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- PDB-7lyj: SARS-CoV-2 frameshifting pseudoknot RNA -

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Basic information

Entry
Database: PDB / ID: 7lyj
TitleSARS-CoV-2 frameshifting pseudoknot RNA
ComponentsRNA (66-MER)
KeywordsRNA / Pseudoknot / tetraloop / triple / SARS / virus / COVID / coronavirus / severe acute respiratory syndrome / frameshift
Function / homologyIRIDIUM HEXAMMINE ION / : / RNA / RNA (> 10)
Function and homology information
Biological speciesSevere acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.11 Å
AuthorsJones, C.P. / Ferre-D'Amare, A.R.
CitationJournal: Rna / Year: 2022
Title: Crystal structure of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) frameshifting pseudoknot.
Authors: Jones, C.P. / Ferre-D'Amare, A.R.
History
DepositionMar 7, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 26, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 8, 2021Group: Database references / Category: citation / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Feb 2, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.3May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA (66-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,24517
Polymers21,2871
Non-polymers95916
Water70339
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, Primarily monomeric at 2 mg/ml, ~45% dimeric at 8 mg/ml
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)115.465, 39.477, 39.398
Angle α, β, γ (deg.)90.000, 98.530, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-104-

MG

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Components

#1: RNA chain RNA (66-MER)


Mass: 21286.672 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Severe acute respiratory syndrome coronavirus 2
#2: Chemical ChemComp-IRI / IRIDIUM HEXAMMINE ION


Mass: 294.400 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: H18IrN6
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 39 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Sequence detailsThe first residue of the RNA (PDB chain A 1 C) corresponds to the SARS-CoV-2 sequence C13476 ...The first residue of the RNA (PDB chain A 1 C) corresponds to the SARS-CoV-2 sequence C13476 (Genome Reference Sequence NC_045512). As residues 39-46 are not biological and were added for crystallization, the biological sequence resumes with residue 47 (PDB chain A 47 C), which corresponds to SARS-CoV-2 sequence C13523.

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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: 2.09 Å3/Da / Density % sol: 41.03 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 36-40% MPD, 40 mM Na cacodylate, pH 5.5, 20 mM MgCl2, 2 mM cobalt hexammine

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 17, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.95→57.094 Å / Num. obs: 12611 / % possible obs: 97.6 % / Redundancy: 6.7 % / Biso Wilson estimate: 47.71 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.102 / Rpim(I) all: 0.044 / Rrim(I) all: 0.111 / Net I/σ(I): 10.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.95-261.43649168220.5110.6281.5731.290.2
8.95-57.095.90.0689011530.9950.030.07428.399.2

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Processing

Software
NameVersionClassification
Aimless0.5.32data scaling
PHENIX1.9_1692refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.11→57.094 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 34.08 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2506 979 9.95 %
Rwork0.2102 8862 -
obs0.2142 9841 95.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 157.58 Å2 / Biso mean: 54.3785 Å2 / Biso min: 28.4 Å2
Refinement stepCycle: final / Resolution: 2.11→57.094 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1408 28 39 1475
Biso mean--60.93 49.39 -
Num. residues----66
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0011586
X-RAY DIFFRACTIONf_angle_d0.2962483
X-RAY DIFFRACTIONf_chiral_restr0.014329
X-RAY DIFFRACTIONf_plane_restr0.00266
X-RAY DIFFRACTIONf_dihedral_angle_d10.255788
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.1101-2.22140.39171320.3409121693
2.2214-2.36060.33141300.2958121492
2.3606-2.54280.32691400.2776126496
2.5428-2.79870.31811420.2878129097
2.7987-3.20370.31861400.2553126496
3.2037-4.03610.21761450.1794127095
4.0361-57.0940.19971500.161134498
Refinement TLS params.

Method: refined / 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)
18.8212-1.9793-1.58778.3807-2.87417.2585-0.0855-0.28540.4357-0.65130.169-0.0554-0.79170.1025-0.03590.4255-0.0838-0.10220.2163-0.05570.337817.41660.58077.4593
25.63751.272-0.21611.40070.24992.6177-0.52040.87441.0098-0.1074-0.2625-0.0082-1.04770.530.84120.8351-0.097-0.33790.56170.09930.60979.53293.4342-8.5894
38.84580.54996.73720.88550.04955.2706-0.16690.3252-0.48310.01920.313-0.0567-0.19260.2872-0.15240.3655-0.0089-0.04150.4209-0.04150.376134.42272.885919.0665
42.4912-0.27470.8821.3549-0.3372.1048-0.08520.5074-0.5482-0.08730.22450.1402-0.1920.2213-0.1690.3759-0.0204-0.09940.3277-0.07290.445345.35224.400625.8466
59.15343.29383.65027.80285.08387.5199-0.51241.09010.8487-0.19780.39-0.0442-0.99981.01710.00690.6536-0.3122-0.18180.76340.20720.411515.32280.6904-8.6345
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 9 )A1 - 9
2X-RAY DIFFRACTION2chain 'A' and (resid 10 through 19 )A10 - 19
3X-RAY DIFFRACTION3chain 'A' and (resid 20 through 40 )A20 - 40
4X-RAY DIFFRACTION4chain 'A' and (resid 41 through 57 )A41 - 57
5X-RAY DIFFRACTION5chain 'A' and (resid 58 through 66 )A58 - 66

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