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- PDB-7o7z: Rabbit 80S ribosome stalled close to the mutated SARS-CoV-2 slipp... -

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Basic information

Entry
Database: PDB / ID: 7o7z
TitleRabbit 80S ribosome stalled close to the mutated SARS-CoV-2 slippery site by a pseudoknot (classified for pseudoknot)
Components
  • (40S ribosomal protein ...) x 18
  • (60S ribosomal protein ...) x 12
  • (Ribosomal Protein ...) x 28
  • 18S rRNA
  • 28S rRNA
  • 5.8S rRNA
  • 5S
  • 60S acidic ribosomal protein P0
  • E-site tRNA
  • P-site Phe-tRNA(Phe)
  • RACK1
  • Replicase polyprotein 1ab
  • Ribosomal_L18_c domain-containing protein
  • eL21
  • eL24
  • eL30
  • eL31
  • eL32
  • eL33
  • eL38
  • eL39
  • eL42
  • eL43
  • eS10
  • mRNA containing SARS-CoV-2 sequence
  • uL22
  • uL23
  • uL29
  • uS14
  • uS15
  • uS9
KeywordsRIBOSOME / Frameshift / virus / pseudoknot
Function / homology
Function and homology information


Major pathway of rRNA processing in the nucleolus and cytosol / GTP hydrolysis and joining of the 60S ribosomal subunit / L13a-mediated translational silencing of Ceruloplasmin expression / SRP-dependent cotranslational protein targeting to membrane / Formation of a pool of free 40S subunits / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / ribosomal subunit / exit from mitosis / optic nerve development ...Major pathway of rRNA processing in the nucleolus and cytosol / GTP hydrolysis and joining of the 60S ribosomal subunit / L13a-mediated translational silencing of Ceruloplasmin expression / SRP-dependent cotranslational protein targeting to membrane / Formation of a pool of free 40S subunits / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / ribosomal subunit / exit from mitosis / optic nerve development / laminin receptor activity / retinal ganglion cell axon guidance / ubiquitin ligase inhibitor activity / positive regulation of signal transduction by p53 class mediator / 90S preribosome / phagocytic cup / protein-RNA complex assembly / ribosomal small subunit export from nucleus / laminin binding / rough endoplasmic reticulum / translation regulator activity / gastrulation / cytosolic ribosome / MDM2/MDM4 family protein binding / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) lyase / cellular response to interleukin-4 / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal large subunit biogenesis / positive regulation of apoptotic signaling pathway / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / small-subunit processome / spindle / cytoplasmic ribonucleoprotein granule / antimicrobial humoral immune response mediated by antimicrobial peptide / rRNA processing / rhythmic process / positive regulation of canonical Wnt signaling pathway / protein guanylyltransferase activity / RNA endonuclease activity producing 3'-phosphomonoesters, hydrolytic mechanism / large ribosomal subunit / regulation of translation / mRNA guanylyltransferase activity / 5'-3' RNA helicase activity / ribosome binding / Lyases; Phosphorus-oxygen lyases / virus receptor activity / Assembly of the SARS-CoV-2 Replication-Transcription Complex (RTC) / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / Maturation of replicase proteins / ribosomal small subunit biogenesis / TRAF3-dependent IRF activation pathway / ribosomal small subunit assembly / ISG15-specific peptidase activity / Transcription of SARS-CoV-2 sgRNAs / retina development in camera-type eye / snRNP Assembly / Translation of Replicase and Assembly of the Replication Transcription Complex / small ribosomal subunit / Replication of the SARS-CoV-2 genome / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / host cell endoplasmic reticulum-Golgi intermediate compartment / double membrane vesicle viral factory outer membrane / 5S rRNA binding / ribosomal large subunit assembly / 3'-5'-RNA exonuclease activity / SARS coronavirus main proteinase / 5'-3' DNA helicase activity / cytosolic small ribosomal subunit / large ribosomal subunit rRNA binding / host cell endosome / small ribosomal subunit rRNA binding / symbiont-mediated degradation of host mRNA / mRNA guanylyltransferase / symbiont-mediated suppression of host ISG15-protein conjugation / symbiont-mediated suppression of host toll-like receptor signaling pathway / G-quadruplex RNA binding / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / omega peptidase activity / defense response to Gram-negative bacterium / SARS-CoV-2 modulates host translation machinery / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / host cell Golgi apparatus / symbiont-mediated suppression of host NF-kappaB cascade / killing of cells of another organism / symbiont-mediated perturbation of host ubiquitin-like protein modification / DNA helicase / cytosolic large ribosomal subunit / perikaryon / single-stranded 3'-5' DNA helicase activity / double-stranded DNA helicase activity / forked DNA-dependent helicase activity / four-way junction helicase activity / methyltransferase cap1 activity / ubiquitinyl hydrolase 1 / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / cysteine-type deubiquitinase activity / cytoplasmic translation
Similarity search - Function
Ribosomal protein L19e, C-terminal domain / 60s Acidic ribosomal protein / 60S acidic ribosomal protein P0 / Viral superfamily 1 RNA helicase core domain / : / 40S ribosomal protein SA / 40S ribosomal protein SA, C-terminal domain / 40S ribosomal protein SA C-terminus / Ribosomal protein L6, N-terminal / Ribosomal protein L6, N-terminal domain ...Ribosomal protein L19e, C-terminal domain / 60s Acidic ribosomal protein / 60S acidic ribosomal protein P0 / Viral superfamily 1 RNA helicase core domain / : / 40S ribosomal protein SA / 40S ribosomal protein SA, C-terminal domain / 40S ribosomal protein SA C-terminus / Ribosomal protein L6, N-terminal / Ribosomal protein L6, N-terminal domain / Ubiquitin-like protein FUBI / Ribosomal protein L30e / Ribosomal L15/L27a, N-terminal / 50S ribosomal protein L10, insertion domain superfamily / Ribosomal protein L23 / 60S ribosomal protein L10P, insertion domain / Insertion domain in 60S ribosomal protein L10P / metallochaperone-like domain / TRASH domain / Ribosomal protein L41 / Ribosomal protein L41 / Ribosomal protein L1, conserved site / : / Ribosomal protein S12e signature. / Ribosomal protein L1 signature. / Ribosomal protein S12e / Ribosomal protein L1 / Ribosomal protein L29e / Ribosomal L29e protein family / Small (40S) ribosomal subunit Asc1/RACK1 / Ribosomal protein S2, eukaryotic / S27a-like superfamily / Ribosomal protein L10e, conserved site / Ribosomal protein L10e signature. / Ribosomal protein L27e, conserved site / Ribosomal protein L27e signature. / Ribosomal protein L10e / 40S Ribosomal protein S10 / Ribosomal protein L38e / Ribosomal protein L38e superfamily / Ribosomal L38e protein family / : / Ribosomal protein S7e signature. / Ribosomal protein L44e signature. / Plectin/S10, N-terminal / Plectin/S10 domain / Ribosomal protein L1, 3-layer alpha/beta-sandwich / Ribosomal protein L24e, conserved site / Ribosomal protein L24e signature. / : / Ribosomal protein S10, eukaryotic/archaeal / Ribosomal protein L19, eukaryotic / Ribosomal protein L19/L19e conserved site / Ribosomal protein L19e signature. / Ribosomal protein L6e signature. / Ribosomal protein S8e subdomain, eukaryotes / Ribosomal protein S25 / S25 ribosomal protein / Ribosomal protein S27a / Ribosomal protein S17e, conserved site / : / Ribosomal protein S27a / Ribosomal protein S17e signature. / Ribosomal protein S27a / Ribosomal protein S3Ae, conserved site / Ribosomal protein S3Ae signature. / Ribosomal protein L44e / Ribosomal protein S30 / Ribosomal protein L44 / Ribosomal protein S30 / Ribosomal protein S2, eukaryotic/archaeal / Ribosomal protein L34e, conserved site / Ribosomal protein L5 eukaryotic, C-terminal / Ribosomal L18 C-terminal region / Ribosomal protein L34e signature. / Ribosomal protein L30e signature 1. / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / Ribosomal protein S27e signature. / Ribosomal protein L23/L25, N-terminal / : / Ribosomal protein L23, N-terminal domain / Ribosomal protein S3, eukaryotic/archaeal / Eukaryotic Ribosomal Protein L27, KOW domain / Ribosomal Protein L6, KOW domain / Ribosomal protein L30e signature 2. / Ribosomal protein L27e / Ribosomal protein S8e, conserved site / Ribosomal protein L27e superfamily / Ribosomal L27e protein family / Ribosomal protein L36e signature. / Ribosomal protein S8e signature. / Ribosomal protein S6, eukaryotic / Ribosomal protein L35Ae, conserved site / Ribosomal protein L30e, conserved site / Ribosomal protein L35Ae signature. / Ribosomal protein S7e / Ribosomal protein L39e, conserved site / Ribosomal protein S7e / Ribosomal protein L39e signature. / 40S ribosomal protein S1/3, eukaryotes
Similarity search - Domain/homology
SPERMIDINE / SPERMINE / : / : / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) ...SPERMIDINE / SPERMINE / : / : / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein eS32 / Large ribosomal subunit protein uL16 / Small ribosomal subunit protein uS4 / Large ribosomal subunit protein eL24 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein eL33 / Small ribosomal subunit protein eS12 / Large ribosomal subunit protein eL29 / Small ribosomal subunit protein uS9 / Large ribosomal subunit protein eL31 / Large ribosomal subunit protein eL21 / Large ribosomal subunit protein uL29 / Small ribosomal subunit protein uS10 / Small ribosomal subunit protein RACK1 / Ubiquitin-ribosomal protein eS31 fusion protein / Large ribosomal subunit protein eL6 / Large ribosomal subunit protein uL1 / Large ribosomal subunit protein uL11 / Large ribosomal subunit protein uL15 / Small ribosomal subunit protein uS15 / Large ribosomal subunit protein uL10 / Large ribosomal subunit protein uL24 / Small ribosomal subunit protein eS1 / Small ribosomal subunit protein eS7 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL6 / Large ribosomal subunit protein eL43 / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein eL14 / Small ribosomal subunit protein uS12 / Large ribosomal subunit protein eL15 / Small ribosomal subunit protein uS11 / 40S ribosomal protein S24 / Large ribosomal subunit protein uL14 / Ubiquitin-like FUBI-ribosomal protein eS30 fusion protein / Small ribosomal subunit protein eS25 / Large ribosomal subunit protein eL30 / Small ribosomal subunit protein uS7 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein eS28 / Small ribosomal subunit protein eS8 / Large ribosomal subunit protein uL3 / Small ribosomal subunit protein uS2 / Small ribosomal subunit protein eS6 / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein uS13 / Small ribosomal subunit protein eS10 / Small ribosomal subunit protein uS17 / Large ribosomal subunit protein eL39 / Large ribosomal subunit protein eL36 / Small ribosomal subunit protein eS17 / Large ribosomal subunit protein uL5 / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein eL27 / Large ribosomal subunit protein eL34 / Small ribosomal subunit protein eS27 / Large ribosomal subunit protein eL38 / Small ribosomal subunit protein uS19 / Large ribosomal subunit protein eL42 / Large ribosomal subunit protein eL32 / Small ribosomal subunit protein uS14 / Replicase polyprotein 1ab / Large ribosomal subunit protein eL19 / Large ribosomal subunit protein eL37
Similarity search - Component
Biological speciesSevere acute respiratory syndrome coronavirus 2
Oryctolagus cuniculus (rabbit)
Bos taurus (domestic cattle)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.4 Å
AuthorsBhatt, P.R. / Scaiola, A. / Leibundgut, M.A. / Atkins, J.F. / Ban, N.
Funding support Switzerland, Ireland, 2items
OrganizationGrant numberCountry
Swiss National Science Foundation31003A_182341 Switzerland
Irish Research CouncilIRCLA/2019/74 Ireland
CitationJournal: Science / Year: 2021
Title: Structural basis of ribosomal frameshifting during translation of the SARS-CoV-2 RNA genome.
Authors: Pramod R Bhatt / Alain Scaiola / Gary Loughran / Marc Leibundgut / Annika Kratzel / Romane Meurs / René Dreos / Kate M O'Connor / Angus McMillan / Jeffrey W Bode / Volker Thiel / David ...Authors: Pramod R Bhatt / Alain Scaiola / Gary Loughran / Marc Leibundgut / Annika Kratzel / Romane Meurs / René Dreos / Kate M O'Connor / Angus McMillan / Jeffrey W Bode / Volker Thiel / David Gatfield / John F Atkins / Nenad Ban /
Abstract: Programmed ribosomal frameshifting is a key event during translation of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA genome that allows synthesis of the viral RNA-dependent ...Programmed ribosomal frameshifting is a key event during translation of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA genome that allows synthesis of the viral RNA-dependent RNA polymerase and downstream proteins. Here, we present the cryo-electron microscopy structure of a translating mammalian ribosome primed for frameshifting on the viral RNA. The viral RNA adopts a pseudoknot structure that lodges at the entry to the ribosomal messenger RNA (mRNA) channel to generate tension in the mRNA and promote frameshifting, whereas the nascent viral polyprotein forms distinct interactions with the ribosomal tunnel. Biochemical experiments validate the structural observations and reveal mechanistic and regulatory features that influence frameshifting efficiency. Finally, we compare compounds previously shown to reduce frameshifting with respect to their ability to inhibit SARS-CoV-2 replication, establishing coronavirus frameshifting as a target for antiviral intervention.
History
DepositionApr 14, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 2, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 9, 2021Group: Structure summary / Category: chem_comp / Item: _chem_comp.name
Revision 1.2Jun 30, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Jul 21, 2021Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / pdbx_validate_torsion / struct_conn
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _struct_conn.pdbx_leaving_atom_flag
Revision 2.0Sep 1, 2021Group: Advisory / Atomic model ...Advisory / Atomic model / Database references / Derived calculations / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / database_2 ...atom_site / database_2 / entity / entity_name_com / entity_poly / entity_poly_seq / entity_src_gen / entity_src_nat / pdbx_poly_seq_scheme / pdbx_struct_mod_residue / pdbx_unobs_or_zero_occ_residues / struct_conn / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _atom_site.label_seq_id / _database_2.pdbx_DOI ..._atom_site.label_seq_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_gene / _entity_src_nat.common_name / _struct_conn.ptnr2_label_seq_id / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq.seq_align_end
Revision 3.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_id
Revision 3.1Apr 24, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 ..._chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _chem_comp_bond.pdbx_aromatic_flag / _chem_comp_bond.value_order

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Structure visualization

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Assembly

Deposited unit
A2: 18S rRNA
AA: 40S ribosomal protein S27
AB: Ribosomal protein S28
AC: Ribosomal protein S27a
AD: 40S ribosomal protein S30
AE: Ribosomal protein eS26
AF: RACK1
AG: uS14
AH: mRNA containing SARS-CoV-2 sequence
AI: E-site tRNA
AT: P-site Phe-tRNA(Phe)
AZ: 40S ribosomal protein SA
Aa: 40S ribosomal protein S3a
Ab: Ribosomal protein uS5
Ac: 40S ribosomal protein S3
Ad: Ribosomal protein eS4
Ae: Ribosomal protein S5
Af: 40S ribosomal protein S6
Ag: 40S ribosomal protein S7
Ah: 40S ribosomal protein S8
Ai: Ribosomal protein S9 (Predicted)
Aj: eS10
Ak: 40S ribosomal protein S11
Al: 40S ribosomal protein S12
Am: uS15
An: 40S ribosomal protein uS11
Ao: 40S ribosomal protein uS19
Ap: uS9
Aq: 40S ribosomal protein eS17
Ar: 40S ribosomal protein S18
As: Ribosomal protein eS19
At: 40S ribosomal protein uS10
Au: Ribosomal protein eS21
Av: Ribosomal protein S15a
Aw: 40S ribosomal protein S23
Ax: 40S ribosomal protein S24
Ay: 40S ribosomal protein S25
Az: 60s ribosomal protein l41
B5: 28S rRNA
B7: 5S
B8: 5.8S rRNA
BA: Ribosomal protein uL2
BB: Ribosomal protein L3
BC: 60S ribosomal protein L4
BD: Ribosomal_L18_c domain-containing protein
BE: 60S ribosomal protein L6
BF: Ribosomal Protein uL30
BG: Ribosomal protein eL8
BH: 60S ribosomal protein L9
BI: 60S ribosomal protein L10
BJ: Ribosomal protein L11
BK: Replicase polyprotein 1ab
BL: Ribosomal protein eL13
BM: Ribosomal protein L14
BN: Ribosomal protein L15
BO: Ribosomal protein uL13
BP: uL22
BQ: Ribosomal Protein eL18
BR: 60S ribosomal protein L19
BS: Ribosomal protein eL20
BT: eL21
BU: Ribosomal protein eL22
BV: Ribosomal protein L23
BW: eL24
BX: uL23
BY: Ribosomal protein L26
BZ: 60S ribosomal protein L27
Ba: 60S ribosomal protein L27a
Bb: 60S ribosomal protein L29
Bc: eL30
Bd: eL31
Be: eL32
Bf: eL33
Bg: 60S ribosomal protein L34
Bh: uL29
Bi: 60S ribosomal protein L36
Bj: Ribosomal protein L37
Bk: eL38
Bl: eL39
Bm: 60S ribosomal protein L40
Bo: eL42
Bp: eL43
Br: Ribosomal protein eL28
Bs: 60S acidic ribosomal protein P0
Bt: Ribosomal protein L12
Bv: Ribosomal protein uL1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,071,783876
Polymers4,056,08786
Non-polymers15,696790
Water38,1382117
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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RNA chain , 7 types, 7 molecules A2AHAIATB5B7B8

#1: RNA chain 18S rRNA


Mass: 603928.250 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: GenBank: GBCT01000564.1
#9: RNA chain mRNA containing SARS-CoV-2 sequence


Mass: 70601.500 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Severe acute respiratory syndrome coronavirus 2
References: GenBank: NC_045512.2
#10: RNA chain E-site tRNA


Mass: 15209.544 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle)
#11: RNA chain P-site Phe-tRNA(Phe)


Mass: 24889.115 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle)
#39: RNA chain 28S rRNA


Mass: 1557519.500 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: GenBank: GBCN01009604.1
#40: RNA chain 5S


Mass: 38851.871 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: GenBank: GBCM01014045.1
#41: RNA chain 5.8S rRNA


Mass: 50809.047 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: GenBank: GBCN01009604.1

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40S ribosomal protein ... , 18 types, 18 molecules AAADAZAaAcAfAgAhAkAlAnAoAqArAtAwAxAy

#2: Protein 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
#5: Protein 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
#12: 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: 32970.023 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TLT8
#13: Protein 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
#15: Protein 40S 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, DNA-(apurinic or apyrimidinic site) lyase
#18: Protein 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
#19: 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
#20: Protein 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
#23: Protein 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
#24: Protein 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
#26: Protein 40S ribosomal protein uS11


Mass: 16302.772 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1T1F0
#27: Protein 40S ribosomal 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
#29: Protein 40S ribosomal 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
#30: Protein 40S ribosomal protein S18


Mass: 17801.814 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TPG3
#32: Protein 40S ribosomal 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
#35: Protein 40S ribosomal protein S23


Mass: 15860.666 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SZ47
#36: Protein 40S ribosomal protein S24


Mass: 15107.924 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1T3D8
#37: Protein 40S ribosomal protein S25


Mass: 13645.028 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TDB3

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Ribosomal Protein ... , 28 types, 28 molecules ABACAEAbAdAeAiAsAuAvBABBBFBGBJBLBMBNBOBQBSBUBVBYBjBrBtBv

#3: Protein 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
#4: Protein Ribosomal protein S27a


Mass: 18004.041 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SK22
#6: Protein Ribosomal protein eS26


Mass: 13047.532 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Depositor reference: GB XP_008254857.1 / Source: (natural) Oryctolagus cuniculus (rabbit)
#14: Protein Ribosomal protein uS5


Mass: 31285.426 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Sequence from GeneBank entry GBAX01005410.1 / Source: (natural) Oryctolagus cuniculus (rabbit)
#16: Protein Ribosomal protein eS4


Mass: 29654.869 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Sequence from GeneBank entry XP_002720153.1 / Source: (natural) Oryctolagus cuniculus (rabbit)
#17: Protein 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
#21: Protein Ribosomal protein S9 (Predicted)


Mass: 22641.564 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: B7NZS8
#31: Protein Ribosomal protein eS19


Mass: 16104.579 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Sequence from GeneBank entry DN883431.1 / Source: (natural) Oryctolagus cuniculus (rabbit)
#33: Protein Ribosomal protein eS21


Mass: 9181.374 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Sequence from UniProt entry DN885342.1 / Source: (natural) Oryctolagus cuniculus (rabbit)
#34: Protein 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
#42: Protein Ribosomal protein uL2


Mass: 28103.855 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Sequence from GeneBank entry XP_002723515.1 / Source: (natural) Oryctolagus cuniculus (rabbit)
#43: Protein Ribosomal protein L3


Mass: 46120.996 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TL06
#47: Protein Ribosomal Protein uL30


Mass: 29201.836 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Sequence from GeneBank entry XP_002710681.1 / Source: (natural) Oryctolagus cuniculus (rabbit)
#48: Protein Ribosomal protein eL8


Mass: 30061.785 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Sequence from GeneBank entry GBCD01000651.1 / Source: (natural) Oryctolagus cuniculus (rabbit)
#51: Protein Ribosomal protein L11


Mass: 20288.465 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TUB8
#53: Protein Ribosomal protein eL13


Mass: 24331.723 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Sequence from GeneBank entry XP_002710580.1 / Source: (natural) Oryctolagus cuniculus (rabbit)
#54: Protein Ribosomal protein L14


Mass: 23870.549 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SZ12
#55: Protein Ribosomal protein L15


Mass: 24207.285 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1T0C1
#56: Protein Ribosomal protein uL13


Mass: 23533.299 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Sequence from GeneBank entry XP_002723961.2 / Source: (natural) Oryctolagus cuniculus (rabbit)
#58: Protein Ribosomal Protein eL18


Mass: 21699.688 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Sequence from GeneBank entry XP_008250645.1 / Source: (natural) Oryctolagus cuniculus (rabbit)
#60: Protein Ribosomal protein eL20


Mass: 20749.391 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Sequence from GeneBank entry GBCK01009614.1 / Source: (natural) Oryctolagus cuniculus (rabbit)
#62: Protein Ribosomal protein eL22


Mass: 14756.909 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Sequence from GeneBank entry CU464830.1 / Source: (natural) Oryctolagus cuniculus (rabbit)
#63: Protein Ribosomal protein L23


Mass: 14892.505 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1T6D1
#66: Protein Ribosomal protein L26


Mass: 17303.363 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SQH0
#77: Protein Ribosomal protein L37


Mass: 11111.032 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: U3KPD5
#83: Protein Ribosomal protein eL28


Mass: 15844.696 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Sequence from GeneBank entry GBCM01003096.1 / Source: (natural) Oryctolagus cuniculus (rabbit)
#85: Protein Ribosomal protein L12


Mass: 17847.619 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SMR7
#86: Protein Ribosomal protein uL1


Mass: 24875.410 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SKZ8

+
Protein , 21 types, 21 molecules AFAGAjAmApBDBKBPBTBWBXBcBdBeBfBhBkBlBoBpBs

#7: Protein RACK1


Mass: 35115.652 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SJB4
#8: Protein uS14


Mass: 6690.821 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1U7M4
#22: Protein eS10


Mass: 18933.846 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TPV3
#25: Protein uS15


Mass: 17259.389 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SP51
#28: Protein uS9


Mass: 19213.465 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SGX4
#45: Protein Ribosomal_L18_c domain-containing protein


Mass: 34523.863 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SYJ6
#52: Protein Replicase polyprotein 1ab / pp1ab / ORF1ab polyprotein


Mass: 121565.844 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Gene: rep, 1a-1b / Production host: Oryctolagus cuniculus (rabbit) / References: UniProt: P0DTD1
#57: Protein uL22


Mass: 21444.221 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TVT6
#61: Protein eL21


Mass: 18609.988 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SHQ2
#64: Protein eL24


Mass: 17825.111 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SE28
#65: Protein uL23


Mass: 17768.246 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SE76
#70: Protein eL30


Mass: 12807.065 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TDL2
#71: Protein eL31


Mass: 14494.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SHG0
#72: Protein eL32


Mass: 15898.932 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1U437
#73: Protein eL33


Mass: 12580.809 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SF08
#75: Protein uL29


Mass: 14566.599 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SIT5
#78: Protein eL38


Mass: 8238.948 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1U001
#79: Protein eL39


Mass: 6455.775 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TTN1
#81: Protein eL42


Mass: 12489.991 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1U344
#82: Protein eL43


Mass: 10299.350 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SY53
#84: Protein 60S acidic ribosomal protein P0


Mass: 34380.504 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SPK4

-
60S ribosomal protein ... , 12 types, 12 molecules AzBCBEBHBIBRBZBaBbBgBiBm

#38: Protein/peptide 60s ribosomal protein l41 / eL41


Mass: 3473.451 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: A0A087WNH4
#44: Protein 60S ribosomal protein L4


Mass: 46430.895 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SVW5
#46: Protein 60S ribosomal protein L6


Mass: 33028.336 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SKF7
#49: Protein 60S ribosomal protein L9


Mass: 21871.418 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SWI6
#50: Protein 60S ribosomal protein L10 / Ribosomal protein L10 (Predicted)


Mass: 24643.057 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: B7NZQ2
#59: Protein 60S ribosomal protein L19


Mass: 23535.281 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: Q3T0W9
#67: Protein 60S ribosomal protein L27


Mass: 15835.831 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TXF6
#68: Protein 60S ribosomal protein L27a


Mass: 16635.551 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SNY0
#69: Protein 60S ribosomal protein L29


Mass: 26721.727 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SGR6
#74: Protein 60S ribosomal protein L34


Mass: 13326.074 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TXG5
#76: Protein 60S ribosomal protein L36


Mass: 12263.834 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TTQ5
#80: Protein 60S ribosomal protein L40


Mass: 14800.474 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)

-
Non-polymers , 6 types, 2907 molecules

#87: Chemical...
ChemComp-SPD / SPERMIDINE / N-(2-AMINO-PROPYL)-1,4-DIAMINOBUTANE / PA(34)


Mass: 145.246 Da / Num. of mol.: 30 / Source method: obtained synthetically / Formula: C7H19N3
#88: Chemical ChemComp-SPM / SPERMINE


Mass: 202.340 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H26N4
#89: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 420 / Source method: obtained synthetically / Formula: Mg
#90: Chemical...
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 329 / Source method: obtained synthetically
#91: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#92: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2117 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1Rabbit 80S ribosome stalled close to the mutated SARS-CoV-2 slippery site by a pseudoknotRIBOSOME#1-#860MULTIPLE SOURCES
2Rabbit 80S ribosome stalledRIBOSOME#1-#8, #12-#861NATURAL
3SARS-CoV-2 slippery site by a pseudoknotCOMPLEX#91RECOMBINANT
4Rabbit 80S ribosome stalledRIBOSOME#10-#111NATURAL
5Replicase polyprotein 1abCOMPLEX#521RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
12Oryctolagus cuniculus (rabbit)9986
23Severe acute respiratory syndrome coronavirus 22697049
34Bos taurus (domestic cattle)9913
45Severe acute respiratory syndrome coronavirus 22697049
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
13synthetic construct (others)32630
25Oryctolagus cuniculus (rabbit)9986
Buffer solutionpH: 7.4
SpecimenConc.: 0.3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R2/2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE-PROPANE / Humidity: 100 % / Chamber temperature: 277 K

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 81000 X / Calibrated magnification: 56604 X / Cs: 2.7 mm / C2 aperture diameter: 100 µm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)
EM imaging opticsEnergyfilter name: GIF Quantum LS / Energyfilter slit width: 20 eV

-
Processing

EM software
IDNameVersionCategory
1RELION3particle selection
2EPU2.8image acquisition
4GctfCTF correction
10cryoSPARC2initial Euler assignment
11cryoSPARC2final Euler assignment
13cryoSPARC23D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 171706 / Symmetry type: POINT

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