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- PDB-9mm6: ROOLefa-octamer-wild type -

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Basic information

Entry
Database: PDB / ID: 9mm6
TitleROOLefa-octamer-wild type
ComponentsRNA (526-MER)
KeywordsRNA / natural RNA nanocage / drug delivery
Function / homology: / : / RNA / RNA (> 10) / RNA (> 100)
Function and homology information
Biological speciesEnterococcus faecalis JH1 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.94 Å
AuthorsLing, X.B. / Fang, W.W. / Ma, J.B. / Korostelev, A.A.
Funding support China, United States, 4items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)NSFC 31971130 China
National Natural Science Foundation of China (NSFC)32471347 China
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM127094 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM150953 United States
CitationJournal: To Be Published
Title: ROOLefa-octamer-wild type
Authors: Ling, X.B. / Fang, W.W. / Ma, J.B. / Korostelev, A.A.
History
DepositionDec 20, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 4, 2025Provider: repository / Type: Initial release
Revision 1.0Jun 4, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jun 4, 2025Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Jun 4, 2025Data content type: Additional map / Part number: 2 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Jun 4, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jun 4, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 4, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 4, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jun 4, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA (526-MER)
E: RNA (526-MER)
I: RNA (526-MER)
M: RNA (526-MER)
Q: RNA (526-MER)
U: RNA (526-MER)
Y: RNA (526-MER)
c: RNA (526-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,504,64862
Polymers1,502,7008
Non-polymers1,94954
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: RNA chain
RNA (526-MER)


Mass: 187837.453 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) Enterococcus faecalis JH1 (bacteria) / References: GenBank: 1899451202
#2: Chemical...
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 43 / Source method: obtained synthetically / Formula: K / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: lncRNA-ROOL2-octamer / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: #1 / Source: NATURAL
Source (natural)Organism: Enterococcus faecalis JH1 (bacteria)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1800 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 51.23 e/Å2 / Film or detector model: GATAN K3 BIOCONTINUUM (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.20.1_4487 / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.94 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 225901 / Symmetry type: POINT
RefinementHighest resolution: 2.94 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00895192
ELECTRON MICROSCOPYf_angle_d0.986148352
ELECTRON MICROSCOPYf_dihedral_angle_d15.547352
ELECTRON MICROSCOPYf_chiral_restr0.05619728
ELECTRON MICROSCOPYf_plane_restr0.0073952

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