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- PDB-7qvp: Human collided disome (di-ribosome) stalled on XBP1 mRNA -

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Basic information

Entry
Database: PDB / ID: 7qvp
TitleHuman collided disome (di-ribosome) stalled on XBP1 mRNA
Components
  • (40S ribosomal protein ...) x 31
  • (60S ribosomal protein ...) x 40
  • (mRNA) x 2
  • 18S ribosomal RNA
  • 28S ribosomal RNA
  • 5.8S ribosomal RNA
  • 5S ribosomal RNA
  • KOW domain-containing protein
  • Receptor of activated protein C kinase 1
  • Ribosomal protein L37
  • Ubiquitin-40S ribosomal protein S27a
  • Ubiquitin-60S ribosomal protein L40
  • tNRA E/E
  • tRNA P/E
  • tRNA P/P
KeywordsTRANSLATION / disome / di-ribosome / XBP1 / ribosome / collision
Function / homology
Function and homology information


Translation initiation complex formation / Formation of the ternary complex, and subsequently, the 43S complex / Ribosomal scanning and start codon recognition / L13a-mediated translational silencing of Ceruloplasmin expression / SRP-dependent cotranslational protein targeting to membrane / Formation of a pool of free 40S subunits / 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) / Major pathway of rRNA processing in the nucleolus and cytosol ...Translation initiation complex formation / Formation of the ternary complex, and subsequently, the 43S complex / Ribosomal scanning and start codon recognition / L13a-mediated translational silencing of Ceruloplasmin expression / SRP-dependent cotranslational protein targeting to membrane / Formation of a pool of free 40S subunits / 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) / Major pathway of rRNA processing in the nucleolus and cytosol / Formation of the ternary complex, and subsequently, the 43S complex / Formation of a pool of free 40S subunits / SRP-dependent cotranslational protein targeting to membrane / Major pathway of rRNA processing in the nucleolus and cytosol / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Translation initiation complex formation / Ribosomal scanning and start codon recognition / L13a-mediated translational silencing of Ceruloplasmin expression / GTP hydrolysis and joining of the 60S ribosomal subunit / negative regulation of protein neddylation / oxidized pyrimidine DNA binding / response to TNF agonist / positive regulation of base-excision repair / negative regulation of formation of translation preinitiation complex / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of endodeoxyribonuclease activity / negative regulation of DNA repair / negative regulation of RNA splicing / mammalian oogenesis stage / GAIT complex / supercoiled DNA binding / activation-induced cell death of T cells / TORC2 complex binding / neural crest cell differentiation / alpha-beta T cell differentiation / NF-kappaB complex / oxidized purine DNA binding / ubiquitin-like protein conjugating enzyme binding / translation at presynapse / positive regulation of ubiquitin-protein transferase activity / Formation of the ternary complex, and subsequently, the 43S complex / erythrocyte homeostasis / rRNA modification in the nucleus and cytosol / laminin receptor activity / protein kinase A binding / negative regulation of ubiquitin protein ligase activity / Ribosomal scanning and start codon recognition / homeostatic process / Translation initiation complex formation / organelle membrane / positive regulation of T cell receptor signaling pathway / macrophage chemotaxis / positive regulation of activated T cell proliferation / fibroblast growth factor binding / lung morphogenesis / male meiosis I / Protein hydroxylation / TOR signaling / SARS-CoV-1 modulates host translation machinery / mTORC1-mediated signalling / T cell proliferation involved in immune response / Peptide chain elongation / iron-sulfur cluster binding / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / Selenocysteine synthesis / positive regulation of signal transduction by p53 class mediator / Formation of a pool of free 40S subunits / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ubiquitin ligase inhibitor activity / Eukaryotic Translation Termination / Response of EIF2AK4 (GCN2) to amino acid deficiency / SRP-dependent cotranslational protein targeting to membrane / blastocyst development / negative regulation of ubiquitin-dependent protein catabolic process / Viral mRNA Translation / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / protein localization to nucleus / GTP hydrolysis and joining of the 60S ribosomal subunit / L13a-mediated translational silencing of Ceruloplasmin expression / erythrocyte development / Major pathway of rRNA processing in the nucleolus and cytosol / protein targeting / protein-RNA complex assembly / 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) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Protein methylation / maturation of LSU-rRNA / spindle assembly / Nuclear events stimulated by ALK signaling in cancer / rough endoplasmic reticulum / laminin binding / translation regulator activity / translation initiation factor binding / gastrulation / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / MDM2/MDM4 family protein binding / positive regulation of microtubule polymerization / cytosolic ribosome / DNA-(apurinic or apyrimidinic site) endonuclease activity
Similarity search - Function
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 protein L2, archaeal-type / Ribosomal L15/L27a, N-terminal / Ribosomal protein L28e ...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 protein L2, archaeal-type / Ribosomal L15/L27a, N-terminal / Ribosomal protein L28e / Ribosomal protein L23 / Ribosomal L28e/Mak16 / Ribosomal L28e protein family / metallochaperone-like domain / TRASH domain / : / 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. / Small (40S) ribosomal subunit Asc1/RACK1 / Ribosomal protein S5, eukaryotic/archaeal / Ribosomal protein S21e / Ribosomal protein S21e superfamily / Ribosomal protein S21e / Ribosomal protein L13e, conserved site / Ribosomal protein L13e signature. / Ribosomal protein S2, eukaryotic / S27a-like superfamily / Ribosomal protein L22e / Ribosomal protein L22e superfamily / Ribosomal L22e protein family / 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 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 L13e / Ribosomal protein S8e subdomain, eukaryotes / Ribosomal protein L13e / 60S ribosomal protein L18a/ L20, 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 L34e signature. / Ribosomal protein L5 eukaryotic, C-terminal / Ribosomal L18 C-terminal region / Ribosomal protein L30e signature 1. / 50S ribosomal protein L18Ae/60S ribosomal protein L20 and L18a / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / Ribosomal L40e family / Ribosomal protein S27e signature. / Ribosomal protein 50S-L18Ae/60S-L20/60S-L18A / 40S ribosomal protein S4, C-terminal domain / Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A / 40S ribosomal protein S4 C-terminus / Ribosomal protein S4e, N-terminal, conserved site / Ribosomal protein S4e signature.
Similarity search - Domain/homology
: / : / : / : / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) ...: / : / : / : / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein eL38 / Large ribosomal subunit protein eL34 / Ribosomal protein L19 / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein RACK1 / Small ribosomal subunit protein uS19 / Ubiquitin-like domain-containing protein / Small ribosomal subunit protein eS19 / Ribosomal protein L37 / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein eS28 / Large ribosomal subunit protein uL14 / Small ribosomal subunit protein uS9 / KOW domain-containing protein / Small ribosomal subunit protein uS15 / 40S ribosomal protein S12 / Large ribosomal subunit protein eL43 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein uS7 / 40S ribosomal protein S26 / 40S ribosomal protein S25 / 40S ribosomal protein S27 / RS14 protein / Large ribosomal subunit protein eL39 / 60S ribosomal protein L27 / Large ribosomal subunit protein uL2 / Small ribosomal subunit protein uS17 / Ubiquitin-ribosomal protein eS31 fusion protein / Ubiquitin-ribosomal protein eL40 fusion protein / Large ribosomal subunit protein eL24 / Large ribosomal subunit protein eL31 / Small ribosomal subunit protein uS13 / Ribosomal protein L36a / Ribosomal protein L15 / Small ribosomal subunit protein eS17 / Small ribosomal subunit protein uS2 / Small ribosomal subunit protein uS5 / Large ribosomal subunit protein eL33 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein uL22 / Small ribosomal subunit protein uS3 / Large ribosomal subunit protein eL13 / Large ribosomal subunit protein uL6 / Large ribosomal subunit protein eL22 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein uL13 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein eL21 / Large ribosomal subunit protein eL28 / Small ribosomal subunit protein eS10 / Large ribosomal subunit protein eL29 / Large ribosomal subunit protein eL14 / Small ribosomal subunit protein uS10 / Small ribosomal subunit protein eS1 / Small ribosomal subunit protein eS7 / Small ribosomal subunit protein eS8 / Large ribosomal subunit protein eL8 / Small ribosomal subunit protein eS4, X isoform / Large ribosomal subunit protein uL23 / Small ribosomal subunit protein eS6 / Small ribosomal subunit protein eS24 / Large ribosomal subunit protein eL30 / Large ribosomal subunit protein eL32 / Large ribosomal subunit protein uL5 / Small ribosomal subunit protein eS32 / Small ribosomal subunit protein eS21 / Large ribosomal subunit protein eL20 / Large ribosomal subunit protein eL6 / Large ribosomal subunit protein eL18 / Ribosomal protein uL16-like / Large ribosomal subunit protein eL36
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 Å
AuthorsDenk, T.G. / Tesina, P. / Beckmann, R.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)BE1814/15-1 Germany
CitationJournal: Nat Commun / Year: 2022
Title: A distinct mammalian disome collision interface harbors K63-linked polyubiquitination of uS10 to trigger hRQT-mediated subunit dissociation.
Authors: Momoko Narita / Timo Denk / Yoshitaka Matsuo / Takato Sugiyama / Chisato Kikuguchi / Sota Ito / Nichika Sato / Toru Suzuki / Satoshi Hashimoto / Iva Machová / Petr Tesina / Roland Beckmann ...Authors: Momoko Narita / Timo Denk / Yoshitaka Matsuo / Takato Sugiyama / Chisato Kikuguchi / Sota Ito / Nichika Sato / Toru Suzuki / Satoshi Hashimoto / Iva Machová / Petr Tesina / Roland Beckmann / Toshifumi Inada /
Abstract: Translational stalling events that result in ribosome collisions induce Ribosome-associated Quality Control (RQC) in order to degrade potentially toxic truncated nascent proteins. For RQC induction, ...Translational stalling events that result in ribosome collisions induce Ribosome-associated Quality Control (RQC) in order to degrade potentially toxic truncated nascent proteins. For RQC induction, the collided ribosomes are first marked by the Hel2/ZNF598 E3 ubiquitin ligase to recruit the RQT complex for subunit dissociation. In yeast, uS10 is polyubiquitinated by Hel2, whereas eS10 is preferentially monoubiquitinated by ZNF598 in human cells for an unknown reason. Here, we characterize the ubiquitination activity of ZNF598 and its importance for human RQT-mediated subunit dissociation using the endogenous XBP1u and poly(A) translation stallers. Cryo-EM analysis of a human collided disome reveals a distinct composite interface, with substantial differences to yeast collided disomes. Biochemical analysis of collided ribosomes shows that ZNF598 forms K63-linked polyubiquitin chains on uS10, which are decisive for mammalian RQC initiation. The human RQT (hRQT) complex composed only of ASCC3, ASCC2 and TRIP4 dissociates collided ribosomes dependent on the ATPase activity of ASCC3 and the ubiquitin-binding capacity of ASCC2. The hRQT-mediated subunit dissociation requires the K63-linked polyubiquitination of uS10, while monoubiquitination of eS10 or uS10 is not sufficient. Therefore, we conclude that ZNF598 functionally marks collided mammalian ribosomes by K63-linked polyubiquitination of uS10 for the trimeric hRQT complex-mediated subunit dissociation.
History
DepositionJan 22, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 12, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 23, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jul 17, 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
A4: mRNA
A5: mRNA
B4: tRNA P/P
B5: tRNA P/E
CC: tNRA E/E
D5: tRNA P/P
L1: 5.8S ribosomal RNA
L5: 28S ribosomal RNA
L6: 28S ribosomal RNA
L7: 5S ribosomal RNA
L8: 5.8S ribosomal RNA
L9: 5S ribosomal RNA
LA: 60S ribosomal protein L8
LB: 60S ribosomal protein L3
LC: 60S ribosomal protein L4
LD: 60S ribosomal protein L5
LE: 60S ribosomal protein L6
LF: 60S ribosomal protein L7
LG: 60S ribosomal protein L7a
LH: 60S ribosomal protein L9
LI: 60S ribosomal protein L10-like
LJ: 60S ribosomal protein L11
LL: 60S ribosomal protein L13
LM: 60S ribosomal protein L14
LN: 60S ribosomal protein L15
LO: 60S ribosomal protein L13a
LP: 60S ribosomal protein L17
LQ: 60S ribosomal protein L18
LR: 60S ribosomal protein L19
LS: 60S ribosomal protein L18a
LT: 60S ribosomal protein L21
LU: 60S ribosomal protein L22
LV: 60S ribosomal protein L23
LW: 60S ribosomal protein L24
LX: 60S ribosomal protein L23a
LY: KOW domain-containing protein
LZ: 60S ribosomal protein L27
La: 60S ribosomal protein L27a
Lb: 60S ribosomal protein L29
Lc: 60S ribosomal protein L30
Ld: 60S ribosomal protein L31
Le: 60S ribosomal protein L32
Lf: 60S ribosomal protein L35a
Lg: 60S ribosomal protein L34
Lh: 60S ribosomal protein L35
Li: 60S ribosomal protein L36
Lj: Ribosomal protein L37
Lk: 60S ribosomal protein L38
Ll: 60S ribosomal protein L39
Lm: Ubiquitin-60S ribosomal protein L40
Ln: 60S ribosomal protein L41
Lo: 60S ribosomal protein L36a
Lp: 60S ribosomal protein L37a
Lr: 60S ribosomal protein L28
MA: 60S ribosomal protein L8
MB: 60S ribosomal protein L3
MC: 60S ribosomal protein L4
MD: 60S ribosomal protein L5
ME: 60S ribosomal protein L6
MF: 60S ribosomal protein L7
MG: 60S ribosomal protein L7a
MH: 60S ribosomal protein L9
MI: 60S ribosomal protein L10-like
MJ: 60S ribosomal protein L11
ML: 60S ribosomal protein L13
MM: 60S ribosomal protein L14
MN: 60S ribosomal protein L15
MO: 60S ribosomal protein L13a
MP: 60S ribosomal protein L17
MQ: 60S ribosomal protein L18
MR: 60S ribosomal protein L19
MS: 60S ribosomal protein L18a
MT: 60S ribosomal protein L21
MU: 60S ribosomal protein L22
MV: 60S ribosomal protein L23
MW: 60S ribosomal protein L24
MX: 60S ribosomal protein L23a
MY: KOW domain-containing protein
MZ: 60S ribosomal protein L27
Ma: 60S ribosomal protein L27a
Mb: 60S ribosomal protein L29
Mc: 60S ribosomal protein L30
Md: 60S ribosomal protein L31
Me: 60S ribosomal protein L32
Mf: 60S ribosomal protein L35a
Mg: 60S ribosomal protein L34
Mh: 60S ribosomal protein L35
Mi: 60S ribosomal protein L36
Mj: Ribosomal protein L37
Mk: 60S ribosomal protein L38
Ml: 60S ribosomal protein L39
Mm: Ubiquitin-60S ribosomal protein L40
Mn: 60S ribosomal protein L41
Mo: 60S ribosomal protein L36a
Mp: 60S ribosomal protein L37a
Mr: 60S ribosomal protein L28
RA: 40S ribosomal protein SA
RB: 40S ribosomal protein S3a
RC: 40S ribosomal protein S2
RD: 40S ribosomal protein S3
RE: 40S ribosomal protein S4, X isoform
RF: 40S ribosomal protein S5
RG: 40S ribosomal protein S6
RH: 40S ribosomal protein S7
RI: 40S ribosomal protein S8
RJ: 40S ribosomal protein S9
RK: 40S ribosomal protein S10
RL: 40S ribosomal protein S11
RN: 40S ribosomal protein S13
RO: 40S ribosomal protein S14
RP: 40S ribosomal protein S15
RQ: 40S ribosomal protein S16
RR: 40S ribosomal protein S17
RS: 40S ribosomal protein S18
RT: 40S ribosomal protein S19
RU: 40S ribosomal protein S20
RV: 40S ribosomal protein S21
RW: 40S ribosomal protein S15a
RX: 40S ribosomal protein S23
RY: 40S ribosomal protein S24
RZ: 40S ribosomal protein S25
Ra: 40S ribosomal protein S26
Rb: 40S ribosomal protein S27
Rc: 40S ribosomal protein S28
Rd: 40S ribosomal protein S29
Re: 40S ribosomal protein S30
Rf: 40S ribosomal protein S12
Rg: Receptor of activated protein C kinase 1
Rh: Ubiquitin-40S ribosomal protein S27a
S2: 18S ribosomal RNA
S3: 18S ribosomal RNA
SA: 40S ribosomal protein SA
SB: 40S ribosomal protein S3a
SC: 40S ribosomal protein S2
SD: 40S ribosomal protein S3
SE: 40S ribosomal protein S4, X isoform
SF: 40S ribosomal protein S5
SG: 40S ribosomal protein S6
SH: 40S ribosomal protein S7
SI: 40S ribosomal protein S8
SJ: 40S ribosomal protein S9
SK: 40S ribosomal protein S10
SL: 40S ribosomal protein S11
SN: 40S ribosomal protein S13
SO: 40S ribosomal protein S14
SP: 40S ribosomal protein S15
SQ: 40S ribosomal protein S16
SR: 40S ribosomal protein S17
SS: 40S ribosomal protein S18
ST: 40S ribosomal protein S19
SU: 40S ribosomal protein S20
SV: 40S ribosomal protein S21
SW: 40S ribosomal protein S15a
SX: 40S ribosomal protein S23
SY: 40S ribosomal protein S24
SZ: 40S ribosomal protein S25
Sa: 40S ribosomal protein S26
Sb: 40S ribosomal protein S27
Sc: 40S ribosomal protein S28
Sd: 40S ribosomal protein S29
Se: 40S ribosomal protein S30
Sg: Receptor of activated protein C kinase 1


Theoretical massNumber of molelcules
Total (without water)7,725,763162
Polymers7,725,763162
Non-polymers00
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 , 9 types, 14 molecules A4A5B4D5B5CCL1L8L5L6L7L9S2S3

#1: RNA chain mRNA


Mass: 4241.363 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#2: RNA chain mRNA


Mass: 3322.866 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
#3: RNA chain tRNA P/P


Mass: 24485.539 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: GenBank: 1850337400
#4: RNA chain tRNA P/E


Mass: 24231.510 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: GenBank: 174924
#5: RNA chain tNRA E/E


Mass: 24004.262 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: GenBank: 176418
#6: RNA chain 5.8S ribosomal RNA


Mass: 50449.812 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: GenBank: 555853
#7: RNA chain 28S ribosomal RNA


Mass: 1690723.500 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
#8: RNA chain 5S ribosomal RNA


Mass: 38998.078 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: GenBank: 23898
#85: RNA chain 18S ribosomal RNA


Mass: 602776.875 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: GenBank: 36162

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60S ribosomal protein ... , 40 types, 78 molecules LAMALBMBLCMCLDMDLEMELFMFLGMGLHMHLIMILJMJLLMLLMMMLNMNLOMOLPLQ...

#9: Protein 60S ribosomal protein L8 / Large ribosomal subunit protein uL2


Mass: 28088.863 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: A0A8B8VPA8
#10: Protein 60S ribosomal protein L3 / HIV-1 TAR RNA-binding protein B / TARBP-B / Large ribosomal subunit protein uL3


Mass: 46211.113 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P39023
#11: Protein 60S ribosomal protein L4 / 60S ribosomal protein L1 / Large ribosomal subunit protein uL4


Mass: 47804.621 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P36578
#12: Protein 60S ribosomal protein L5 / Large ribosomal subunit protein uL18


Mass: 34426.789 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P46777
#13: Protein 60S ribosomal protein L6 / Large ribosomal subunit protein eL6 / Neoplasm-related protein C140 / Tax-responsive enhancer ...Large ribosomal subunit protein eL6 / Neoplasm-related protein C140 / Tax-responsive enhancer element-binding protein 107 / TaxREB107


Mass: 32810.176 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q02878
#14: Protein 60S ribosomal protein L7 / Large ribosomal subunit protein uL30


Mass: 29290.973 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P18124
#15: Protein 60S ribosomal protein L7a / Large ribosomal subunit protein eL8 / PLA-X polypeptide / Surfeit locus protein 3


Mass: 30061.785 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62424
#16: Protein 60S ribosomal protein L9 / Large ribosomal subunit protein uL6


Mass: 21899.471 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P32969
#17: Protein 60S ribosomal protein L10-like / Large ribosomal subunit protein uL16-like


Mass: 24570.949 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q96L21
#18: Protein 60S ribosomal protein L11 / CLL-associated antigen KW-12 / Large ribosomal subunit protein uL5


Mass: 20288.465 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62913
#19: Protein 60S ribosomal protein L13 / Breast basic conserved protein 1 / Large ribosomal subunit protein eL13


Mass: 24321.682 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P26373
#20: Protein 60S ribosomal protein L14 / CAG-ISL 7 / Large ribosomal subunit protein eL14


Mass: 23485.016 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P50914
#21: Protein 60S ribosomal protein L15


Mass: 24207.285 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: L8Y0W1
#22: Protein 60S ribosomal protein L13a / 23 kDa highly basic protein / Large ribosomal subunit protein uL13


Mass: 23633.412 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P40429
#23: Protein 60S ribosomal protein L17 / 60S ribosomal protein L23 / Large ribosomal subunit protein uL22 / PD-1


Mass: 17888.822 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P18621
#24: Protein 60S ribosomal protein L18 / Large ribosomal subunit protein eL18


Mass: 21687.676 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q07020
#25: Protein 60S ribosomal protein L19


Mass: 23535.281 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: A0A2J8KH59
#26: Protein 60S ribosomal protein L18a / Large ribosomal subunit protein eL20


Mass: 20808.514 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q02543
#27: Protein 60S ribosomal protein L21 / Large ribosomal subunit protein eL21


Mass: 18609.988 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P46778
#28: Protein 60S ribosomal protein L22 / EBER-associated protein / EAP / Epstein-Barr virus small RNA-associated protein / Heparin-binding ...EBER-associated protein / EAP / Epstein-Barr virus small RNA-associated protein / Heparin-binding protein HBp15 / Large ribosomal subunit protein eL22


Mass: 14813.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P35268
#29: Protein 60S ribosomal protein L23


Mass: 14892.505 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: A0A3P9HH38
#30: Protein 60S ribosomal protein L24 / Ribosomal protein L24


Mass: 17825.111 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: F2X267
#31: Protein 60S ribosomal protein L23a / Large ribosomal subunit protein uL23


Mass: 17740.193 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62750
#33: Protein 60S ribosomal protein L27


Mass: 15835.831 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: A0A851LWS6
#34: Protein 60S ribosomal protein L27a / Large ribosomal subunit protein uL15


Mass: 16604.535 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P46776
#35: Protein 60S ribosomal protein L29 / Cell surface heparin-binding protein HIP / Large ribosomal subunit protein eL29


Mass: 17804.275 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P47914
#36: Protein 60S ribosomal protein L30 / Large ribosomal subunit protein eL30


Mass: 12805.092 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62888
#37: Protein 60S ribosomal protein L31


Mass: 14494.938 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: G7NZE1
#38: Protein 60S ribosomal protein L32 / Large ribosomal subunit protein eL32


Mass: 15898.932 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62910
#39: Protein 60S ribosomal protein L35a / Cell growth-inhibiting gene 33 protein / Large ribosomal subunit protein eL33


Mass: 12564.743 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P18077
#40: Protein 60S ribosomal protein L34 / Large ribosomal subunit protein eL34


Mass: 13326.074 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: A0A1U7T3M5
#41: Protein 60S ribosomal protein L35 / Large ribosomal subunit protein uL29


Mass: 14593.624 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P42766
#42: Protein 60S ribosomal protein L36 / Large ribosomal subunit protein eL36


Mass: 12290.859 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9Y3U8
#44: Protein 60S ribosomal protein L38


Mass: 8238.948 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: A0A1A7W9T9
#45: Protein 60S ribosomal protein L39


Mass: 6426.759 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: A0A7N4PFJ2
#47: Protein/peptide 60S ribosomal protein L41 / HG12 / Large ribosomal subunit protein eL41


Mass: 3473.451 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62945
#48: Protein 60S ribosomal protein L36a


Mass: 12476.973 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: J3KQN4
#49: Protein 60S ribosomal protein L37a


Mass: 10299.350 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: A0A6I9ZMF9
#50: Protein 60S ribosomal protein L28 / Large ribosomal subunit protein eL28


Mass: 15784.622 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P46779
#51: Protein 60S ribosomal protein L17 / 60S ribosomal protein L23 / Large ribosomal subunit protein uL22 / PD-1


Mass: 21443.170 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P18621

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Protein , 5 types, 9 molecules LYMYLjMjLmMmRgSgRh

#32: Protein KOW domain-containing protein


Mass: 17303.363 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: A0A5N3X333
#43: Protein Ribosomal protein L37


Mass: 10379.280 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: A0A2Y9RW09
#46: Protein Ubiquitin-60S ribosomal protein L40


Mass: 14758.394 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: A0A8C8Y9V5
#83: Protein Receptor of activated protein C kinase 1


Mass: 35115.652 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: A0A2K6K8B0
#84: Protein Ubiquitin-40S ribosomal protein S27a / Ubiquitin carboxyl extension protein 80


Mass: 18004.041 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: A0A8C0T835

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40S ribosomal protein ... , 31 types, 61 molecules RASARBSBRCSCRDSDRESERFSFRGSGRHSHRISIRJSJRKSKRLSLRNSNROSORPSP...

#52: 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 / Colon carcinoma laminin-binding protein / Laminin receptor 1 / LamR / Laminin-binding protein precursor p40 / LBP/p40 / Multidrug resistance-associated protein MGr1-Ag / NEM/1CHD4 / Small ribosomal subunit protein uS2


Mass: 32883.938 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P08865
#53: Protein 40S ribosomal protein S3a / Small ribosomal subunit protein eS1 / v-fos transformation effector protein / Fte-1


Mass: 30002.061 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P61247
#54: Protein 40S ribosomal protein S2 / 40S ribosomal protein S4 / Protein LLRep3 / Small ribosomal subunit protein uS5


Mass: 31376.516 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P15880
#55: Protein 40S ribosomal protein S3 / Small ribosomal subunit protein uS3


Mass: 26729.369 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
References: UniProt: P23396, DNA-(apurinic or apyrimidinic site) lyase
#56: Protein 40S ribosomal protein S4, X isoform / SCR10 / Single copy abundant mRNA protein / Small ribosomal subunit protein eS4


Mass: 29654.869 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62701
#57: Protein 40S ribosomal protein S5


Mass: 22913.453 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: A0A6J0Y1Z7
#58: Protein 40S ribosomal protein S6 / Phosphoprotein NP33 / Small ribosomal subunit protein eS6


Mass: 28751.906 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62753
#59: Protein 40S ribosomal protein S7


Mass: 22168.914 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62082
#60: Protein 40S ribosomal protein S8 / Small ribosomal subunit protein eS8


Mass: 24263.387 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62241
#61: Protein 40S ribosomal protein S9


Mass: 22641.564 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: A0A6J0B498
#62: Protein 40S ribosomal protein S10 / Small ribosomal subunit protein eS10


Mass: 18933.846 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P46783
#63: Protein 40S ribosomal protein S11


Mass: 18468.826 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: A0A8B8VW69
#64: Protein 40S ribosomal protein S13


Mass: 17259.389 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: A0A663F1C0
#65: Protein 40S ribosomal protein S14


Mass: 16302.772 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: A0A7L0BEC6
#66: Protein 40S ribosomal protein S15


Mass: 17076.207 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: A0A2K6QL61
#67: Protein 40S ribosomal protein S16


Mass: 16477.377 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: A0A4W2HV66
#68: Protein 40S ribosomal protein S17 / Small ribosomal subunit protein eS17


Mass: 15578.156 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P08708
#69: Protein 40S ribosomal protein S18


Mass: 17759.777 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: H0WTR0
#70: Protein 40S ribosomal protein S19


Mass: 16091.562 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: A0A2Y9E7Q1
#71: Protein 40S ribosomal protein S20


Mass: 13398.763 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P60868
#72: Protein 40S ribosomal protein S21 / Small ribosomal subunit protein eS21


Mass: 9124.389 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P63220
#73: Protein 40S ribosomal protein S15a


Mass: 14865.555 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: A0A2K5QKS6
#74: Protein 40S ribosomal protein S23


Mass: 15844.666 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: A0A340WVW7
#75: Protein 40S ribosomal protein S24 / Small ribosomal subunit protein eS24


Mass: 15463.333 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62847
#76: Protein 40S ribosomal protein S25


Mass: 13776.224 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: A0A6J3IG71
#77: Protein 40S ribosomal protein S26


Mass: 11619.796 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: A0A6J2NCX2
#78: Protein 40S ribosomal protein S27


Mass: 9480.186 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: A0A7J8BG50
#79: Protein 40S ribosomal protein S28


Mass: 7855.052 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: A0A3M0JHZ8
#80: Protein 40S ribosomal protein S29


Mass: 6690.821 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: A0A2J8WKD7
#81: Protein 40S ribosomal protein S30


Mass: 6668.938 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: A0A2K6U587
#82: Protein 40S ribosomal protein S12


Mass: 14538.987 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: A0A671DUR2

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Details

Has ligand of interestN

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: human collided disome stalled on XBP1 staller / Type: RIBOSOME / Entity ID: all / Source: NATURAL
Source (natural)Organism: Homo sapiens (human)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen 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: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3500 nm / Nominal defocus min: 400 nm
Image recordingElectron dose: 43.6 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

Software
NameVersionClassificationNB
phenix.real_space_refine1.14_3260refinement
PHENIX1.14_3260refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 53848 / Symmetry type: POINT
RefinementStereochemistry target values: CDL v1.2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0078449653
ELECTRON MICROSCOPYf_angle_d0.967663480
ELECTRON MICROSCOPYf_chiral_restr0.051783564
ELECTRON MICROSCOPYf_plane_restr0.007241305
ELECTRON MICROSCOPYf_dihedral_angle_d16.4142245219

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