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- PDB-7syl: Structure of the HCV IRES bound to the 40S ribosomal subunit, clo... -

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Basic information

Entry
Database: PDB / ID: 7syl
TitleStructure of the HCV IRES bound to the 40S ribosomal subunit, closed conformation. Structure 6(delta dII)
Components
  • (40S ribosomal protein ...) x 6
  • 18S rRNA18S ribosomal RNA
  • 60s ribosomal protein l41
  • HCV IRESHepatitis C virus internal ribosome entry site
  • RACK1Receptor for activated C kinase 1
  • eS1
  • eS10
  • eS12
  • eS17
  • eS19
  • eS25 (S25)
  • eS26 (S26)
  • eS27
  • eS28
  • eS29
  • eS30
  • eS6
  • eS8
  • uS10
  • uS11
  • uS12
  • uS13
  • uS15
  • uS17
  • uS19
  • uS3
  • uS4
  • uS5 (S2)
  • uS7
  • uS8
  • uS9
KeywordsRIBOSOME / HCV / IRES / 40S
Function / homology
Function and homology information


ribosomal subunit / DNA-(apurinic or apyrimidinic site) lyase / structural constituent of ribosome / translation
Similarity search - Function
Ribosomal protein S21e signature. / Ribosomal protein S12e signature. / Ribosomal protein S19e signature. / 40S Ribosomal protein S10 / Plectin/S10, N-terminal / Plectin/S10 domain / Ribosomal protein S17e signature. / Ribosomal protein S7e signature. / Ribosomal protein S3Ae signature. / Ribosomal protein S27e signature. ...Ribosomal protein S21e signature. / Ribosomal protein S12e signature. / Ribosomal protein S19e signature. / 40S Ribosomal protein S10 / Plectin/S10, N-terminal / Plectin/S10 domain / Ribosomal protein S17e signature. / Ribosomal protein S7e signature. / Ribosomal protein S3Ae signature. / Ribosomal protein S27e signature. / Ribosomal protein S4e signature. / Ribosomal protein S8e signature. / Ribosomal S24e conserved site / Ribosomal protein S24e signature. / Ribosomal protein S24e / Ribosomal protein S24e / Ribosomal protein S6e signature. / Ribosomal protein S28e signature. / Ubiquitin domain signature. / Ribosomal protein S2 signature 2. / Ribosomal protein S3 signature. / Ribosomal protein S10 signature. / Ribosomal protein S14 signature. / Ribosomal protein S2 signature 1. / Type-2 KH domain profile. / Ribosomal protein S19 signature. / Ribosomal protein S7 signature. / Ribosomal protein S17 signature. / Ribosomal protein S13 signature. / Ribosomal protein S13 family profile. / Ribosomal protein S8 signature. / Ribosomal protein S4 signature. / Ribosomal protein S15 signature. / S4 RNA-binding domain profile. / Ribosomal protein S11 signature. / Ribosomal protein S9 signature. / Ubiquitin domain profile. / Ribosomal protein S12 signature. / Ribosomal protein L23/L15e core domain superfamily / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
: / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein eS32 / 40S ribosomal protein S24 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein eS12 / Small ribosomal subunit protein uS9 ...: / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein eS32 / 40S ribosomal protein S24 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein eS12 / Small ribosomal subunit protein uS9 / Small ribosomal subunit protein uS10 / Small ribosomal subunit protein RACK1 / Ubiquitin-ribosomal protein eS31 fusion protein / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein eS1 / Small ribosomal subunit protein eS7 / Small ribosomal subunit protein uS12 / Ubiquitin-like FUBI-ribosomal protein eS30 fusion protein / Small ribosomal subunit protein uS7 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein eS28 / Small ribosomal subunit protein eS8 / Small ribosomal subunit protein eS4 / Small ribosomal subunit protein uS2 / Small ribosomal subunit protein eS6 / Small ribosomal subunit protein eS21 / Small ribosomal subunit protein eS19 / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein uS13 / Plectin/eS10 N-terminal domain-containing protein / Small ribosomal subunit protein uS17 / Small ribosomal subunit protein eS17 / Small ribosomal subunit protein eS27 / Small ribosomal subunit protein uS19 / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein uS14
Similarity search - Component
Biological specieshepatitis C virus genotype 1a
Oryctolagus cuniculus (rabbit)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.5 Å
AuthorsBrown, Z.P. / Abaeva, I.S. / De, S. / Hellen, C.U.T. / Pestova, T.V. / Frank, J.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM139453 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM55440 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R35GM122602 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)1R01AI123406 United States
CitationJournal: EMBO J / Year: 2022
Title: Molecular architecture of 40S translation initiation complexes on the hepatitis C virus IRES.
Authors: Zuben P Brown / Irina S Abaeva / Swastik De / Christopher U T Hellen / Tatyana V Pestova / Joachim Frank /
Abstract: Hepatitis C virus mRNA contains an internal ribosome entry site (IRES) that mediates end-independent translation initiation, requiring a subset of eukaryotic initiation factors (eIFs). Biochemical ...Hepatitis C virus mRNA contains an internal ribosome entry site (IRES) that mediates end-independent translation initiation, requiring a subset of eukaryotic initiation factors (eIFs). Biochemical studies revealed that direct binding of the IRES to the 40S ribosomal subunit places the initiation codon into the P site, where it base pairs with eIF2-bound Met-tRNAiMet forming a 48S initiation complex. Subsequently, eIF5 and eIF5B mediate subunit joining, yielding an elongation-competent 80S ribosome. Initiation can also proceed without eIF2, in which case Met-tRNAiMet is recruited directly by eIF5B. However, the structures of initiation complexes assembled on the HCV IRES, the transitions between different states, and the accompanying conformational changes have remained unknown. To fill these gaps, we now obtained cryo-EM structures of IRES initiation complexes, at resolutions up to 3.5 Å, that cover all major stages from the initial ribosomal association, through eIF2-containing 48S initiation complexes, to eIF5B-containing complexes immediately prior to subunit joining. These structures provide insights into the dynamic network of 40S/IRES contacts, highlight the role of IRES domain II, and reveal conformational changes that occur during the transition from eIF2- to eIF5B-containing 48S complexes and prepare them for subunit joining.
History
DepositionNov 25, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 13, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 1, 2023Group: Database references / Refinement description
Category: citation / citation_author / pdbx_initial_refinement_model
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
2: 18S rRNA
B: 40S ribosomal protein SA
C: eS1
D: uS5 (S2)
E: uS3
F: 40S ribosomal protein S4
G: uS7
H: eS6
I: 40S ribosomal protein S7
J: eS8
K: uS4
L: eS10
M: uS17
N: eS12
O: uS15
P: uS11
Q: uS19
R: uS9
S: eS17
T: uS13
U: eS19
V: uS10
W: 40S ribosomal protein S21
X: uS8
Y: uS12
Z: 40S ribosomal protein S24
a: eS25 (S25)
b: eS26 (S26)
c: eS27
d: eS28
e: eS29
f: eS30
g: 40S ribosomal protein S27a
h: RACK1
n: 60s ribosomal protein l41
z: HCV IRES
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,389,78338
Polymers1,389,65236
Non-polymers1312
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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RNA chain , 2 types, 2 molecules 2z

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


Mass: 603100.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#36: RNA chain HCV IRES / Hepatitis C virus internal ribosome entry site


Mass: 128746.109 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) hepatitis C virus genotype 1a / Production host: Escherichia coli (E. coli) / References: GenBank: 149384897

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40S ribosomal protein ... , 6 types, 6 molecules BFIWZg

#2: Protein 40S ribosomal protein SA / / 37 kDa laminin receptor precursor / 37LRP / 37/67 kDa laminin receptor / LRP/LR / 67 kDa laminin ...37 kDa laminin receptor precursor / 37LRP / 37/67 kDa laminin receptor / LRP/LR / 67 kDa laminin receptor / 67LR / Laminin receptor 1 / LamR / Laminin-binding protein precursor p40 / LBP/p40


Mass: 32958.016 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TLT8
#6: Protein 40S ribosomal protein S4 /


Mass: 29654.869 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TK17
#9: Protein 40S ribosomal protein S7 /


Mass: 47356.172 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SVB0
#23: Protein 40S ribosomal protein S21 /


Mass: 9124.389 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TM82
#26: Protein 40S ribosomal protein S24 /


Mass: 15237.104 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: A0A5F9CNN4
#33: Protein 40S ribosomal protein S27a / / Ubiquitin carboxyl extension protein 80 / Ubiquitin-40S ribosomal protein S27a


Mass: 21431.742 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SK22

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Protein , 27 types, 27 molecules CDEGHJKLMNOPQRSTUVXYabcdefh

#3: Protein eS1 / 40S ribosomal protein S3a


Mass: 30002.061 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SS70
#4: Protein uS5 (S2)


Mass: 24441.846 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#5: Protein uS3 / Ribosomal protein S3


Mass: 31146.607 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TNM3
#7: Protein uS7 / 40S ribosomal protein S5


Mass: 22913.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TFM5
#8: Protein eS6 / 40S ribosomal protein S6


Mass: 28751.906 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TM55
#10: Protein eS8 / 40S ribosomal protein S8


Mass: 24263.387 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TJW1
#11: Protein uS4 / Ribosomal protein S9


Mass: 22641.564 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: B7NZS8
#12: Protein eS10


Mass: 17156.865 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TPV3
#13: Protein uS17 / 40S ribosomal protein S11


Mass: 18468.826 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TRM4
#14: Protein eS12 / 40S ribosomal protein S12


Mass: 14538.987 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SFR8
#15: Protein uS15 / Ribosomal protein S13


Mass: 17259.389 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SP51
#16: Protein uS11


Mass: 18133.984 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1U472
#17: Protein uS19


Mass: 17049.182 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1U0Q2
#18: Protein uS9 / Ribosomal protein S16


Mass: 19213.465 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SGX4
#19: Protein eS17


Mass: 15552.119 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TU13
#20: Protein uS13


Mass: 17759.777 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TPG3
#21: Protein eS19


Mass: 16235.796 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TN62
#22: Protein uS10


Mass: 13398.763 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SIZ2
#24: Protein uS8 / Ribosomal protein S15a


Mass: 14865.555 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TG89
#25: Protein uS12


Mass: 15844.666 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SZ47
#27: Protein eS25 (S25)


Mass: 13645.028 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#28: Protein eS26 (S26)


Mass: 11645.794 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#29: Protein eS27 / 40S ribosomal protein S27


Mass: 9480.186 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TZ76
#30: Protein eS28 / Ribosomal protein S28


Mass: 7855.052 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TIB4
#31: Protein eS29


Mass: 6690.821 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1U7M4
#32: Protein eS30 / 40S ribosomal protein S30


Mass: 14498.884 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1T8A2
#34: Protein RACK1 / Receptor for activated C kinase 1


Mass: 35115.652 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SJB4

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Protein/peptide / Non-polymers , 2 types, 3 molecules n

#35: Protein/peptide 60s ribosomal protein l41 /


Mass: 3473.451 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: A0A087WNH4
#37: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn

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Details

Has ligand of interestN

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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: 40S ribosomal small subunit with HCV IRES / Type: RIBOSOME / Entity ID: #1-#36 / Source: MULTIPLE SOURCES
Molecular weightValue: 2 MDa / Experimental value: NO
Buffer solutionpH: 7.5
SpecimenConc.: 7.5E-5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: H2/O2 mixture for 25 seconds at 25W power / Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R0.6/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE-PROPANE / Humidity: 100 % / Chamber temperature: 277.15 K / Details: 4 second blot time, force 3

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI F30
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 52000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm / Cs: 2.26 mm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN
Image recordingAverage exposure time: 4 sec. / Electron dose: 70.9 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.19.1_4122: / Classification: refinement
EM software
IDNameVersionCategory
2Leginonimage acquisition
4CTFFINDCTF correction
7UCSF Chimera1.15model fitting
8Coot0.9.3model fitting
10PHENIX1.19.1-4122model refinement
11RELION3.1initial Euler assignment
14RELION3.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 29657 / Num. of class averages: 1 / Symmetry type: POINT
Atomic model building
IDPDB-IDPdb chain-ID 3D fitting-ID
16D9J

6d9j

1
25FLX

5flx

z1
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00484092
ELECTRON MICROSCOPYf_angle_d0.848122434
ELECTRON MICROSCOPYf_dihedral_angle_d15.82727707
ELECTRON MICROSCOPYf_chiral_restr0.04415194
ELECTRON MICROSCOPYf_plane_restr0.0078632

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