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- PDB-3b31: Crystal structure of domain III of the Cricket Paralysis Virus IR... -

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Basic information

Entry
Database: PDB / ID: 3b31
TitleCrystal structure of domain III of the Cricket Paralysis Virus IRES RNA
Components
  • RNA (29-MER)
  • RNA (5'-R(P*UP*AP*AP*GP*AP*AP*AP*UP*UP*UP*AP*CP*CP*U)-3')
KeywordsRNA / IRES / RNA structure / translation initiation / tRNA anticodon / hybrid state / tRNA mimicry
Function / homologyIRIDIUM HEXAMMINE ION / PHOSPHATE ION / RNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.4 Å
AuthorsKieft, J.S. / Costantino, D.A. / Pfingsten, J.S. / Rambo, R.P.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2008
Title: tRNA-mRNA mimicry drives translation initiation from a viral IRES.
Authors: Costantino, D.A. / Pfingsten, J.S. / Rambo, R.P. / Kieft, J.S.
History
DepositionOct 19, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 25, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_ref_seq / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RNA (29-MER)
B: RNA (5'-R(P*UP*AP*AP*GP*AP*AP*AP*UP*UP*UP*AP*CP*CP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,7216
Polymers13,7432
Non-polymers9784
Water2,630146
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.724, 58.724, 98.989
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: RNA chain RNA (29-MER)


Mass: 9326.556 Da / Num. of mol.: 1 / Fragment: residues 6174-6202 / Mutation: U6178A, A6198U, A6199G / Source method: obtained synthetically
Details: RNA made by in vitro transcription. This naturally occurs in Cricket Paralysis Virus
#2: RNA chain RNA (5'-R(P*UP*AP*AP*GP*AP*AP*AP*UP*UP*UP*AP*CP*CP*U)-3')


Mass: 4416.675 Da / Num. of mol.: 1 / Fragment: residues 6203-6216 / Source method: obtained synthetically / Details: CrPV IGR IRES RNA
#3: Chemical ChemComp-IRI / IRIDIUM HEXAMMINE ION


Mass: 294.400 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: H18IrN6
#4: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 146 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 3.1 Å3/Da / Density % sol: 60.34 %
Crystal growTemperature: 303 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1.4 M lithium sulfate, 40 mM magnesium acetate, 50 mM HEPES-NaOH, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 303K
Components of the solutions
IDNameCrystal-IDSol-ID
1lithium sulfate11
2magnesium acetate11
3HEPES-NaOH11
4lithium sulfate12
5magnesium acetate12
6HEPES-NaOH12

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Data collection

Diffraction
IDCrystal-ID
11
21
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
ROTATING ANODERIGAKU11.5418
SYNCHROTRONALS 12.3.121.1055, 1.1053
Detector
TypeIDDetector
RIGAKU RAXIS IV++1IMAGE PLATE
ADSC QUANTUM 3152CCD
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2MADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.54181
21.10551
31.10531
ReflectionResolution: 2.4→23.2 Å / Num. all: 7247 / Num. obs: 7225 / % possible obs: 99.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 31.9 % / Rmerge(I) obs: 0.09 / Rsym value: 0.09 / Net I/σ(I): 27.2
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 18.3 % / Mean I/σ(I) obs: 2 / Num. unique all: 696 / % possible all: 99.7

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHENIXmodel building
CNS1.1refinement
ELVESdata reduction
MOSFLMdata reduction
CCP4data scaling
PHENIXphasing
RefinementMethod to determine structure: MAD / Resolution: 2.4→23.2 Å / σ(F): 2 / σ(I): 2
RfactorNum. reflection% reflection
Rfree0.2686 774 -
Rwork0.2393 --
all-7247 -
obs-7225 99.7 %
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.917 Å20 Å20 Å2
2---2.917 Å20 Å2
3---5.834 Å2
Refinement stepCycle: LAST / Resolution: 2.4→23.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 913 25 146 1084
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0053
X-RAY DIFFRACTIONc_angle_deg1.35

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