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Basic information

Entry
Database: PDB / ID: 7jrs
TitleCrystal structures of artificially designed homomeric RNA nanoarchitectures
ComponentsRNA 3D nanocage
KeywordsRNA / nano structure / dimeric parallelogram
Function / homologyRNA / RNA (> 10) / RNA (> 100)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.21 Å
AuthorsLiu, D. / Shao, Y. / Piccirilli, J.A. / Weizmann, Y.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)1555361 United States
CitationJournal: Sci Adv / Year: 2021
Title: Structures of artificially designed discrete RNA nanoarchitectures at near-atomic resolution.
Authors: Liu, D. / Shao, Y. / Piccirilli, J.A. / Weizmann, Y.
History
DepositionAug 12, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 8, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 6, 2021Group: 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.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA 3D nanocage
B: RNA 3D nanocage


Theoretical massNumber of molelcules
Total (without water)83,7922
Polymers83,7922
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4620 Å2
ΔGint-22 kcal/mol
Surface area43130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.623, 64.795, 69.578
Angle α, β, γ (deg.)85.700, 64.250, 79.910
Int Tables number1
Space group name H-MP1

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Components

#1: RNA chain RNA 3D nanocage


Mass: 41895.992 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.89 Å3/Da / Density % sol: 57.47 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: 20 mM MgCl2, 0.3 mM spermine tetrahydrochloride, 50 mM sodium succinate pH 5.5, 3.0 M Ammonium Sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Apr 11, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 3.21→50 Å / Num. obs: 15105 / % possible obs: 97.8 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 29.6
Reflection shellResolution: 3.21→3.27 Å / Rmerge(I) obs: 0.804 / Num. unique obs: 790 / % possible all: 95.9

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.25data extraction
HKL-2000718data reduction
HKL-2000718data scaling
PHENIX1.11.1_2575phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ID: 4CS1

4cs1


Resolution: 3.21→38.289 Å / SU ML: 0.55 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 39.53 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2966 1517 10.04 %
Rwork0.2745 13588 -
obs0.2768 15105 98.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 243.78 Å2 / Biso mean: 151.8488 Å2 / Biso min: 88.97 Å2
Refinement stepCycle: final / Resolution: 3.21→38.289 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 5554 0 0 5554
Num. residues----258
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0016218
X-RAY DIFFRACTIONf_angle_d0.3189702
X-RAY DIFFRACTIONf_chiral_restr0.0171290
X-RAY DIFFRACTIONf_plane_restr0.001258
X-RAY DIFFRACTIONf_dihedral_angle_d12.5243090
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.2102-3.31370.43381310.3734120195
3.3137-3.43210.43061350.3754124699
3.4321-3.56940.46391390.3728124299
3.5694-3.73170.3281360.3192121799
3.7317-3.92830.40681410.2929125099
3.9283-4.17410.33041400.2897124699
4.1741-4.4960.36771410.3233123699
4.496-4.94760.3351420.3183126599
4.9476-5.66150.33221370.2831124799
5.6615-7.12540.29181400.291124599
7.1254-38.2890.21531350.2169119395

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