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- PDB-4v92: Kluyveromyces lactis 80S ribosome in complex with CrPV-IRES -

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Basic information

Entry
Database: PDB / ID: 4v92
TitleKluyveromyces lactis 80S ribosome in complex with CrPV-IRES
Components
  • 18S RRNA18S ribosomal RNA
  • ES1
  • ES10
  • ES12
  • ES17
  • ES19
  • ES21
  • ES24
  • ES25
  • ES26
  • ES27
  • ES28
  • ES30
  • ES31
  • ES4
  • ES6
  • ES7
  • ES8
  • RACK1Receptor for activated C kinase 1
  • RNA OF CRICKET-PARALYSIS-VIRUS-IRES
  • US10
  • US11
  • US12
  • US13
  • US14
  • US15
  • US17
  • US19
  • US2
  • US3
  • US4
  • US5
  • US7
  • US8
  • US9
KeywordsRIBOSOME / EUKARYOTIC / TRANSLATION / INITIATION / IRES
Function / homologyRNA / RNA (> 10) / RNA (> 100) / RNA (> 1000)
Function and homology information
Biological speciesKLUYVEROMYCES LACTIS (yeast)
CRICKET PARALYSIS VIRUS
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsFernandez, I.S. / Bai, X. / Scheres, S.H.W. / Ramakrishnan, V.
CitationJournal: Cell / Year: 2014
Title: Initiation of translation by cricket paralysis virus IRES requires its translocation in the ribosome.
Authors: Israel S Fernández / Xiao-Chen Bai / Garib Murshudov / Sjors H W Scheres / V Ramakrishnan /
Abstract: The cricket paralysis virus internal ribosome entry site (CrPV-IRES) is a folded structure in a viral mRNA that allows initiation of translation in the absence of any host initiation factors. By ...The cricket paralysis virus internal ribosome entry site (CrPV-IRES) is a folded structure in a viral mRNA that allows initiation of translation in the absence of any host initiation factors. By using recent advances in single-particle electron cryomicroscopy, we have solved the structure of CrPV-IRES bound to the ribosome of the yeast Kluyveromyces lactis in both the canonical and rotated states at overall resolutions of 3.7 and 3.8 Å, respectively. In both states, the pseudoknot PKI of the CrPV-IRES mimics a tRNA/mRNA interaction in the decoding center of the A site of the 40S ribosomal subunit. The structure and accompanying factor-binding data show that CrPV-IRES binding mimics a pretranslocation rather than initiation state of the ribosome. Translocation of the IRES by elongation factor 2 (eEF2) is required to bring the first codon of the mRNA into the A site and to allow the start of translation.
History
DepositionMar 21, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 9, 2014Provider: repository / Type: Initial release
SupersessionDec 10, 2014ID: 4CUX, 4CUY
Revision 1.1Dec 10, 2014Group: Other
Revision 1.2Apr 22, 2015Group: Other
Revision 2.0Aug 2, 2017Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations
Category: atom_site / em_software ...atom_site / em_software / pdbx_validate_close_contact / struct_conn
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _em_software.fitting_id / _em_software.image_processing_id / _em_software.name / _pdbx_validate_close_contact.auth_atom_id_1
Revision 2.1Dec 11, 2019Group: Other / Category: atom_sites / pdbx_database_status
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] ..._atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3] / _pdbx_database_status.process_site

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Structure visualization

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Assembly

Deposited unit
A2: 18S RRNA
AZ: RNA OF CRICKET-PARALYSIS-VIRUS-IRES
BA: US2
BB: ES1
BC: US5
BD: US3
BE: ES4
BF: US7
BG: ES6
BH: ES7
BI: ES8
BJ: US4
BK: ES10
BL: US17
BM: ES12
BN: US15
BO: US11
BP: US19
BQ: US9
BR: ES17
BS: US13
BT: ES19
BU: US10
BV: ES21
BW: US8
BX: US12
BY: ES24
BZ: ES25
Ba: ES26
Bb: ES27
Bc: ES28
Bd: US14
Be: ES30
Bf: ES31
Bg: RACK1


Theoretical massNumber of molelcules
Total (without water)1,164,74335
Polymers1,164,74335
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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RNA chain , 2 types, 2 molecules A2AZ

#1: RNA chain 18S RRNA / 18S ribosomal RNA


Mass: 569191.250 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: 18S RRNA / Source: (natural) KLUYVEROMYCES LACTIS (yeast)
#2: RNA chain RNA OF CRICKET-PARALYSIS-VIRUS-IRES


Mass: 60767.703 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: CRICKET-PARALYSIS-VIRUS-IRES / Source: (natural) CRICKET PARALYSIS VIRUS

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Protein , 33 types, 33 molecules BABBBCBDBEBFBGBHBIBJBKBLBMBNBOBPBQBRBSBTBUBVBWBXBYBZBaBbBcBd...

#3: Protein US2


Mass: 22811.074 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) KLUYVEROMYCES LACTIS (yeast)
#4: Protein ES1


Mass: 23982.734 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) KLUYVEROMYCES LACTIS (yeast)
#5: Protein US5


Mass: 23084.850 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) KLUYVEROMYCES LACTIS (yeast)
#6: Protein US3


Mass: 24631.713 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) KLUYVEROMYCES LACTIS (yeast)
#7: Protein ES4


Mass: 29338.133 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) KLUYVEROMYCES LACTIS (yeast)
#8: Protein US7


Mass: 22822.223 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) KLUYVEROMYCES LACTIS (yeast)
#9: Protein ES6


Mass: 25778.867 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) KLUYVEROMYCES LACTIS (yeast)
#10: Protein ES7


Mass: 21000.492 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) KLUYVEROMYCES LACTIS (yeast)
#11: Protein ES8


Mass: 21018.000 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) KLUYVEROMYCES LACTIS (yeast)
#12: Protein US4


Mass: 20608.047 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) KLUYVEROMYCES LACTIS (yeast)
#13: Protein ES10


Mass: 11054.485 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) KLUYVEROMYCES LACTIS (yeast)
#14: Protein US17


Mass: 16272.149 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) KLUYVEROMYCES LACTIS (yeast)
#15: Protein ES12


Mass: 12926.904 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) KLUYVEROMYCES LACTIS (yeast)
#16: Protein US15


Mass: 16928.748 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) KLUYVEROMYCES LACTIS (yeast)
#17: Protein US11


Mass: 13446.426 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) KLUYVEROMYCES LACTIS (yeast)
#18: Protein US19


Mass: 13060.371 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) KLUYVEROMYCES LACTIS (yeast)
#19: Protein US9


Mass: 15329.792 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) KLUYVEROMYCES LACTIS (yeast)
#20: Protein ES17


Mass: 13882.165 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) KLUYVEROMYCES LACTIS (yeast)
#21: Protein US13


Mass: 16340.733 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) KLUYVEROMYCES LACTIS (yeast)
#22: Protein ES19


Mass: 15713.815 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) KLUYVEROMYCES LACTIS (yeast)
#23: Protein US10


Mass: 11819.814 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) KLUYVEROMYCES LACTIS (yeast)
#24: Protein ES21


Mass: 9758.829 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) KLUYVEROMYCES LACTIS (yeast)
#25: Protein US8


Mass: 14518.867 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) KLUYVEROMYCES LACTIS (yeast)
#26: Protein US12


Mass: 15654.417 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) KLUYVEROMYCES LACTIS (yeast)
#27: Protein ES24


Mass: 15231.650 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) KLUYVEROMYCES LACTIS (yeast)
#28: Protein ES25


Mass: 7366.631 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) KLUYVEROMYCES LACTIS (yeast)
#29: Protein ES26


Mass: 11022.989 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) KLUYVEROMYCES LACTIS (yeast)
#30: Protein ES27


Mass: 8762.195 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) KLUYVEROMYCES LACTIS (yeast)
#31: Protein ES28


Mass: 7116.281 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) KLUYVEROMYCES LACTIS (yeast)
#32: Protein US14


Mass: 6206.189 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) KLUYVEROMYCES LACTIS (yeast)
#33: Protein ES30


Mass: 6284.500 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) KLUYVEROMYCES LACTIS (yeast)
#34: Protein ES31


Mass: 6572.660 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) KLUYVEROMYCES LACTIS (yeast)
#35: Protein RACK1 / Receptor for activated C kinase 1


Mass: 34437.766 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) KLUYVEROMYCES LACTIS (yeast)

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Kluyveromyces lactis 80S ribosome in complex with CrPV-IRES
Type: RIBOSOME
Buffer solutionpH: 6.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: CARBON
VitrificationInstrument: FEI VITROBOT MARK I / Cryogen name: PROPANE / Details: LIQUID ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS / Date: Jul 7, 2013
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 47000 X / Nominal defocus max: 3 nm / Nominal defocus min: 1.8 nm / Cs: 2.7 mm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k)
Image scansNum. digital images: 1900
Radiation wavelengthRelative weight: 1

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Processing

EM software
IDNameCategory
1REFMACmodel fitting
2UCSF Chimeramodel fitting
3RELION3D reconstruction
CTF correctionDetails: EACH PARTICLE
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionMethod: RELIONList of Walmart brands / Resolution: 3.7 Å / Num. of particles: 18132 / Nominal pixel size: 1.34 Å / Symmetry type: POINT
Atomic model buildingB value: 60 / Protocol: FLEXIBLE FIT / Space: RECIPROCAL / Target criteria: R-FACTOR, FSC / Details: METHOD--FLEXIBLE
Atomic model buildingPDB-ID: 3B31

3b31

RefinementHighest resolution: 3.7 Å
Refinement stepCycle: LAST / Highest resolution: 3.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 41597 0 0 41597

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