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- PDB-7jju: Crystal structure of en exoribonuclease-resistant RNA (xrRNA) fro... -

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Basic information

Entry
Database: PDB / ID: 7jju
TitleCrystal structure of en exoribonuclease-resistant RNA (xrRNA) from Potato leafroll virus (PLRV)
ComponentsPotato leafroll virus xrRNA
KeywordsRNA / RNA structure viral RNA exonuclease resistance RNA pseudoknot polerovirus plant virus
Function / homologyCACODYLATE ION / Guanidinium / IRIDIUM HEXAMMINE ION / RNA / RNA (> 10)
Function and homology information
Biological speciesPotato leafroll virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.604 Å
AuthorsSteckelberg, A.-L. / Vicens, Q. / Auffinger, P. / Costantino, D.C. / Nix, J.C. / Kieft, J.S.
Funding support United States, Germany, 7items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM118070 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI133348 United States
German Research Foundation (DFG)STE2509/201 Germany
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P30GM124169-01 United States
Department of Energy (DOE, United States)DE-AC02-05CH11231 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P30CA046934 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: Rna / Year: 2020
Title: The crystal structure of a Polerovirus exoribonuclease-resistant RNA shows how diverse sequences are integrated into a conserved fold.
Authors: Steckelberg, A.L. / Vicens, Q. / Costantino, D.A. / Nix, J.C. / Kieft, J.S.
History
DepositionJul 27, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 9, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 25, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Potato leafroll virus xrRNA
B: Potato leafroll virus xrRNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,59026
Polymers33,3442
Non-polymers4,24724
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6930 Å2
ΔGint-13 kcal/mol
Surface area17760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.190, 72.190, 137.140
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Components on special symmetry positions
IDModelComponents
11B-511-

IRI

21B-511-

IRI

31B-511-

IRI

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Components

#1: RNA chain Potato leafroll virus xrRNA


Mass: 16671.771 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Potato leafroll virus
#2: Chemical
ChemComp-GZ6 / Guanidinium


Mass: 60.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: CH6N3
#3: Chemical
ChemComp-CAC / CACODYLATE ION / dimethylarsinate


Mass: 136.989 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6AsO2
#4: Chemical
ChemComp-IRI / IRIDIUM HEXAMMINE ION


Mass: 294.400 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: H18IrN6
Has ligand of interestN

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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: 2.61 Å3/Da / Density % sol: 52.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 1 microL RNA solution (5 mg/mL RNA in 30 mM HEPES pH 7.5, 20 mM MgCl2, 100 mM KCl) + 1 microL crystallization solution (10% 2-methyl-2,4-pentanediol, 40 mM Sodium Cacodylate (pH 6.0), 12 mM ...Details: 1 microL RNA solution (5 mg/mL RNA in 30 mM HEPES pH 7.5, 20 mM MgCl2, 100 mM KCl) + 1 microL crystallization solution (10% 2-methyl-2,4-pentanediol, 40 mM Sodium Cacodylate (pH 6.0), 12 mM Spermine, 150 mM KCl, 100 mM Guanidinium HCl) over a reservoir of 500 microL of 30% 2-methyl-2,4-pentanediol and 100mM Guanidinium HCl.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 0.9234 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: Sep 13, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9234 Å / Relative weight: 1
ReflectionResolution: 2.604→49.72 Å / Num. obs: 11689 / % possible obs: 99.64 % / Redundancy: 41.3 % / Biso Wilson estimate: 63.33 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.09956 / Rpim(I) all: 0.01561 / Rrim(I) all: 0.1008 / Net I/σ(I): 30.86
Reflection shellResolution: 2.604→2.697 Å / Redundancy: 38 % / Rmerge(I) obs: 1.663 / Mean I/σ(I) obs: 2.53 / Num. unique obs: 1135 / CC1/2: 0.914 / CC star: 0.977 / Rrim(I) all: 1.685 / % possible all: 99.56

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Processing

Software
NameVersionClassification
XDS20191015data processing
PHENIXdev_3885refinement
XDS20191015data reduction
XSCALE20191015data scaling
PHENIX1.13_2998phasing
RefinementMethod to determine structure: SAD / Resolution: 2.604→49.72 Å / SU ML: 0.4318 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 33.4161
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2534 1097 5.19 %
Rwork0.2246 20043 -
obs0.2261 11669 99.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 62.95 Å2
Refine analyzeLuzzati coordinate error obs: 0.43 Å
Refinement stepCycle: LAST / Resolution: 2.604→49.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 2162 178 0 2340
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00122576
X-RAY DIFFRACTIONf_angle_d0.44064058
X-RAY DIFFRACTIONf_chiral_restr0.0202504
X-RAY DIFFRACTIONf_plane_restr0.0018110
X-RAY DIFFRACTIONf_dihedral_angle_d15.59621274
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.720.38931340.37922491X-RAY DIFFRACTION99.36
2.72-2.870.4181150.38342543X-RAY DIFFRACTION99.77
2.87-3.040.32131230.31952521X-RAY DIFFRACTION99.77
3.05-3.280.24971410.23052512X-RAY DIFFRACTION99.85
3.28-3.610.26671630.23592483X-RAY DIFFRACTION99.85
3.61-4.130.27051420.20542488X-RAY DIFFRACTION99.85
4.13-5.210.21391530.18682508X-RAY DIFFRACTION99.92
5.21-49.720.21181260.18582497X-RAY DIFFRACTION98.87
Refinement TLS params.Method: refined / Origin x: 36.2585465093 Å / Origin y: 34.4735384395 Å / Origin z: 50.0891628021 Å
111213212223313233
T0.371293507091 Å2-0.0579352098153 Å2-0.0197157645462 Å2-0.57778040642 Å20.0273952723862 Å2--0.424772021271 Å2
L1.75714935257 °2-0.0473451211635 °22.03503727268 °2-0.550821517128 °20.186423207295 °2--1.22750660508 °2
S0.249402707224 Å °-0.0550833055514 Å °-0.176059854106 Å °0.0172582673651 Å °0.0705787461172 Å °0.0255333603242 Å °-0.0374251346067 Å °0.0093560229534 Å °-0.376246256221 Å °
Refinement TLS groupSelection details: all

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