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- PDB-2il9: Crystal Structure of Plautia Stali Intestine Virus Intergenic Reg... -

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Basic information

Entry
Database: PDB / ID: 2il9
TitleCrystal Structure of Plautia Stali Intestine Virus Intergenic Region Internal Ribosome Entry Site Ribosomal Binding Domain RNA at 3.1 Angstroms
ComponentsRibosomal Binding Domain of the IRES RNA
KeywordsRNA / IRES / ribosomal binding domain / PSIV / under wound helix / double-nested pseudoknot
Function / homologyRNA / RNA (> 10) / RNA (> 100)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3.1 Å
AuthorsPfingsten, J.S. / Costantino, D.A. / Kieft, J.S.
CitationJournal: Science / Year: 2006
Title: Structural basis for ribosome recruitment and manipulation by a viral IRES RNA
Authors: Pfingsten, J.S. / Costantino, D.A. / Kieft, J.S.
History
DepositionOct 2, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 13, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 21, 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: Ribosomal Binding Domain of the IRES RNA
M: Ribosomal Binding Domain of the IRES RNA


Theoretical massNumber of molelcules
Total (without water)91,1522
Polymers91,1522
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)133.570, 133.570, 160.425
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63
DetailsTwo molecules in ASU form a domain-swap dimer. Region 1 of chain A and region 2 of chain M form the biological unit. Likewise region 1 of chain M and region 2 of chain A form the second copy of the biological unit.

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Components

#1: RNA chain Ribosomal Binding Domain of the IRES RNA


Mass: 45575.941 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: Sequence occurs naturally in Plautia Stali Intestine Virus

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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

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
14.5372.86
2
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
3031vapor diffusion, sitting drop5.615% MPD, 150 mM MgAcetate, 0.5 mM Spermidine; cryoprotected with 20% MPD, 150 mM MgAcetate, 50 mM Na-MES pH 5.6, 5 mM Iridium (III) hexammine, vapor diffusion, sitting drop, temperature 303K
3032vapor diffusion, sitting drop5.615% MPD, 100 mM MgAcetate, 0.5 mM Spermidine; cryoprotected with 20% MPD, 100 mM MgAcetate, 50 mM Na-MES pH 5.6, 5% isopropanol, vapor diffusion, sitting drop, temperature 303K
Components of the solutions
IDNameCrystal-IDSol-ID
1MPD11
2MgAcetate11
3Spermidine11
4MPD12
5MgAcetate12
6Spermidine12
7Iridium (III) hexammine13
8MPD13
9MgAcetate13
10Na-MES13
11MPD21
12MgAcetate21
13Spermidine21
14MPD22
15MgAcetate22
16Spermidine22
17isopropanol23
18MPD23
19MgAcetate23
20Na-MES23

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
SYNCHROTRONALS 8.2.111.1053,1.1057,1.1004
ROTATING ANODERIGAKU21.5418
Detector
TypeIDDetectorDate
ADSC QUANTUM 2101CCDApr 25, 2006
RIGAKU RAXIS IV2IMAGE PLATEMay 29, 2006
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1MADMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.10531
21.10571
31.10041
41.54181
ReflectionResolution: 3.1→16.97 Å / Num. obs: 26973

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Phasing

PhasingMethod: MAD
Phasing set
ID
1
2
3
Phasing MADD res high: 3.41 Å / D res low: 45 Å / FOM : 0.36 / Reflection: 20229
Phasing MAD set
Clust-IDExpt-IDSet-IDWavelength (Å)F double prime refinedF prime refined
13 wavelength11.105317.87-15.67
13 wavelength21.105710.21-25.95
13 wavelength31.10049.54-10.26
Phasing MAD set site
IDAtom type symbolB isoFract xFract yFract zOccupancy
1Pt600.230.4390.9950.427
2Pt600.7620.2130.4450.334
3Pt600.4390.230.1230.369
4Pt600.340.0570.0510.261
5Pt600.450.2150.1750.341
6Pt600.2090.5590.3790.27
7Pt600.2040.6460.2280.248
Phasing MAD shell
Resolution (Å)FOM Reflection
12.14-450.46936
7.7-12.140.551657
6.04-7.70.572122
5.12-6.040.512516
4.53-5.120.412835
4.1-4.530.333120
3.78-4.10.23427
3.52-3.780.153616

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Processing

Software
NameVersionClassificationNB
SOLVE2.03phasing
CNS1.1refinement
PDB_EXTRACT2data extraction
CrystalClear(MSC/RIGAKU)data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 3.1→16.97 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 74429.094 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.294 2683 9.9 %RANDOM
Rwork0.253 ---
obs-26973 92.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 37 Å2 / ksol: 0.27 e/Å3
Displacement parametersBiso mean: 87.6 Å2
Baniso -1Baniso -2Baniso -3
1--1.15 Å213.95 Å20 Å2
2---1.15 Å20 Å2
3---2.29 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.5 Å0.41 Å
Luzzati d res low-5 Å
Luzzati sigma a0.57 Å0.47 Å
Refinement stepCycle: LAST / Resolution: 3.1→16.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 5665 0 0 5665
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1
X-RAY DIFFRACTIONc_dihedral_angle_d15.1
X-RAY DIFFRACTIONc_improper_angle_d1.39
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 3.1→3.29 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.391 397 10.1 %
Rwork0.336 3521 -
obs-3918 80.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramirhex.top
X-RAY DIFFRACTION5irhex.paramion.top

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