77350.959
2.635-2.7120.962210820.962210820.0151000.962
2.712-2.7950.952208340.952208340.0221000.952
2.795-2.8870.935198950.935198950.0271000.935
2.887-2.9880.914192040.914192040.011000.914
2.988-3.1010.885185530.885185530.021000.885
3.101-3.2270.855180420.855180420.0281000.855
3.227-3.3710.816171440.816171440.0221000.816
3.371-3.5350.758165460.758165460.0141000.758
3.535-3.7270.71155440.71155441000.71
3.727-3.9520.65148320.65148321000.65
3.952-4.2250.572138430.572138431000.572
4.225-4.5640.605129620.605129620.0071000.605
4.564-4.9990.681118590.681118590.1471000.681
4.999-5.5890.783107850.783107850.331000.783
5.589-6.4530.6394450.6394450.5121000.63
6.453-7.9010.62580140.62580140.8031000.625
7.901-11.1660.25661610.25661610.9621000.256
11.166-214.8040.16234050.16234050.9941000.162

+
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