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- PDB-2agn: Fitting of hepatitis C virus internal ribosome entry site domains... -

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Entry
Database: PDB / ID: 2agn
TitleFitting of hepatitis C virus internal ribosome entry site domains into the 15 A Cryo-EM map of a HCV IRES-80S ribosome (H. sapiens) complex
Components
  • 6 nt A-RNA helix
  • HCV IRES DOMAIN II
  • HCV IRES IIIABC
  • HCV IRES SUB-DOMAIN IIIB
  • HCV-1B IRES RNA SUB-DOMAIN IIID
KeywordsRNA / HCV / IRES
Function / homologyRNA / RNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 15 Å
AuthorsBoehringer, D. / Thermann, R. / Ostareck-Lederer, A. / Lewis, J.D. / Stark, H.
CitationJournal: Structure / Year: 2005
Title: Structure of the hepatitis C virus IRES bound to the human 80S ribosome: remodeling of the HCV IRES.
Authors: Daniel Boehringer / Rolf Thermann / Antje Ostareck-Lederer / Joe D Lewis / Holger Stark /
Abstract: Initiation of translation of the hepatitis C virus (HCV) polyprotein is driven by an internal ribosome entry site (IRES) RNA that bypasses much of the eukaryotic translation initiation machinery. ...Initiation of translation of the hepatitis C virus (HCV) polyprotein is driven by an internal ribosome entry site (IRES) RNA that bypasses much of the eukaryotic translation initiation machinery. Here, single-particle electron cryomicroscopy has been used to study the mechanism of HCV IRES-mediated initiation. A HeLa in vitro translation system was used to assemble human IRES-80S ribosome complexes under near physiological conditions; these were stalled before elongation. Domain 2 of the HCV IRES is bound to the tRNA exit site, touching the L1 stalk of the 60S subunit, suggesting a mechanism for the removal of the HCV IRES in the progression to elongation. Domain 3 of the HCV IRES positions the initiation codon in the ribosomal mRNA binding cleft by binding helix 28 at the head of the 40S subunit. The comparison with the previously published binary 40S-HCV IRES complex reveals structural rearrangements in the two pseudoknot structures of the HCV IRES in translation initiation.
History
DepositionJul 27, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 25, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 18, 2013Group: Structure summary
Revision 1.4Dec 18, 2019Group: Data collection / Database references / Source and taxonomy
Category: database_2 / em_image_scans ...database_2 / em_image_scans / em_software / pdbx_entity_src_syn
Item: _em_software.image_processing_id
Revision 1.5Mar 13, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type

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Structure visualization

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Assembly

Deposited unit
A: HCV-1B IRES RNA SUB-DOMAIN IIID
B: HCV IRES SUB-DOMAIN IIIB
C: HCV IRES DOMAIN II
D: 6 nt A-RNA helix
E: HCV IRES IIIABC


Theoretical massNumber of molelcules
Total (without water)65,5325
Polymers65,5325
Non-polymers00
Water0
1


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

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Components

#1: RNA chain HCV-1B IRES RNA SUB-DOMAIN IIID / Coordinate model: P atoms only


Mass: 9450.667 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: RNA chain HCV IRES SUB-DOMAIN IIIB / Coordinate model: P atoms only


Mass: 9595.754 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: RNA chain HCV IRES DOMAIN II / Coordinate model: P atoms only


Mass: 24776.691 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: RNA chain 6 nt A-RNA helix / Coordinate model: P atoms only


Mass: 4547.780 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#5: RNA chain HCV IRES IIIABC / Coordinate model: P atoms only


Mass: 17161.283 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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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: HCV IRES-80S ribosome complex / Type: RIBOSOME
Buffer solutionpH: 8.1
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: perforated corbon foil on a copper grid
VitrificationCryogen name: ETHANE / Details: plunging into liquid ethane

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Electron microscopy imaging

MicroscopyModel: FEI/PHILIPS CM200FEG / Date: Oct 1, 2003
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 50000 X / Calibrated magnification: 50000 X / Nominal defocus max: 4000 nm / Nominal defocus min: 2000 nm / Cs: 2 mm
Specimen holderTemperature: 77 K / Tilt angle max: 0 ° / Tilt angle min: 0 °
Image recordingElectron dose: 20 e/Å2 / Film or detector model: GENERIC FILM / Details: Kodak SO-163
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

EM software
IDNameVersionCategory
1IMAGIC3D reconstruction
2Amira2.3model fitting
CTF correctionDetails: phase reversal
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionMethod: angular reconstitution / Resolution: 15 Å / Num. of particles: 24100 / Nominal pixel size: 3.6 Å / Actual pixel size: 3.6 Å
Details: This entry contains only phosphorus atom in the coordinate.
Symmetry type: POINT
Atomic model buildingSpace: REAL
Atomic model building
IDPDB-ID 3D fitting-IDAccession codeInitial refinement model-IDSource nameType
11P5P

1p5p

11P5P1PDBexperimental model
21F84

1f84

11F842PDBexperimental model
31KH6

1kh6

11KH63PDBexperimental model
41KP7

1kp7

11KP74PDBexperimental model
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms0 183 0 0 183

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