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- PDB-7zpq: Structure of the RQT-bound 80S ribosome from S. cerevisiae (C1) -

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Entry
Database: PDB / ID: 7zpq
TitleStructure of the RQT-bound 80S ribosome from S. cerevisiae (C1)
Components
  • (40S ribosomal protein ...) x 22
  • (60S ribosomal protein ...) x 33
  • 18S ribosomal RNA
  • 25S ribosomal RNA
  • 5.8S ribosomal RNA
  • 5S ribosomal RNA
  • Guanine nucleotide-binding protein subunit beta-like protein
  • RPL10 isoform 1
  • RPL11B isoform 1
  • RPL24A isoform 1
  • RPL32 isoform 1
  • RPL38 isoform 1
  • RPL41A isoform 1
  • RPL4A isoform 1
  • RPL5 isoform 1
  • RPS15 isoform 1
  • RPS2 isoform 1
  • RPS20 isoform 1
  • RPS22A isoform 1
  • RPS26B isoform 1
  • RPS28A isoform 1
  • RPS29A isoform 1
  • RPS3 isoform 1
  • RPS31 isoform 1
  • RQC trigger complex subunit CUE3
  • RQT4 isoform 1
  • Rps5p
  • SLH1 isoform 1
  • tRNA
KeywordsRIBOSOME / collision / RNA binding / RQT / RQC
Function / homology
Function and homology information


: / primary metabolic process / ribosomal subunit / regulation of amino acid metabolic process / negative regulation of glucose mediated signaling pathway / ribosome disassembly / mTORC1-mediated signalling / Protein hydroxylation / ribosome-associated ubiquitin-dependent protein catabolic process / pre-mRNA 5'-splice site binding ...: / primary metabolic process / ribosomal subunit / regulation of amino acid metabolic process / negative regulation of glucose mediated signaling pathway / ribosome disassembly / mTORC1-mediated signalling / Protein hydroxylation / ribosome-associated ubiquitin-dependent protein catabolic process / pre-mRNA 5'-splice site binding / GDP-dissociation inhibitor activity / K63-linked polyubiquitin modification-dependent protein binding / nonfunctional rRNA decay / Formation of the ternary complex, and subsequently, the 43S complex / Translation initiation complex formation / response to cycloheximide / Ribosomal scanning and start codon recognition / cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / Major pathway of rRNA processing in the nucleolus and cytosol / mRNA destabilization / SRP-dependent cotranslational protein targeting to membrane / GTP hydrolysis and joining of the 60S ribosomal subunit / negative regulation of mRNA splicing, via spliceosome / preribosome, large subunit precursor / 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) / positive regulation of protein kinase activity / negative regulation of translational frameshifting / L13a-mediated translational silencing of Ceruloplasmin expression / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / G-protein alpha-subunit binding / ribosomal large subunit export from nucleus / 90S preribosome / regulation of translational fidelity / ribosomal subunit export from nucleus / protein-RNA complex assembly / maturation of LSU-rRNA / 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) / translation regulator activity / rescue of stalled cytosolic ribosome / cytosolic ribosome / cellular response to amino acid starvation / protein kinase C binding / ubiquitin binding / ribosomal large subunit biogenesis / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / positive regulation of apoptotic signaling pathway / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / macroautophagy / maturation of SSU-rRNA / translational initiation / small-subunit processome / helicase activity / maintenance of translational fidelity / modification-dependent protein catabolic process / protein tag activity / cytoplasmic stress granule / rRNA processing / ribosome biogenesis / ribosome binding / ribosomal small subunit biogenesis / ribosomal small subunit assembly / 5S rRNA binding / ribosomal large subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / gene expression / cytosolic large ribosomal subunit / nucleic acid binding / cytoplasmic translation / negative regulation of translation / rRNA binding / protein ubiquitination / structural constituent of ribosome / hydrolase activity / ribosome / translation / G protein-coupled receptor signaling pathway / ribonucleoprotein complex / negative regulation of gene expression / response to antibiotic / mRNA binding / ubiquitin protein ligase binding / regulation of DNA-templated transcription / nucleolus / mitochondrion / RNA binding / zinc ion binding / nucleoplasm / ATP binding / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
CUE domain-containing protein 3, CUE domain / : / Zinc finger, C2HC5-type / Activating signal cointegrator 1-like / Putative zinc finger motif, C2HC5-type / CUE domain / Domain that may be involved in binding ubiquitin-conjugating enzymes (UBCs) / Ubiquitin system component CUE / CUE domain profile. / Sec63 Brl domain ...CUE domain-containing protein 3, CUE domain / : / Zinc finger, C2HC5-type / Activating signal cointegrator 1-like / Putative zinc finger motif, C2HC5-type / CUE domain / Domain that may be involved in binding ubiquitin-conjugating enzymes (UBCs) / Ubiquitin system component CUE / CUE domain profile. / Sec63 Brl domain / Sec63 domain / Sec63 Brl domain / : / : / Ribosomal protein S26e signature. / Ribosomal protein L41 / Ribosomal protein L41 / Ribosomal protein S21e, conserved site / Ribosomal protein S21e signature. / Ribosomal protein L13e, conserved site / Ribosomal protein L13e signature. / Ribosomal protein S26e / Ribosomal protein S26e superfamily / Ribosomal protein S26e / : / Ribosomal protein S12e signature. / Ribosomal protein L29e / Ribosomal L29e protein family / Ribosomal protein S12e / Ribosomal protein L27e, conserved site / Small (40S) ribosomal subunit Asc1/RACK1 / Ribosomal protein L27e signature. / Ribosomal protein S5, eukaryotic/archaeal / Ribosomal protein L22e / Ribosomal protein L22e superfamily / Ribosomal L22e protein family / Ribosomal protein S21e / Ribosomal protein S21e superfamily / Ribosomal protein S21e / Ribosomal protein S19e, conserved site / Ribosomal protein S19e signature. / Ribosomal protein S2, eukaryotic / Ribosomal protein L38e / Ribosomal protein L38e superfamily / Ribosomal L38e protein family / Ribosomal protein L13e / Ribosomal protein L13e / Ribosomal protein L19, eukaryotic / Ribosomal protein L10e, conserved site / Ribosomal protein L10e signature. / S27a-like superfamily / Ribosomal protein L44e signature. / Ribosomal protein L19/L19e conserved site / 40S Ribosomal protein S10 / Ribosomal protein L19e signature. / Ribosomal protein L24e, conserved site / : / Ribosomal protein L24e signature. / 60S ribosomal protein L18a/ L20, eukaryotes / Ribosomal protein L10e / Ribosomal protein L6e signature. / Plectin/S10, N-terminal / Plectin/S10 domain / Ribosomal protein L18/L18-A/B/e, conserved site / Ribosomal protein L18e signature. / Ribosomal protein L34e, conserved site / Ribosomal protein L34e signature. / : / Ribosomal protein L5 eukaryotic, C-terminal / Ribosomal L18 C-terminal region / Ribosomal protein S10, eukaryotic/archaeal / Ribosomal L40e family / Ribosomal protein L23/L25, N-terminal / Ribosomal protein L23, N-terminal domain / Ribosomal protein S30 / : / Ribosomal protein S30 / Ribosomal protein L44e / Ribosomal protein L44 / Ribosomal protein S7e signature. / Ribosomal protein S25 / 50S ribosomal protein L18Ae/60S ribosomal protein L20 and L18a / S25 ribosomal protein / Ribosomal protein L30e signature 1. / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein L40e superfamily / Ribosomal protein L36e signature. / Ribosomal protein 50S-L18Ae/60S-L20/60S-L18A / Ribosomal protein S8e subdomain, eukaryotes / Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A / Ribosomal protein 60S L18 and 50S L18e / Ribosomal protein S27a / Ribosomal protein S17e, conserved site / Ribosomal protein S27a / Ribosomal protein S17e signature. / Ribosomal protein S27a / Ribosomal protein L35Ae, conserved site / Ribosomal protein L35Ae signature. / Eukaryotic Ribosomal Protein L27, KOW domain
Similarity search - Domain/homology
: / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Rps5p / Small ribosomal subunit protein eS1 / RPS22A isoform 1 ...: / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Rps5p / Small ribosomal subunit protein eS1 / RPS22A isoform 1 / RPS31 isoform 1 / RPL38 isoform 1 / RPL10 isoform 1 / RPS29A isoform 1 / RPS20 isoform 1 / RPS2 isoform 1 / 60S ribosomal protein L29 / RPL24A isoform 1 / RPL11B isoform 1 / 40S ribosomal protein S25 / 40S ribosomal protein S26 / RPL5 isoform 1 / 40S ribosomal protein S8 / RPL32 isoform 1 / 40S ribosomal protein S3 / RPL4A isoform 1 / Large ribosomal subunit protein uL3 / RPS15 isoform 1 / RPS28A isoform 1 / 40S ribosomal protein S12 / RQT4 isoform 1 / SLH1 isoform 1 / 60S ribosomal protein L41 / Small ribosomal subunit protein uS2A / Small ribosomal subunit protein uS4A / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein eL39 / Large ribosomal subunit protein uL30A / Large ribosomal subunit protein uL6A / Large ribosomal subunit protein eL6B / Large ribosomal subunit protein uL22A / Large ribosomal subunit protein uL24A / Large ribosomal subunit protein eL33A / Large ribosomal subunit protein eL36A / Large ribosomal subunit protein eL15A / Large ribosomal subunit protein eL22A / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein eS19A / Small ribosomal subunit protein eS21A / 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 eL43A / Large ribosomal subunit protein eL42A / 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 / 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 / Large ribosomal subunit protein eL30 / Small ribosomal subunit protein eS17B / Large ribosomal subunit protein eL8A / Large ribosomal subunit protein uL13A / Small ribosomal subunit protein eS7A / Small ribosomal subunit protein eS27A / Large ribosomal subunit protein eL14A / Small ribosomal subunit protein RACK1 / Small ribosomal subunit protein uS11B / Large ribosomal subunit protein eL37A / RQC trigger complex subunit CUE3 / Large ribosomal subunit protein eL34A / Large ribosomal subunit protein eL21A / Small ribosomal subunit protein eS10A / Large ribosomal subunit protein eL13A
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.47 Å
AuthorsBest, K.M. / Ikeuchi, K. / Kater, L. / Best, D.M. / Musial, J. / Matsuo, Y. / Berninghausen, O. / Becker, T. / Inada, T. / Beckmann, R.
Funding supportEuropean Union, Germany, 3items
OrganizationGrant numberCountry
European Research Council (ERC)885711European Union
German Research Foundation (DFG)BE 1814/15-1 Germany
German Research Foundation (DFG)RTG1721 Germany
Citation
Journal: Nat Commun / Year: 2023
Title: Structural basis for clearing of ribosome collisions by the RQT complex.
Authors: Katharina Best / Ken Ikeuchi / Lukas Kater / Daniel Best / Joanna Musial / Yoshitaka Matsuo / Otto Berninghausen / Thomas Becker / Toshifumi Inada / Roland Beckmann /
Abstract: Translation of aberrant messenger RNAs can cause stalling of ribosomes resulting in ribosomal collisions. Collided ribosomes are specifically recognized to initiate stress responses and quality ...Translation of aberrant messenger RNAs can cause stalling of ribosomes resulting in ribosomal collisions. Collided ribosomes are specifically recognized to initiate stress responses and quality control pathways. Ribosome-associated quality control facilitates the degradation of incomplete translation products and requires dissociation of the stalled ribosomes. A central event is therefore the splitting of collided ribosomes by the ribosome quality control trigger complex, RQT, by an unknown mechanism. Here we show that RQT requires accessible mRNA and the presence of a neighboring ribosome. Cryogenic electron microscopy of RQT-ribosome complexes reveals that RQT engages the 40S subunit of the lead ribosome and can switch between two conformations. We propose that the Ski2-like helicase 1 (Slh1) subunit of RQT applies a pulling force on the mRNA, causing destabilizing conformational changes of the small ribosomal subunit, ultimately resulting in subunit dissociation. Our findings provide conceptual framework for a helicase-driven ribosomal splitting mechanism.
#1: Journal: Acta Crystallogr D Struct Biol / Year: 2018
Title: Real-space refinement in PHENIX for cryo-EM and crystallography.
Authors: Afonine, P.V. / Poon, B.K. / Read, R.J. / Sobolev, O.V. / Terwilliger, T.C. / Urzhumtsev, A. / Adams, P.D.
History
DepositionApr 28, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 22, 2023Provider: repository / Type: Initial release
Revision 1.1Mar 1, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Jul 24, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond / em_admin / Item: _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
2: 18S ribosomal RNA
3: 5.8S ribosomal RNA
4: 5S ribosomal RNA
5: 25S ribosomal RNA
6: tRNA
AA: 40S ribosomal protein S0-A
AB: 40S ribosomal protein S1
AC: RPS2 isoform 1
AD: RPS3 isoform 1
AE: 40S ribosomal protein S4-A
AF: Rps5p
AG: 40S ribosomal protein S6-A
AH: 40S ribosomal protein S7-A
AI: 40S ribosomal protein S8
AJ: 40S ribosomal protein S9-A
AK: 40S ribosomal protein S10-A
AL: 40S ribosomal protein S11-A
AM: 40S ribosomal protein S12
AN: 40S ribosomal protein S13
AO: 40S ribosomal protein S14-B
AP: RPS15 isoform 1
AQ: 40S ribosomal protein S16-A
AR: 40S ribosomal protein S17-B
AS: 40S ribosomal protein S18-A
AT: 40S ribosomal protein S19-A
AU: RPS20 isoform 1
AV: 40S ribosomal protein S21-A
AW: RPS22A isoform 1
AX: 40S ribosomal protein S23-A
AY: 40S ribosomal protein S24-A
AZ: 40S ribosomal protein S25
Aa: RPS26B isoform 1
Ab: 40S ribosomal protein S27-A
Ac: RPS28A isoform 1
Ad: RPS29A isoform 1
Ae: 40S ribosomal protein S30-A
Af: RPS31 isoform 1
Ag: Guanine nucleotide-binding protein subunit beta-like protein
BA: 60S ribosomal protein L2-A
BB: 60S ribosomal protein L3
BC: RPL4A isoform 1
BD: RPL5 isoform 1
BE: 60S ribosomal protein L6-B
BF: 60S ribosomal protein L7-A
BG: 60S ribosomal protein L8-A
BH: 60S ribosomal protein L9-A
BI: RPL10 isoform 1
BJ: RPL11B isoform 1
BK: 60S ribosomal protein L13-A
BL: 60S ribosomal protein L14-A
BM: 60S ribosomal protein L15-A
BN: 60S ribosomal protein L16-A
BO: 60S ribosomal protein L17-A
BP: 60S ribosomal protein L18-A
BQ: 60S ribosomal protein L19-A
BR: 60S ribosomal protein L20-A
BS: 60S ribosomal protein L21-A
BT: 60S ribosomal protein L22-A
BU: 60S ribosomal protein L23-A
BV: RPL24A isoform 1
BW: 60S ribosomal protein L25
BX: 60S ribosomal protein L26-A
BY: 60S ribosomal protein L27-A
BZ: 60S ribosomal protein L28
Ba: 60S ribosomal protein L29
Bb: 60S ribosomal protein L30
Bc: 60S ribosomal protein L31-A
Bd: RPL32 isoform 1
Be: 60S ribosomal protein L33-A
Bf: 60S ribosomal protein L34-A
Bg: 60S ribosomal protein L35-A
Bh: 60S ribosomal protein L36-A
Bi: 60S ribosomal protein L37-A
Bj: RPL38 isoform 1
Bk: 60S ribosomal protein L39
Bl: 60S ribosomal protein L40-A
Bm: RPL41A isoform 1
Bn: 60S ribosomal protein L42-A
Bo: 60S ribosomal protein L43-A
CA: SLH1 isoform 1
CB: RQC trigger complex subunit CUE3
CC: RQT4 isoform 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,377,263177
Polymers3,374,58582
Non-polymers2,67995
Water00
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 , 5 types, 5 molecules 23456

#1: 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: 1329886537
#2: 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: 1331532632
#3: 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: 1329886537
#4: 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)
#5: RNA chain tRNA


Mass: 24445.512 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: GenBank: 176436

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40S ribosomal protein ... , 22 types, 22 molecules AAABAEAGAHAIAJAKALAMANAOAQARASATAVAXAYAZAbAe

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


Mass: 22811.074 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: RM11-1a / References: UniProt: B3LI22
#7: Protein 40S ribosomal protein S1


Mass: 28798.467 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5PRY4
#10: Protein 40S ribosomal protein S4-A / RP5 / S7 / Small ribosomal subunit protein eS4-A / YS6


Mass: 29167.926 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P0CX35
#12: Protein 40S ribosomal protein S6-A / RP9 / S10 / Small ribosomal subunit protein eS6-A / YS4


Mass: 26181.445 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P0CX37
#13: Protein 40S ribosomal protein S7-A / RP30 / RP40 / Small ribosomal subunit protein eS7-A


Mass: 21000.492 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P26786
#14: Protein 40S ribosomal protein S8


Mass: 22537.803 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5Q1H1
#15: Protein 40S ribosomal protein S9-A / RP21 / S13 / Small ribosomal subunit protein uS4-A / YP28 / YS11


Mass: 21081.549 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c / References: UniProt: O13516
#16: Protein 40S ribosomal protein S10-A / Small ribosomal subunit protein eS10-A


Mass: 11042.562 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c / References: UniProt: Q08745
#17: Protein 40S ribosomal protein S11-A / RP41 / S18 / Small ribosomal subunit protein uS17-A / YS12


Mass: 16460.330 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P0CX47
#18: Protein 40S ribosomal protein S12


Mass: 13028.008 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5Q8I3
#19: Protein 40S ribosomal protein S13 / S27a / Small ribosomal subunit protein uS15 / YS15


Mass: 16928.748 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P05756
#20: Protein 40S ribosomal protein S14-B / RP59B / Small ribosomal subunit protein uS11-B


Mass: 13446.426 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P39516
#22: Protein 40S ribosomal protein S16-A / RP61R / Small ribosomal subunit protein uS9-A


Mass: 15659.216 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P0CX51
#23: Protein 40S ribosomal protein S17-B / RP51B / Small ribosomal subunit protein eS17-B


Mass: 15820.413 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P14127
#24: Protein 40S ribosomal protein S18-A / Small ribosomal subunit protein uS13-A


Mass: 16940.443 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P0CX55
#25: Protein 40S ribosomal protein S19-A / RP55A / S16a / Small ribosomal subunit protein eS19-A / YP45 / YS16A


Mass: 15810.930 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P07280
#27: Protein 40S ribosomal protein S21-A / S26 / Small ribosomal subunit protein eS21-A / YS25


Mass: 9758.829 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P0C0V8
#29: Protein 40S ribosomal protein S23-A / RP37 / S28 / Small ribosomal subunit protein uS12-A / YS14


Mass: 15942.699 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P0CX29
#30: Protein 40S ribosomal protein S24-A / RP50 / Small ribosomal subunit protein eS24-A


Mass: 15231.650 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P0CX31
#31: Protein 40S ribosomal protein S25


Mass: 9540.301 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5PZ18
#33: Protein 40S ribosomal protein S27-A / RP61 / Small ribosomal subunit protein eS27-A / YS20


Mass: 8762.195 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P35997
#36: Protein 40S ribosomal protein S30-A / Small ribosomal subunit protein eS30-A


Mass: 6779.086 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P0CX33

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Protein , 21 types, 21 molecules ACADAFAPAUAWAaAcAdAfAgBCBDBIBJBVBdBjCACBCC

#8: Protein RPS2 isoform 1


Mass: 23084.850 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5PWF7
#9: Protein RPS3 isoform 1


Mass: 24631.713 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5Q3Q1
#11: Protein Rps5p


Mass: 22908.338 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A1L4AA68
#21: Protein RPS15 isoform 1


Mass: 13265.591 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5Q6F2
#26: Protein RPS20 isoform 1


Mass: 11363.321 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5PVE9
#28: Protein RPS22A isoform 1


Mass: 14518.867 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5PSE9
#32: Protein RPS26B isoform 1


Mass: 11022.989 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5Q0E8
#34: Protein RPS28A isoform 1


Mass: 7116.281 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5Q700
#35: Protein RPS29A isoform 1


Mass: 6335.303 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5PV92
#37: Protein RPS31 isoform 1


Mass: 8388.049 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5PU37
#38: Protein Guanine nucleotide-binding protein subunit beta-like protein / Receptor for activated C kinase / Receptor of activated protein kinase C 1 / RACK1 / Small ...Receptor for activated C kinase / Receptor of activated protein kinase C 1 / RACK1 / Small ribosomal subunit protein RACK1


Mass: 34151.484 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P38011
#41: Protein RPL4A isoform 1


Mass: 39027.926 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5Q3W0
#42: Protein RPL5 isoform 1


Mass: 33415.387 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5Q0W8
#47: Protein RPL10 isoform 1


Mass: 25080.062 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5PUZ5
#48: Protein RPL11B isoform 1


Mass: 19266.082 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5PYM2
#60: Protein RPL24A isoform 1


Mass: 14617.215 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5PY83
#68: Protein RPL32 isoform 1


Mass: 14478.054 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5Q1M9
#74: Protein RPL38 isoform 1


Mass: 8714.363 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5PUL8
#80: Protein SLH1 isoform 1


Mass: 225127.078 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: SLH1, GI527_G0002706 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A8H8UL01
#81: Protein RQC trigger complex subunit CUE3 / CUE domain-containing protein 3 / Coupling of ubiquitin conjugation to ER degradation protein 3


Mass: 34241.949 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: CUE3, RQT3, YGL110C, G3060 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P53137
#82: Protein RQT4 isoform 1


Mass: 60903.078 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: RQT4, GI527_G0003667 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A8H4C0K6

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60S ribosomal protein ... , 33 types, 33 molecules BABBBEBFBGBHBKBLBMBNBOBPBQBRBSBTBUBWBXBYBZBaBbBcBeBfBgBhBiBk...

#39: Protein 60S ribosomal protein L2-A / L5 / Large ribosomal subunit protein uL2-A / RP8 / YL6


Mass: 27089.158 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P0CX45
#40: Protein 60S ribosomal protein L3


Mass: 43719.602 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5Q627
#43: Protein 60S ribosomal protein L6-B / L17 / Large ribosomal subunit protein eL6-B / RP18 / YL16


Mass: 20042.578 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P05739
#44: Protein 60S ribosomal protein L7-A / L6 / Large ribosomal subunit protein uL30-A / RP11 / YL8


Mass: 25240.377 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P05737
#45: Protein 60S ribosomal protein L8-A / L4 / L4-2 / L7a-1 / Large ribosomal subunit protein eL8-A / 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) / Strain: ATCC 204508 / S288c / References: UniProt: P17076
#46: Protein 60S ribosomal protein L9-A / L8 / Large ribosomal subunit protein uL6-A / RP24 / YL11


Mass: 21605.061 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P05738
#49: Protein 60S ribosomal protein L13-A / Large ribosomal subunit protein eL13-A


Mass: 21885.234 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c / References: UniProt: Q12690
#50: Protein 60S ribosomal protein L14-A / Large ribosomal subunit protein eL14-A


Mass: 14976.794 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P36105
#51: Protein 60S ribosomal protein L15-A / L13 / Large ribosomal subunit protein eL15-A / 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) / Strain: ATCC 204508 / S288c / References: UniProt: P05748
#52: Protein 60S ribosomal protein L16-A / L13a / L21 / Large ribosomal subunit protein uL13-A / RP22 / YL15


Mass: 22028.951 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P26784
#53: Protein 60S ribosomal protein L17-A / L20A / Large ribosomal subunit protein uL22-A / YL17


Mass: 20458.322 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P05740
#54: Protein 60S ribosomal protein L18-A / Large ribosomal subunit protein eL18-A / RP28


Mass: 20478.059 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P0CX49
#55: Protein 60S ribosomal protein L19-A / L23 / Large ribosomal subunit protein eL19-A / 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) / Strain: ATCC 204508 / S288c / References: UniProt: P0CX82
#56: Protein 60S ribosomal protein L20-A / L18a / Large ribosomal subunit protein eL20-A


Mass: 20347.654 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P0CX23
#57: Protein 60S ribosomal protein L21-A / Large ribosomal subunit protein eL21-A


Mass: 18148.066 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c / References: UniProt: Q02753
#58: Protein 60S ribosomal protein L22-A / L1c / Large ribosomal subunit protein eL22-A / RP4 / YL31


Mass: 11263.863 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P05749
#59: Protein 60S ribosomal protein L23-A / L17a / Large ribosomal subunit protein uL14-A / YL32


Mass: 14362.755 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P0CX41
#61: Protein 60S ribosomal protein L25 / Large ribosomal subunit protein uL23 / 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) / Strain: ATCC 204508 / S288c / References: UniProt: P04456
#62: Protein 60S ribosomal protein L26-A / L33 / Large ribosomal subunit protein uL24-A / YL33


Mass: 14005.475 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P05743
#63: Protein 60S ribosomal protein L27-A / Large ribosomal subunit protein eL27-A


Mass: 15437.166 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: AKFLKAGKVAVVVRGRYAGKKVVIVKPHDEGSKSHPFGHALVAGIERYPLKVTKKHGAKKVAKRTKIKPF IKVVNYNHLLPTRYTLDVEAFKSVVSTETFEQPSQREEAKKVVKKAFEERHQAGKNQWFFSKLRF
Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P0C2H6
#64: Protein 60S ribosomal protein L28 / L27a / L29 / Large ribosomal subunit protein uL15 / 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) / Strain: ATCC 204508 / S288c / References: UniProt: P02406
#65: Protein 60S ribosomal protein L29


Mass: 6560.688 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5PWR1
#66: Protein 60S ribosomal protein L30 / L32 / Large ribosomal subunit protein eL30 / RP73 / YL38


Mass: 10487.266 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P14120
#67: Protein 60S ribosomal protein L31-A / L34 / Large ribosomal subunit protein eL31-A / YL28


Mass: 12649.754 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P0C2H8
#69: Protein 60S ribosomal protein L33-A / L37 / Large ribosomal subunit protein eL33-A / RP47 / YL37


Mass: 12045.935 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P05744
#70: Protein 60S ribosomal protein L34-A / Large ribosomal subunit protein eL34-A


Mass: 12608.831 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P87262
#71: Protein 60S ribosomal protein L35-A / Large ribosomal subunit protein uL29-A


Mass: 13811.444 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P0CX84
#72: Protein 60S ribosomal protein L36-A / L39 / Large ribosomal subunit protein eL36-A / YL39


Mass: 11020.063 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P05745
#73: Protein 60S ribosomal protein L37-A / L43 / Large ribosomal subunit protein eL37-A / YL35 / YP55


Mass: 9588.045 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P49166
#75: Protein/peptide 60S ribosomal protein L39 / L46 / Large ribosomal subunit protein eL39 / YL40


Mass: 6227.444 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P04650
#76: Protein 60S ribosomal protein L40-A / CEP52 / Large ribosomal subunit protein eL40-A


Mass: 6032.321 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P0CH08
#78: Protein 60S ribosomal protein L42-A / L41 / Large ribosomal subunit protein eL42-A / YL27 / YP44


Mass: 11840.159 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P0CX27
#79: Protein 60S ribosomal protein L43-A / L37a / Large ribosomal subunit protein eL43-A / YL35


Mass: 9981.756 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P0CX25

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Protein/peptide , 1 types, 1 molecules Bm

#77: Protein/peptide RPL41A isoform 1 / RPL41B isoform 1


Mass: 3354.243 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A8H8UMB4

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Non-polymers , 2 types, 95 molecules

#83: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 86 / Source method: obtained synthetically / Formula: Mg
#84: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Zn

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Details

Has ligand of interestN

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Experimental details

-
Experiment

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

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1ribosome with bound RQT components (Slh1, Cue3 and Rqt4)RIBOSOME#1-#820NATURAL
2RQT complex (Slh1, Cue3 and Rqt4)COMPLEX#80-#821RECOMBINANT
3ribosomeCOMPLEX#1-#791NATURAL
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
11Saccharomyces cerevisiae (brewer's yeast)4932
22Saccharomyces cerevisiae (brewer's yeast)4932
33Saccharomyces cerevisiae (brewer's yeast)4932
Source (recombinant)Organism: Saccharomyces cerevisiae (brewer's yeast)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid type: Quantifoil R3/3
VitrificationInstrument: FEI VITROBOT MARK II / Cryogen name: ETHANE

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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: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 43.6 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

Software
NameVersionClassificationNB
phenix.real_space_refine1.19.1_4122refinement
PHENIX1.19.1_4122refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.47 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 194186 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 22.14 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.003233781
ELECTRON MICROSCOPYf_angle_d0.5562341585
ELECTRON MICROSCOPYf_chiral_restr0.036242596
ELECTRON MICROSCOPYf_plane_restr0.004523656
ELECTRON MICROSCOPYf_dihedral_angle_d14.677778390

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