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- PDB-5m1j: Nonstop ribosomal complex bound with Dom34 and Hbs1 -

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Basic information

Entry
Database: PDB / ID: 5m1j
TitleNonstop ribosomal complex bound with Dom34 and Hbs1
Components
  • (40S ribosomal protein ...) x 31
  • (60S ribosomal protein ...) x 40
  • 18S ribosomal RNA
  • 25S ribosomal RNA
  • 5.8S ribosomal RNA
  • 5S ribosomal RNA
  • Guanine nucleotide-binding protein subunit beta-like protein
  • Protein DOM34
  • Protein HBS1
  • Ubiquitin-40S ribosomal protein S31
  • Ubiquitin-60S ribosomal protein L40
  • nonstop mRNA
  • yeast Phe-tRNA-Phe
KeywordsRIBOSOME / mRNA surveillance
Function / homology
Function and homology information


Eukaryotic Translation Elongation / RNA surveillance / Dom34-Hbs1 complex / nuclear-transcribed mRNA catabolic process, no-go decay / nuclear-transcribed mRNA catabolic process, non-stop decay / HSF1 activation / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, LSU-rRNA,5S) / Negative regulators of DDX58/IFIH1 signaling / regulation of amino acid metabolic process / negative regulation of glucose mediated signaling pathway ...Eukaryotic Translation Elongation / RNA surveillance / Dom34-Hbs1 complex / nuclear-transcribed mRNA catabolic process, no-go decay / nuclear-transcribed mRNA catabolic process, non-stop decay / HSF1 activation / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, LSU-rRNA,5S) / Negative regulators of DDX58/IFIH1 signaling / regulation of amino acid metabolic process / negative regulation of glucose mediated signaling pathway / positive regulation of translational fidelity / RMTs methylate histone arginines / Protein methylation / mTORC1-mediated signalling / Protein hydroxylation / ribosome disassembly / ribosome-associated ubiquitin-dependent protein catabolic process / GDP-dissociation inhibitor activity / regulation of polysaccharide biosynthetic process / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / Formation of the ternary complex, and subsequently, the 43S complex / Translation initiation complex formation / Ribosomal scanning and start codon recognition / preribosome, small subunit precursor / nonfunctional rRNA decay / transporter complex / cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / response to cycloheximide / Major pathway of rRNA processing in the nucleolus and cytosol / mRNA destabilization / lipopolysaccharide transport / SRP-dependent cotranslational protein targeting to membrane / GTP hydrolysis and joining of the 60S ribosomal subunit / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / negative regulation of translational frameshifting / Formation of a pool of free 40S subunits / positive regulation of protein kinase activity / preribosome, large subunit precursor / L13a-mediated translational silencing of Ceruloplasmin expression / Gram-negative-bacterium-type cell outer membrane assembly / positive regulation of translational initiation / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / translational elongation / ribosomal large subunit export from nucleus / G-protein alpha-subunit binding / 90S preribosome / Ub-specific processing proteases / translation elongation factor activity / ribosomal subunit export from nucleus / regulation of translational fidelity / endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / protein-RNA complex assembly / translational termination / maturation of LSU-rRNA / ribosomal small subunit export from nucleus / translation regulator activity / DNA-(apurinic or apyrimidinic site) endonuclease activity / Neutrophil degranulation / RNA endonuclease activity / rescue of stalled ribosome / protein kinase C binding / cellular response to amino acid starvation / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / positive regulation of translation / ribosomal large subunit biogenesis / ribosome assembly / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / meiotic cell cycle / maturation of SSU-rRNA / macroautophagy / small-subunit processome / translational initiation / modification-dependent protein catabolic process / protein tag activity / maintenance of translational fidelity / cell outer membrane / cytoplasmic stress granule / rRNA processing / ribosome biogenesis / ribosome binding / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / 5S rRNA binding / small ribosomal subunit rRNA binding / ribosomal large subunit assembly / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / cytosolic large ribosomal subunit / cytoplasmic translation / protein ubiquitination / negative regulation of translation / rRNA binding / structural constituent of ribosome / ribosome / translation / G protein-coupled receptor signaling pathway / negative regulation of gene expression
Similarity search - Function
Translation release factor pelota / HBS1-like protein, N-terminal / Pelota/DOM34, N-terminal domain / HBS1 N-terminus / eRF1 domain 2 / eRF1 domain 2 / eRF1 domain 1/Pelota-like / eRF1 domain 3 / eRF1, domain 2 superfamily / eRF1 domain 1 ...Translation release factor pelota / HBS1-like protein, N-terminal / Pelota/DOM34, N-terminal domain / HBS1 N-terminus / eRF1 domain 2 / eRF1 domain 2 / eRF1 domain 1/Pelota-like / eRF1 domain 3 / eRF1, domain 2 superfamily / eRF1 domain 1 / eRF1 domain 3 / eRF1_1 / : / GTP-eEF1A C-terminal domain-like / : / LptD, C-terminal / LPS-assembly protein LptD / : / LPS transport system D / Organic solvent tolerance-like, N-terminal / LptA/(LptD N-terminal domain) LPS transport protein / Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal / Group II dsDNA virus coat/capsid protein / : / Tr-type G domain, conserved site / Translational (tr)-type guanine nucleotide-binding (G) domain signature. / Ribosomal protein L13e / : / Ribosomal protein S26e signature. / Ribosomal protein L41 / Ribosomal protein L41 / Ribosomal protein S21e, conserved site / Ribosomal protein S21e signature. / Ribosomal protein S26e / Ribosomal protein S26e superfamily / Ribosomal protein S26e / : / Ribosomal protein S12e signature. / Ribosomal protein S12e / Ribosomal protein L29e / Ribosomal L29e protein family / Ribosomal protein S19e, conserved site / Ribosomal protein S19e signature. / Ribosomal protein S5, eukaryotic/archaeal / Small (40S) ribosomal subunit Asc1/RACK1 / Ribosomal protein S21e / Ribosomal protein S21e superfamily / Ribosomal protein S21e / Ribosomal protein S2, eukaryotic / Ribosomal protein L22e / Ribosomal protein L22e superfamily / Ribosomal L22e protein family / Ribosomal protein L27e, conserved site / Ribosomal protein L27e signature. / Ribosomal protein L10e, conserved site / Ribosomal protein L10e signature. / S27a-like superfamily / Ribosomal protein L38e / Ribosomal protein L38e superfamily / Ribosomal L38e protein family / Ribosomal protein L10e / 40S Ribosomal protein S10 / : / Ribosomal protein L44e signature. / Ribosomal protein S7e signature. / Ribosomal protein L24e, conserved site / Ribosomal protein L24e signature. / Ribosomal protein L19/L19e conserved site / Ribosomal protein L19, eukaryotic / Ribosomal protein L19e signature. / Plectin/S10, N-terminal / Plectin/S10 domain / : / 60S ribosomal protein L18a/ L20, eukaryotes / Ribosomal protein L6e signature. / Ribosomal protein S10, eukaryotic/archaeal / Ribosomal protein S8e subdomain, eukaryotes / : / Ribosomal protein S17e, conserved site / Ribosomal protein S17e signature. / Ribosomal protein S25 / S25 ribosomal protein / Ribosomal protein L44e / Ribosomal protein S3Ae, conserved site / Ribosomal protein L44 / Ribosomal protein S3Ae signature. / Ribosomal protein S30 / Ribosomal protein S30 / Ribosomal protein S27a / Ribosomal protein L34e, conserved site / Ribosomal protein S27a / Ribosomal protein L34e signature. / Ribosomal protein S27a / Ribosomal protein S2, eukaryotic/archaeal / Ribosomal protein L5 eukaryotic, C-terminal / 50S ribosomal protein L18Ae/60S ribosomal protein L20 and L18a / Ribosomal L18 C-terminal region / Ribosomal L40e family / Ribosomal protein 50S-L18Ae/60S-L20/60S-L18A / Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A
Similarity search - Domain/homology
N-acetyl-L-phenylalanine / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / : / : / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) ...N-acetyl-L-phenylalanine / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / : / : / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS4A / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein eL24A / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein eL39 / Large ribosomal subunit protein uL30A / Large ribosomal subunit protein uL6A / Large ribosomal subunit protein uL22A / Large ribosomal subunit protein uL24A / Large ribosomal subunit protein eL33A / Large ribosomal subunit protein eL36A / Large ribosomal subunit protein eL29 / Large ribosomal subunit protein eL15A / Large ribosomal subunit protein eL22A / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein uS15 / Ubiquitin-ribosomal protein eS31 fusion protein / Small ribosomal subunit protein uS11A / Small ribosomal subunit protein eS19A / Small ribosomal subunit protein eS21A / Small ribosomal subunit protein uS8A / Large ribosomal subunit protein uL5A / Small ribosomal subunit protein eS28B / Large ribosomal subunit protein eL27A / Large ribosomal subunit protein eL31A / Ubiquitin-ribosomal protein eL40A fusion protein / Large ribosomal subunit protein eL20A / Large ribosomal subunit protein eL43B / Large ribosomal subunit protein eL42B / Small ribosomal subunit protein uS12A / Small ribosomal subunit protein eS24A / Small ribosomal subunit protein eS30A / Small ribosomal subunit protein eS4A / Small ribosomal subunit protein eS6A / Small ribosomal subunit protein eS8A / Large ribosomal subunit protein uL14A / Large ribosomal subunit protein uL2A / Small ribosomal subunit protein uS17A / Large ribosomal subunit protein eL18A / Small ribosomal subunit protein uS9A / Small ribosomal subunit protein uS13A / Large ribosomal subunit protein eL19A / Large ribosomal subunit protein uL29A / Small ribosomal subunit protein eS32B / Large ribosomal subunit protein uL4A / Putative major capsid protein p72 / Large ribosomal subunit protein uL3 / Small ribosomal subunit protein eS17B / Large ribosomal subunit protein eL8A / Small ribosomal subunit protein uS5 / Large ribosomal subunit protein uL18 / Small ribosomal subunit protein uS7 / Large ribosomal subunit protein uL13A / Small ribosomal subunit protein eS7A / Elongation factor 1 alpha-like protein / Small ribosomal subunit protein uS2A / Protein DOM34 / Small ribosomal subunit protein eS1A / Small ribosomal subunit protein eS27A / Large ribosomal subunit protein eL14A / Small ribosomal subunit protein RACK1 / Large ribosomal subunit protein eL32 / Small ribosomal subunit protein uS10 / Small ribosomal subunit protein eS26B / Small ribosomal subunit protein uS14A / Large ribosomal subunit protein uL16 / Small ribosomal subunit protein eS12 / Large ribosomal subunit protein eL37A / Large ribosomal subunit protein eL38 / Large ribosomal subunit protein eL34A / Small ribosomal subunit protein uS19 / Large ribosomal subunit protein eL6A / Large ribosomal subunit protein eL21A / Small ribosomal subunit protein eS10A / LPS-assembly protein LptD / Small ribosomal subunit protein eS25A
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsHilal, T. / Yamamoto, H. / Loerke, J. / Buerger, J. / Mielke, T. / Spahn, C.M.T.
Funding support Germany, 2items
OrganizationGrant numberCountry
German Research FoundationSFB740, FOR1805 Germany
HFSPRGP0062/2012 Germany
CitationJournal: Nat Commun / Year: 2016
Title: Structural insights into ribosomal rescue by Dom34 and Hbs1 at near-atomic resolution.
Authors: Tarek Hilal / Hiroshi Yamamoto / Justus Loerke / Jörg Bürger / Thorsten Mielke / Christian M T Spahn /
Abstract: The surveillance of mRNA translation is imperative for homeostasis. Monitoring the integrity of the message is essential, as the translation of aberrant mRNAs leads to stalling of the translational ...The surveillance of mRNA translation is imperative for homeostasis. Monitoring the integrity of the message is essential, as the translation of aberrant mRNAs leads to stalling of the translational machinery. During ribosomal rescue, arrested ribosomes are specifically recognized by the conserved eukaryotic proteins Dom34 and Hbs1, to initiate their recycling. Here we solve the structure of Dom34 and Hbs1 bound to a yeast ribosome programmed with a nonstop mRNA at 3.3 Å resolution using cryo-electron microscopy. The structure shows that Domain N of Dom34 is inserted into the upstream mRNA-binding groove via direct stacking interactions with conserved nucleotides of 18S rRNA. It senses the absence of mRNA at the A-site and part of the mRNA entry channel by direct competition. Thus, our analysis establishes the structural foundation for the recognition of aberrantly stalled 80S ribosomes by the Dom34·Hbs1·GTP complex during Dom34-mediated mRNA surveillance pathways.
History
DepositionOct 7, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 18, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 2, 2017Group: Data collection / Derived calculations
Category: em_software / pdbx_struct_conn_angle / struct_conn
Item: _em_software.name
Revision 1.2Feb 20, 2019Group: Data collection / Experimental preparation / Source and taxonomy
Category: em_admin / em_sample_support ...em_admin / em_sample_support / pdbx_database_proc / pdbx_entity_src_syn / pdbx_struct_ref_seq_depositor_info
Item: _em_admin.last_update / _pdbx_entity_src_syn.ncbi_taxonomy_id ..._em_admin.last_update / _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_scientific / _pdbx_struct_ref_seq_depositor_info.db_seq_one_letter_code
Revision 1.3May 15, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id

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Structure visualization

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Assembly

Deposited unit
A1: Protein DOM34
A2: 40S ribosomal protein S0-A
a2: 40S ribosomal protein S26-B
B2: 40S ribosomal protein S1-A
b2: 40S ribosomal protein S27-A
C2: 40S ribosomal protein S2
c2: 40S ribosomal protein S28-B
D2: 40S ribosomal protein S3
d2: 40S ribosomal protein S29-A
E2: 40S ribosomal protein S4-A
e2: 40S ribosomal protein S30-A
F2: 40S ribosomal protein S5
G2: 40S ribosomal protein S6-A
g2: Guanine nucleotide-binding protein subunit beta-like protein
H2: 40S ribosomal protein S7-A
I2: 40S ribosomal protein S8-A
J2: 40S ribosomal protein S9-A
K2: 40S ribosomal protein S10-A
L2: 40S ribosomal protein S11-A
M2: 40S ribosomal protein S12
N2: 40S ribosomal protein S13
O2: 40S ribosomal protein S14-A
P2: 40S ribosomal protein S15
Q2: 40S ribosomal protein S16-A
R2: 40S ribosomal protein S17-B
S2: 40S ribosomal protein S18-A
T2: 40S ribosomal protein S19-A
U2: 40S ribosomal protein S20
V2: 40S ribosomal protein S21-A
W2: 40S ribosomal protein S22-A
X2: 40S ribosomal protein S23-A
Y2: 40S ribosomal protein S24-A
Z2: 40S ribosomal protein S25-A
22: 18S ribosomal RNA
f2: Ubiquitin-40S ribosomal protein S31
14: 25S ribosomal RNA
34: 5S ribosomal RNA
44: 5.8S ribosomal RNA
a5: 60S ribosomal protein L28
A5: 60S ribosomal protein L2-A
b5: 60S ribosomal protein L29
B5: 60S ribosomal protein L3
c5: 60S ribosomal protein L30
C5: 60S ribosomal protein L4-A
D5: 60S ribosomal protein L5
d5: 60S ribosomal protein L31-A
e5: 60S ribosomal protein L32
f5: 60S ribosomal protein L33-A
F5: 60S ribosomal protein L7-A
g5: 60S ribosomal protein L34-A
G5: 60S ribosomal protein L8-A
h5: 60S ribosomal protein L35-A
H5: 60S ribosomal protein L9-A
i5: 60S ribosomal protein L36-A
I5: 60S ribosomal protein L10
J5: 60S ribosomal protein L11-A
j5: 60S ribosomal protein L37-A
k5: 60S ribosomal protein L38
l5: 60S ribosomal protein L39
L5: 60S ribosomal protein L13-A
m5: Ubiquitin-60S ribosomal protein L40
M5: 60S ribosomal protein L14-A
N5: 60S ribosomal protein L15-A
o5: 60S ribosomal protein L42-B
p5: 60S ribosomal protein L43-B
P5: 60S ribosomal protein L17-A
Q5: 60S ribosomal protein L18-A
S5: 60S ribosomal protein L20-A
U5: 60S ribosomal protein L22-A
V5: 60S ribosomal protein L23-A
Z5: 60S ribosomal protein L27-A
K5: 60S ribosomal protein L16-A
n5: 60S ribosomal protein L41-B
R5: 60S ribosomal protein L19-A
X5: 60S ribosomal protein L25
Y5: 60S ribosomal protein L26-A
T5: 60S ribosomal protein L21-A
E5: 60S ribosomal protein L6-A
W5: 60S ribosomal protein L24-A
A6: Protein HBS1
X7: nonstop mRNA
A3: yeast Phe-tRNA-Phe
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,195,2681150
Polymers3,168,30182
Non-polymers26,9671068
Water23413
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 5 types, 5 molecules A1g2f2m5A6

#1: Protein Protein DOM34


Mass: 43574.344 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Hexahistidine-tagged protein
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: DOM34, YNL001W, N2016 / Production host: Escherichia coli (E. coli)
References: UniProt: P33309, Hydrolases; Acting on ester bonds
#14: Protein Guanine nucleotide-binding protein subunit beta-like protein / Receptor for activated C kinase / Receptor of activated protein kinase C 1 / RACK1


Mass: 34710.023 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P38011
#35: Protein Ubiquitin-40S ribosomal protein S31


Mass: 8101.675 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P05759
#61: Protein Ubiquitin-60S ribosomal protein L40


Mass: 6032.321 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P0CH08
#80: Protein Protein HBS1


Mass: 68812.383 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Hexahistidine tagged protein
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: HBS1, YKR084C, YKR404 / Production host: Escherichia coli (E. coli) / References: UniProt: P32769

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40S ribosomal protein ... , 31 types, 31 molecules A2a2B2b2C2c2D2d2E2e2F2G2H2I2J2K2L2M2N2O2P2Q2R2S2T2U2V2W2X2Y2Z2

#2: Protein 40S ribosomal protein S0-A / Nucleic acid-binding protein NAB1A


Mass: 22940.188 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P32905
#3: Protein 40S ribosomal protein S26-B


Mass: 11151.117 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P39939
#4: Protein 40S ribosomal protein S1-A / RP10A


Mass: 24312.199 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P33442
#5: Protein 40S ribosomal protein S27-A / RP61 / YS20


Mass: 8762.195 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P35997
#6: Protein 40S ribosomal protein S2 / Omnipotent suppressor protein SUP44 / RP12 / S4 / YS5


Mass: 23212.979 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P25443
#7: Protein 40S ribosomal protein S28-B / S33 / YS27


Mass: 7116.281 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P0C0X0
#8: Protein 40S ribosomal protein S3 / RP13 / YS3


Mass: 24702.791 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P05750
#9: Protein 40S ribosomal protein S29-A / S36 / YS29


Mass: 6335.303 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P41057
#10: Protein 40S ribosomal protein S4-A / RP5 / S7 / YS6


Mass: 29338.133 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P0CX35
#11: Protein 40S ribosomal protein S30-A


Mass: 6779.086 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P0CX33
#12: Protein 40S ribosomal protein S5 / RP14 / S2 / YS8


Mass: 22908.338 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P26783
#13: Protein 40S ribosomal protein S6-A / RP9 / S10 / YS4


Mass: 25895.072 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P0CX37
#15: Protein 40S ribosomal protein S7-A / RP30 / RP40


Mass: 21000.492 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P26786
#16: Protein 40S ribosomal protein S8-A / RP19 / S14 / YS9


Mass: 22406.609 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P0CX39
#17: Protein 40S ribosomal protein S9-A / RP21 / S13 / YP28 / YS11


Mass: 21210.662 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: O13516
#18: Protein 40S ribosomal protein S10-A


Mass: 11571.100 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q08745
#19: Protein 40S ribosomal protein S11-A / RP41 / S18 / YS12


Mass: 17654.738 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P0CX47
#20: Protein 40S ribosomal protein S12


Mass: 13327.331 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P48589
#21: Protein 40S ribosomal protein S13 / S27a / YS15


Mass: 16928.748 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P05756
#22: Protein 40S ribosomal protein S14-A / RP59A


Mass: 13446.426 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P06367
#23: Protein 40S ribosomal protein S15 / RIG protein / RP52 / S21 / YS21


Mass: 14155.720 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q01855
#24: Protein 40S ribosomal protein S16-A / RP61R


Mass: 15659.216 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P0CX51
#25: Protein 40S ribosomal protein S17-B / RP51B


Mass: 14268.545 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P14127
#26: Protein 40S ribosomal protein S18-A


Mass: 16940.443 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P0CX55
#27: Protein 40S ribosomal protein S19-A / RP55A / S16a / YP45 / YS16A


Mass: 15810.930 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P07280
#28: Protein 40S ribosomal protein S20


Mass: 12190.175 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P38701
#29: Protein 40S ribosomal protein S21-A / S26 / YS25


Mass: 9758.829 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P0C0V8
#30: Protein 40S ribosomal protein S22-A / RP50 / S24 / YP58 / YS22


Mass: 14518.867 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P0C0W1
#31: Protein 40S ribosomal protein S23-A / RP37 / S28 / YS14


Mass: 15942.699 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P0CX29
#32: Protein 40S ribosomal protein S24-A / RP50


Mass: 15231.650 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P0CX31
#33: Protein 40S ribosomal protein S25-A / RP45 / S31 / YS23


Mass: 8001.377 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q3E792

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RNA chain , 6 types, 6 molecules 22143444X7A3

#34: RNA chain 18S ribosomal RNA


Mass: 579126.562 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: GenBank: 874346701
#36: RNA chain 25S ribosomal RNA


Mass: 1097493.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: GenBank: 834774822
#37: RNA chain 5S ribosomal RNA


Mass: 38951.105 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: GenBank: 1039024045
#38: RNA chain 5.8S ribosomal RNA


Mass: 50682.922 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: GenBank: 1102645687
#81: RNA chain nonstop mRNA


Mass: 6494.952 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthetic mRNA / Source: (synth.) synthetic construct (others)
#82: RNA chain yeast Phe-tRNA-Phe


Mass: 24890.121 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: N-acetylated Phe-tRNA / Source: (natural) Saccharomyces cerevisiae (brewer's yeast)

+
60S ribosomal protein ... , 40 types, 40 molecules a5A5b5B5c5C5D5d5e5f5F5g5G5h5H5i5I5J5j5k5l5L5M5N5o5p5P5Q5S5U5...

#39: Protein 60S ribosomal protein L28 / L27a / L29 / RP44 / RP62 / YL24


Mass: 16630.471 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P02406
#40: Protein 60S ribosomal protein L2-A / L5 / RP8 / YL6


Mass: 27217.289 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P0CX45
#41: Protein 60S ribosomal protein L29 / YL43


Mass: 6560.688 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P05747
#42: Protein 60S ribosomal protein L3 / Maintenance of killer protein 8 / RP1 / Trichodermin resistance protein / YL1


Mass: 43719.602 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P14126
#43: Protein 60S ribosomal protein L30 / L32 / RP73 / YL38


Mass: 10558.344 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P14120
#44: Protein 60S ribosomal protein L4-A / L2 / RP2 / YL2


Mass: 39027.926 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P10664
#45: Protein 60S ribosomal protein L5 / L1 / L1a / Ribosomal 5S RNA-binding protein / YL3


Mass: 33633.633 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P26321
#46: Protein 60S ribosomal protein L31-A / L34 / YL28


Mass: 12649.754 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P0C2H8
#47: Protein 60S ribosomal protein L32


Mass: 14478.054 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P38061
#48: Protein 60S ribosomal protein L33-A / L37 / RP47 / YL37


Mass: 12045.935 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P05744
#49: Protein 60S ribosomal protein L7-A / L6 / RP11 / YL8


Mass: 25240.377 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P05737
#50: Protein 60S ribosomal protein L34-A


Mass: 12608.831 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P87262
#51: Protein 60S ribosomal protein L8-A / L4 / L4-2 / L7a-1 / Maintenance of killer protein 7 / RP6 / YL5


Mass: 25814.998 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P17076
#52: Protein 60S ribosomal protein L35-A


Mass: 13811.444 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P0CX84
#53: Protein 60S ribosomal protein L9-A / L8 / RP24 / YL11


Mass: 21605.061 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P05738
#54: Protein 60S ribosomal protein L36-A / L39 / YL39


Mass: 11020.063 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P05745
#55: Protein 60S ribosomal protein L10 / L9 / Ubiquinol-cytochrome C reductase complex subunit VI-requiring protein


Mass: 25279.271 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P41805
#56: Protein 60S ribosomal protein L11-A / L16 / RP39 / YL22


Mass: 19266.082 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P0C0W9
#57: Protein 60S ribosomal protein L37-A / L43 / YL35 / YP55


Mass: 9746.199 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P49166
#58: Protein 60S ribosomal protein L38


Mass: 8714.363 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P49167
#59: Protein/peptide 60S ribosomal protein L39 / L46 / YL40


Mass: 6227.444 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P04650
#60: Protein 60S ribosomal protein L13-A


Mass: 21885.234 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q12690
#62: Protein 60S ribosomal protein L14-A


Mass: 14976.794 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P36105
#63: Protein 60S ribosomal protein L15-A / L13 / RP15R / YL10 / YP18


Mass: 24351.162 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P05748
#64: Protein 60S ribosomal protein L42-B / L41 / Maintenance of killer protein 18 / YL27 / YP44


Mass: 12115.462 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P0CX28
#65: Protein 60S ribosomal protein L43-B / L37a / YL35


Mass: 9981.756 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P0CX26
#66: Protein 60S ribosomal protein L17-A / L20A / YL17


Mass: 20458.322 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P05740
#67: Protein 60S ribosomal protein L18-A / RP28


Mass: 20478.059 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P0CX49
#68: Protein 60S ribosomal protein L20-A / L18a


Mass: 20478.852 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P0CX23
#69: Protein 60S ribosomal protein L22-A / L1c / RP4 / YL31


Mass: 11263.863 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P05749
#70: Protein 60S ribosomal protein L23-A / L17a / YL32


Mass: 14362.755 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P0CX41
#71: Protein 60S ribosomal protein L27-A


Mass: 15437.166 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P0C2H6
#72: Protein 60S ribosomal protein L16-A / L13a / L21 / RP22 / YL15


Mass: 22028.951 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P26784
#73: Protein/peptide 60S ribosomal protein L41-B / L47 / YL41


Mass: 3354.243 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P0CX87
#74: Protein 60S ribosomal protein L19-A / L23 / RP15L / RP33 / YL14


Mass: 21631.121 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P0CX82
#75: Protein 60S ribosomal protein L25 / RP16L / YL25 / YP42'


Mass: 13771.176 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P04456
#76: Protein 60S ribosomal protein L26-A / L33 / YL33


Mass: 14134.588 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P05743
#77: Protein 60S ribosomal protein L21-A


Mass: 18148.066 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q02753
#78: Protein 60S ribosomal protein L6-A / L17 / RP18 / YL16


Mass: 19869.369 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q02326
#79: Protein 60S ribosomal protein L24-A / L30 / RP29 / YL21


Mass: 11369.424 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P04449

-
Non-polymers , 5 types, 1081 molecules

#83: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#84: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1058 / Source method: obtained synthetically / Formula: Mg
#85: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER


Mass: 522.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O13P3
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM
#86: Chemical ChemComp-5CR / N-acetyl-L-phenylalanine


Type: L-peptide linking / Mass: 207.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H13NO3
#87: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 13 / 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

ComponentName: Nonstop ribosomal complex bound with Dom34-Hbs1-GMPPNP
Type: RIBOSOME / Entity ID: #1-#82 / Source: MULTIPLE SOURCES
Molecular weightValue: 3.6 MDa / Experimental value: NO
Buffer solutionpH: 7.6
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

-
Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
MicroscopyModel: FEI POLARA 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 80645 X / Nominal defocus max: 4500 nm / Nominal defocus min: 500 nm / Cs: 2 mm
Specimen holderCryogen: NITROGEN
Image recordingAverage exposure time: 5 sec. / Electron dose: 25 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of real images: 4797
Image scansMovie frames/image: 25 / Used frames/image: 1-25

-
Processing

SoftwareName: PHENIX / Version: dev_2415: / Classification: refinement
EM software
IDNameVersionCategory
2Leginon3.1image acquisition
4SPIDER14CTF correction
5CTFFIND4CTF correction
8UCSF Chimeramodel fitting
9Cootmodel fitting
11SPIDER14initial Euler assignment
12FREALIGN9.11final Euler assignment
13RELION1.4classification
14FREALIGN9.113D reconstruction
15PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 520612
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 73391 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
RefinementHighest resolution: 3.3 Å
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.011228976
ELECTRON MICROSCOPYf_angle_d0.649335579
ELECTRON MICROSCOPYf_dihedral_angle_d12.82150647
ELECTRON MICROSCOPYf_chiral_restr0.03741997
ELECTRON MICROSCOPYf_plane_restr0.00622339

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