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- PDB-5cnr: Crystal structure-guided design of self-assembling RNA nano triangles -

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Basic information

Entry
Database: PDB / ID: 5cnr
TitleCrystal structure-guided design of self-assembling RNA nano triangles
Components
  • RNA (5'-R(*AP*GP*AP*GP*GP*AP*CP*GP*GP*CP*G)-3')
  • RNA (5'-R(*GP*UP*CP*UP*AP*CP*CP*CP*AP*CP*CP*UP*CP*GP*CP*C)-3')
KeywordsRNA / seneca valley virus / nanotriangle / self-assembly
Function / homologyRNA / RNA (> 10)
Function and homology information
Biological speciesSeneca valley virus
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.59 Å
AuthorsBoerneke, M. / Dibrov, S. / Hermann, T.
Funding support United States, 1items
OrganizationGrant numberCountry
UCSD Academic SenateRM069B United States
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2016
Title: Crystal-Structure-Guided Design of Self-Assembling RNA Nanotriangles.
Authors: Boerneke, M.A. / Dibrov, S.M. / Hermann, T.
History
DepositionJul 18, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 9, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 23, 2016Group: Database references
Revision 1.2Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA (5'-R(*GP*UP*CP*UP*AP*CP*CP*CP*AP*CP*CP*UP*CP*GP*CP*C)-3')
B: RNA (5'-R(*AP*GP*AP*GP*GP*AP*CP*GP*GP*CP*G)-3')
E: RNA (5'-R(*GP*UP*CP*UP*AP*CP*CP*CP*AP*CP*CP*UP*CP*GP*CP*C)-3')
F: RNA (5'-R(*AP*GP*AP*GP*GP*AP*CP*GP*GP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,2225
Polymers17,1874
Non-polymers351
Water0
1
A: RNA (5'-R(*GP*UP*CP*UP*AP*CP*CP*CP*AP*CP*CP*UP*CP*GP*CP*C)-3')
B: RNA (5'-R(*AP*GP*AP*GP*GP*AP*CP*GP*GP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,6293
Polymers8,5932
Non-polymers351
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1170 Å2
ΔGint-8 kcal/mol
Surface area5340 Å2
MethodPISA
2
E: RNA (5'-R(*GP*UP*CP*UP*AP*CP*CP*CP*AP*CP*CP*UP*CP*GP*CP*C)-3')
F: RNA (5'-R(*AP*GP*AP*GP*GP*AP*CP*GP*GP*CP*G)-3')


Theoretical massNumber of molelcules
Total (without water)8,5932
Polymers8,5932
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area960 Å2
ΔGint0 kcal/mol
Surface area5460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.934, 59.934, 262.622
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

#1: RNA chain RNA (5'-R(*GP*UP*CP*UP*AP*CP*CP*CP*AP*CP*CP*UP*CP*GP*CP*C)-3')


Mass: 4968.999 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Seneca valley virus
#2: RNA chain RNA (5'-R(*AP*GP*AP*GP*GP*AP*CP*GP*GP*CP*G)-3')


Mass: 3624.258 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Seneca valley virus
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.64 Å3/Da / Density % sol: 53.42 %
Crystal growTemperature: 281 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: drop: 20% MPD, 55 mM NaCl, 12 mM spermine, 40 mM Tris well: 18% MPD, 120 mM NaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-D / Wavelength: 1.54 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jan 13, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.59→48.3 Å / Num. obs: 5011 / % possible obs: 83.2 % / Redundancy: 17.6 % / Rsym value: 0.076 / Net I/σ(I): 35.5
Reflection shellResolution: 2.59→2.68 Å / Redundancy: 2 % / % possible all: 11.7

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Processing

Software
NameVersionClassification
PHENIX1.7.3_928refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4P97

4p97


Resolution: 2.59→19.403 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 33.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2444 500 10.03 %
Rwork0.1925 --
obs0.1979 4985 83.82 %
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 91.673 Å2 / ksol: 0.298 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--21.4768 Å20 Å2-0 Å2
2---21.4768 Å20 Å2
3----52.3477 Å2
Refinement stepCycle: LAST / Resolution: 2.59→19.403 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1136 1 0 1137
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0021266
X-RAY DIFFRACTIONf_angle_d0.4451966
X-RAY DIFFRACTIONf_dihedral_angle_d14.08632
X-RAY DIFFRACTIONf_chiral_restr0.051266
X-RAY DIFFRACTIONf_plane_restr0.00254
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5963-2.85680.4811530.4279474X-RAY DIFFRACTION36
2.8568-3.26850.41521410.32091271X-RAY DIFFRACTION98
3.2685-4.11160.26211480.24731338X-RAY DIFFRACTION100
4.1116-19.40320.19861580.14181402X-RAY DIFFRACTION100
Refinement TLS params.

Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.4743-0.48920.62730.575-0.60490.8175-0.0690.51820.1884-0.757-0.4073-0.5961.11670.51050.00120.73320.07740.05380.7677-0.1790.878148.03419.191314.9542
20.1278-0.20310.04860.45450.09820.2167-0.21470.8948-0.1075-0.11130.1664-0.6507-0.1178-0.69490.0010.7613-0.0074-0.02080.589-0.02860.711545.93971.1546319.9836
30.24250.09930.29360.05890.18160.486-0.67570.19550.5104-0.28930.2143-0.12260.1176-0.11090.00060.717-0.04970.11970.5672-0.10610.800751.109713.715315.601
40.5954-0.24390.39160.9703-0.6950.57830.03480.952-1.113-0.35580.8787-0.06190.53390.41620.01370.6469-0.0321-0.04240.9556-0.05531.07869.543619.8698319.0855
55.4197-0.67890.20310.75990.42930.3298-0.4373-0.92630.09951.47560.4195-0.50351.34810.13970.60661.7978-0.0785-0.44492.02050.24520.715870.3314-10.4381357.8871
60.0046-0.02020.00470.0691-0.01840.0068-0.0899-0.20280.50010.83890.7471-1.0786-0.6920.34150.0061.03740.0893-0.20181.4578-0.18770.721478.525-24.8887367.4228
73.7834-1.0847-1.67890.35010.49150.7462-0.941-0.4720.0443-0.50190.0801-0.11310.33050.4012-1.52261.39510.1623-0.40071.9950.02970.629675.3178-10.7416359.4929
80.075-0.3101-0.09321.54180.52620.18530.1724-0.2893-0.90521.70910.4424-0.17360.71030.5820.70821.5402-0.2033-0.01881.8470.53610.961287.23684.6765362.7994
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 3:11)
2X-RAY DIFFRACTION2chain 'A' and (resseq 12:18)
3X-RAY DIFFRACTION3chain 'B' and (resseq 37:42)
4X-RAY DIFFRACTION4chain 'B' and (resseq 43:47)
5X-RAY DIFFRACTION5chain 'E' and (resseq 3:13)
6X-RAY DIFFRACTION6chain 'E' and (resseq 14:18)
7X-RAY DIFFRACTION7chain 'F' and (resseq 37:42)
8X-RAY DIFFRACTION8chain 'F' and (resseq 43:47)

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