PDB-9mnc: Human 80S ribosome bound to small molecule SW393071

ID or keywords:

Entry

Database: PDB / ID: 9mnc

Title

Human 80S ribosome bound to small molecule SW393071

Components

(Large ribosomal subunit protein ...) x 41
(Small ribosomal subunit protein ...) x 30
18S rRNA
28S rRNA
5.8S rRNA
5S rRNA
FAU ubiquitin-like and ribosomal protein S30
Isoform 3 of Small ribosomal subunit protein eS24
Receptor of activated protein C kinase 1
Ubiquitin-40S ribosomal protein S27a

Keywords

RIBOSOME / Translation / ligand

Function / homology

Function and homology information

embryonic brain development / translation at presynapse / exit from mitosis / optic nerve development / response to insecticide / regulation of translation involved in cellular response to UV / eukaryotic 80S initiation complex / ribosomal protein import into nucleus / regulation of G1 to G0 transition / negative regulation of endoplasmic reticulum unfolded protein response ...embryonic brain development / translation at presynapse / exit from mitosis / optic nerve development / response to insecticide / regulation of translation involved in cellular response to UV / eukaryotic 80S initiation complex / ribosomal protein import into nucleus / regulation of G1 to G0 transition / negative regulation of endoplasmic reticulum unfolded protein response / negative regulation of formation of translation preinitiation complex / axial mesoderm development / retinal ganglion cell axon guidance / oxidized pyrimidine DNA binding / response to TNF agonist / positive regulation of base-excision repair / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / protein-DNA complex disassembly / positive regulation of respiratory burst involved in inflammatory response / positive regulation of gastrulation / 90S preribosome assembly / protein tyrosine kinase inhibitor activity / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of ubiquitin-protein transferase activity / IRE1-RACK1-PP2A complex / positive regulation of DNA-templated transcription initiation / alpha-beta T cell differentiation / positive regulation of Golgi to plasma membrane protein transport / nucleolus organization / TNFR1-mediated ceramide production / positive regulation of DNA damage response, signal transduction by p53 class mediator / GAIT complex / negative regulation of RNA splicing / TORC2 complex binding / neural crest cell differentiation / supercoiled DNA binding / G1 to G0 transition / NF-kappaB complex / negative regulation of DNA repair / cytoplasmic translational initiation / cysteine-type endopeptidase activator activity involved in apoptotic process / oxidized purine DNA binding / middle ear morphogenesis / rRNA modification in the nucleus and cytosol / negative regulation of intrinsic apoptotic signaling pathway in response to hydrogen peroxide / regulation of establishment of cell polarity / negative regulation of bicellular tight junction assembly / ubiquitin-like protein conjugating enzyme binding / negative regulation of phagocytosis / erythrocyte homeostasis / cytoplasmic side of rough endoplasmic reticulum membrane / Formation of the ternary complex, and subsequently, the 43S complex / ion channel inhibitor activity / protein kinase A binding / laminin receptor activity / homeostatic process / pigmentation / Ribosomal scanning and start codon recognition / positive regulation of mitochondrial depolarization / macrophage chemotaxis / Translation initiation complex formation / lung morphogenesis / negative regulation of Wnt signaling pathway / positive regulation of natural killer cell proliferation / fibroblast growth factor binding / Protein hydroxylation / monocyte chemotaxis / BH3 domain binding / negative regulation of translational frameshifting / regulation of adenylate cyclase-activating G protein-coupled receptor signaling pathway / TOR signaling / mTORC1-mediated signalling / SARS-CoV-1 modulates host translation machinery / iron-sulfur cluster binding / positive regulation of GTPase activity / regulation of cell division / cellular response to ethanol / Peptide chain elongation / Selenocysteine synthesis / Formation of a pool of free 40S subunits / negative regulation of protein binding / blastocyst development / Eukaryotic Translation Termination / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / protein serine/threonine kinase inhibitor activity / SRP-dependent cotranslational protein targeting to membrane / Response of EIF2AK4 (GCN2) to amino acid deficiency / negative regulation of respiratory burst involved in inflammatory response / ubiquitin ligase inhibitor activity / Viral mRNA Translation / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / protein localization to nucleus / negative regulation of ubiquitin-dependent protein catabolic process / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / positive regulation of signal transduction by p53 class mediator / GTP hydrolysis and joining of the 60S ribosomal subunit / L13a-mediated translational silencing of Ceruloplasmin expression / Major pathway of rRNA processing in the nucleolus and cytosol / protein targeting / regulation of translational fidelity
Similarity search - Function

40S ribosomal protein SA / Ribosomal protein L6, N-terminal / Ribosomal protein L6, N-terminal domain / 40S ribosomal protein SA, C-terminal domain / 40S ribosomal protein SA C-terminus / Ubiquitin-like protein FUBI / Ribosomal protein L30e / Ribosomal L15/L27a, N-terminal / Ribosomal protein L28e / : ...40S ribosomal protein SA / Ribosomal protein L6, N-terminal / Ribosomal protein L6, N-terminal domain / 40S ribosomal protein SA, C-terminal domain / 40S ribosomal protein SA C-terminus / Ubiquitin-like protein FUBI / Ribosomal protein L30e / Ribosomal L15/L27a, N-terminal / Ribosomal protein L28e / : / Ribosomal protein L23 / Ribosomal protein L2, archaeal-type / Ribosomal L28e/Mak16 / Ribosomal L28e protein family / metallochaperone-like domain / TRASH domain / : / Ribosomal protein S26e signature. / Ribosomal protein L41 / Ribosomal protein L41 / Ribosomal protein L13e, conserved site / Ribosomal protein L13e signature. / Ribosomal protein S21e, conserved site / Ribosomal protein S21e signature. / : / Ribosomal protein S12e signature. / Ribosomal protein S26e / Ribosomal protein L29e / Ribosomal protein S26e superfamily / Ribosomal protein S26e / Ribosomal L29e protein family / Ribosomal protein S12e / Ribosomal protein L22e / Ribosomal protein L22e superfamily / Ribosomal L22e protein family / Ribosomal protein L27e, conserved site / Ribosomal protein L27e signature. / Small (40S) ribosomal subunit Asc1/RACK1 / Ribosomal protein L13e / Ribosomal protein L13e / Ribosomal protein L38e / Ribosomal protein S5, eukaryotic/archaeal / Ribosomal protein L38e superfamily / Ribosomal L38e protein family / Ribosomal protein S19e, conserved site / : / Ribosomal protein S19e signature. / Ribosomal protein L19, eukaryotic / Ribosomal protein S21e / Ribosomal protein S21e superfamily / Ribosomal protein S21e / Ribosomal protein L6e signature. / 60S ribosomal protein L18a/ L20, eukaryotes / Ribosomal protein S2, eukaryotic / Ribosomal protein L10e, conserved site / Ribosomal protein L10e signature. / Ribosomal protein L19/L19e conserved site / Ribosomal protein L19e signature. / Ribosomal protein L44e signature. / Ribosomal protein L24e, conserved site / Ribosomal protein L24e signature. / Ribosomal protein L18/L18-A/B/e, conserved site / Ribosomal protein L18e signature. / 40S Ribosomal protein S10 / Ribosomal protein L10e / S27a-like superfamily / Ribosomal protein L34e, conserved site / Ribosomal protein L34e signature. / Plectin/S10, N-terminal / Plectin/S10 domain / Ribosomal protein L5 eukaryotic, C-terminal / Ribosomal L18 C-terminal region / Ribosomal protein L23/L25, N-terminal / Ribosomal protein L23, N-terminal domain / 50S ribosomal protein L18Ae/60S ribosomal protein L20 and L18a / : / Ribosomal L40e family / Ribosomal protein L30e signature 1. / Ribosomal protein 50S-L18Ae/60S-L20/60S-L18A / Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A / Ribosomal protein L36e signature. / Ribosomal protein S10, eukaryotic/archaeal / Ribosomal protein S30 / Ribosomal protein S30 / Ribosomal protein L44e / Ribosomal protein L44 / Ribosomal protein 60S L18 and 50S L18e / Ribosomal protein L35Ae, conserved site / Ribosomal protein L35Ae signature. / Eukaryotic Ribosomal Protein L27, KOW domain / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein L40e superfamily / Ribosomal protein S25 / : / S25 ribosomal protein / Ribosomal protein L27e / Ribosomal protein L27e superfamily / Ribosomal L27e protein family / Ribosomal Protein L6, KOW domain
Similarity search - Domain/homology

: / : / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein eS17 / Small ribosomal subunit protein uS2 ...: / : / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / 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 / Small ribosomal subunit protein eS12 / Large ribosomal subunit protein eL13 / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein uL6 / Large ribosomal subunit protein eL22 / Large ribosomal subunit protein uL4 / Small ribosomal subunit protein eS19 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein uL13 / Small ribosomal subunit protein eS27 / 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 uS4 / Small ribosomal subunit protein uS7 / Small ribosomal subunit protein eS10 / Large ribosomal subunit protein eL34 / Large ribosomal subunit protein eL14 / Small ribosomal subunit protein uS10 / Small ribosomal subunit protein eS1 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein eL15 / Large ribosomal subunit protein eL27 / Large ribosomal subunit protein eL43 / Large ribosomal subunit protein eL37 / Small ribosomal subunit protein eS7 / Small ribosomal subunit protein eS8 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS9 / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein uS13 / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein uS17 / Large ribosomal subunit protein eL8 / Small ribosomal subunit protein eS4, X isoform / Large ribosomal subunit protein uL23 / Small ribosomal subunit protein eS6 / Large ribosomal subunit protein uL14 / Small ribosomal subunit protein uS19 / Small ribosomal subunit protein eS24 / Small ribosomal subunit protein eS25 / Small ribosomal subunit protein eS26 / Small ribosomal subunit protein eS28 / Ubiquitin-like FUBI-ribosomal protein eS30 fusion protein / Large ribosomal subunit protein eL30 / Large ribosomal subunit protein eL39 / Large ribosomal subunit protein eL31 / Large ribosomal subunit protein eL32 / Large ribosomal subunit protein uL5 / Large ribosomal subunit protein uL2 / Small ribosomal subunit protein eS32 / Ubiquitin-ribosomal protein eS31 fusion protein / Ubiquitin-ribosomal protein eL40 fusion protein / Large ribosomal subunit protein eL38 / Small ribosomal subunit protein eS21 / Small ribosomal subunit protein RACK1 / Large ribosomal subunit protein eL24 / Large ribosomal subunit protein eL42 / Large ribosomal subunit protein eL19 / Large ribosomal subunit protein eL20 / Large ribosomal subunit protein eL6 / Large ribosomal subunit protein eL18 / 60S ribosomal protein L29 / Large ribosomal subunit protein eL36
Similarity search - Component

Biological species

Homo sapiens (human)

Method

ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.33 Å

Authors

Erzberger, J.P. / Cruz, V.E.

Funding support

United States, 1items

Citation

Journal: To Be Published
Title: Human 80S ribosome bound to small molecule SW393071
Authors: Cruz, V.E. / Erzberger, J.P.

History

Deposition	Dec 20, 2024	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jun 24, 2026	Provider: repository / Type: Initial release
Revision 1.0	Jun 24, 2026	Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0	Jun 24, 2026	Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0	Jun 24, 2026	Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0	Jun 24, 2026	Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0	Jun 24, 2026	Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0	Jun 24, 2026	Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9mnc.cif.gz	6.6 MB	Display	PDBx/mmCIF format
PDB format	pdb9mnc.ent.gz		Display	PDB format
PDBx/mmJSON format	9mnc.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/mn/9mnc ftp://data.pdbj.org/pub/pdb/validation_reports/mn/9mnc	HTTPS FTP

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Related structure data

Related structure data	48420MC M: map data used to model this data C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#121 - Jan 2010 70S Ribosomes similarity (83) #130 - Oct 2010 Riboswitches similarity (2) #16 - Apr 2001 Aminoacyl-tRNA Synthetases similarity (1) #10 - Oct 2000 Ribosome similarity (84) #157 - Jan 2013 Transfer-Messenger RNA similarity (3) #260 - Aug 2021 Ribonuclease P similarity (8) #253 - Jan 2021 Expressome similarity (3) #181 - Jan 2015 Cascade and CRISPR similarity (1) #229 - Jan 2019 Fluorescent RNA Aptamers similarity (1) #161 - May 2013 Ricin similarity (235) #146 - Feb 2012 Aminoglycoside Antibiotics similarity (3) #15 - Mar 2001 Transfer RNA similarity (1) #249 - Sep 2020 SARS-CoV-2 RNA-dependent RNA Polymerase similarity (1) #60 - Dec 2004 Ubiquitin similarity (83) #210 - Jun 2017 Adenine Riboswitch in Action similarity (1) #87 - Mar 2007 Zinc Fingers similarity (1) #266 - Feb 2022 Oligosaccharyltransferase similarity (114) #245 - May 2020 Spliceosomes similarity (3) #226 - Oct 2018 Aminoglycoside Antibiotics and Resistance similarity (3) #262 - Oct 2021 Fifty Years of Open Access to PDB Structures similarity (3) #65 - May 2005 Self-splicing RNA similarity (2) #105 - Sep 2008 Ribonuclease A similarity (1) #98 - Feb 2008 Small Interfering RNA similarity (1) #234 - Jun 2019 MDM2 and Cancer similarity (79) #230 - Feb 2019 Initiation Factor eIF4E similarity (8) #227 - Nov 2018 Telomerase similarity (2) #106 - Oct 2008 Poly(A) Polymerase similarity (5) #143 - Nov 2011 Toll-like Receptors similarity (5) #104 - Aug 2008 Selenocysteine Synthase similarity (2) #81 - Sep 2006 Elongation Factors similarity (1) #89 - May 2007 Aconitase and Iron Regulatory Protein 1 similarity (1) #122 - Feb 2010 Enhanceosome similarity (7) #88 - Apr 2007 Clathrin similarity (1) #205 - Jan 2017 Nuclear Pore Complex similarity (6) #150 - Jun 2012 Sliding Clamps similarity (5) #241 - Jan 2020 Twenty Years of Molecules similarity (1) #172 - Apr 2014 RecA and Rad51 similarity (8) #68 - Aug 2005 Neurotrophins similarity (3) #43 - Jul 2003 Src Tyrosine Kinase similarity (3) #56 - Aug 2004 Caspases similarity (3) #165 - Sep 2013 Designed Protein Cages similarity (1) #62 - Feb 2005 Major Histocompatibility Complex similarity (1) #86 - Feb 2007 Exosomes similarity (1) #44 - Aug 2003 Calmodulin similarity (1) #126 - Jun 2010 Epidermal Growth Factor similarity (1) #91 - Jul 2007 Thymine Dimers similarity (1) #255 - Mar 2021 Cisplatin and DNA similarity (2) #196 - Apr 2016 Lead Poisoning similarity (1) #28 - Apr 2002 Anthrax Toxin similarity (1) #163 - Jul 2013 HIV Capsid similarity (1) #195 - Mar 2016 RAF Protein Kinases similarity (1) #112 - Apr 2009 Oct and Sox Transcription Factors similarity (1)

PDB pages

PDBj /

wwPDB /

NCBI

Related items in Molecule of the Month

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Deposited unit

L1: 5.8S rRNA

L5: 28S rRNA

L8: Large ribosomal subunit protein uL18

L9: 5S rRNA

LB: Large ribosomal subunit protein uL3

LC: Large ribosomal subunit protein uL4

LD: Large ribosomal subunit protein uL2

LE: Large ribosomal subunit protein uL24

LF: Large ribosomal subunit protein uL30

LG: Large ribosomal subunit protein eL8

LH: Large ribosomal subunit protein uL6

LI: Large ribosomal subunit protein eL32

LJ: Large ribosomal subunit protein uL5

LK: Large ribosomal subunit protein eL6

LM: Large ribosomal subunit protein eL14

LN: Large ribosomal subunit protein eL15

LO: Large ribosomal subunit protein uL29

LP: Large ribosomal subunit protein eL37

LQ: Large ribosomal subunit protein eL13

LR: Large ribosomal subunit protein eL19

LS: Large ribosomal subunit protein eL20

LT: Large ribosomal subunit protein eL21

LU: Large ribosomal subunit protein eL39

LV: Large ribosomal subunit protein uL14

LW: Large ribosomal subunit protein eL24

LY: Large ribosomal subunit protein uL13

LZ: Large ribosomal subunit protein eL27

La: Large ribosomal subunit protein uL15

Lb: Large ribosomal subunit protein eL29

Lc: Large ribosomal subunit protein eL30

Ld: Large ribosomal subunit protein eL31

Le: Large ribosomal subunit protein eL42

Lf: Large ribosomal subunit protein eL33

Lg: Large ribosomal subunit protein eL34

Lh: Large ribosomal subunit protein uL22

Li: Large ribosomal subunit protein eL36

Lj: Large ribosomal subunit protein eL18

Lk: Large ribosomal subunit protein eL38

Ll: Large ribosomal subunit protein eL28

Lm: Large ribosomal subunit protein eL22

Ln: Large ribosomal subunit protein uL23

Lo: Large ribosomal subunit protein eL40

Lp: Large ribosomal subunit protein eL43

Lz: Large ribosomal subunit protein uL16

S1: Small ribosomal subunit protein eS1

SA: Small ribosomal subunit protein uS2

SC: Small ribosomal subunit protein uS5

SD: Small ribosomal subunit protein uS7

SE: Small ribosomal subunit protein eS4, X isoform

SG: Small ribosomal subunit protein eS6

SH: Small ribosomal subunit protein eS7

SI: Small ribosomal subunit protein eS8

SJ: Small ribosomal subunit protein uS4

SK: Small ribosomal subunit protein uS3

SL: Small ribosomal subunit protein uS17

SM: Small ribosomal subunit protein eS10

SN: Small ribosomal subunit protein uS15

SO: Small ribosomal subunit protein uS11

SP: Small ribosomal subunit protein uS19

SQ: Small ribosomal subunit protein uS9

SS: Small ribosomal subunit protein eS17

ST: Small ribosomal subunit protein uS13

SU: Small ribosomal subunit protein eS19

SV: Small ribosomal subunit protein eS21

SW: Small ribosomal subunit protein uS8

SX: Small ribosomal subunit protein uS12

SY: Isoform 3 of Small ribosomal subunit protein eS24

SZ: Small ribosomal subunit protein uS10

Sa: Small ribosomal subunit protein eS26

Sb: Small ribosomal subunit protein eS27

Sc: Small ribosomal subunit protein eS25

Sd: Small ribosomal subunit protein eS28

Se: FAU ubiquitin-like and ribosomal protein S30

Sf: Small ribosomal subunit protein uS14

Sg: Receptor of activated protein C kinase 1

So: Small ribosomal subunit protein eS32

Sy: Small ribosomal subunit protein eS12

Sz: Ubiquitin-40S ribosomal protein S27a

S2: 18S rRNA

hetero molecules

3.8 MDa, 79 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software
Evidence: electron microscopy, not applicable

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RNA chain , 4 types, 4 molecules L1L5L9S2

#1: RNA chain	5.8S rRNA Mass: 50463.840 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: GenBank: 555853
#2: RNA chain	28S rRNA Mass: 1640938.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
#4: RNA chain	5S rRNA Mass: 38998.078 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: GenBank: 23898
#79: RNA chain	18S rRNA Mass: 603582.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)

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Large ribosomal subunit protein ... , 41 types, 41 molecules L8LBLCLDLELFLGLHLILJLKLMLNLOLPLQLRLSLTLULVLWLYLZLaLbLcLdLeLf...

#3: Protein	Large ribosomal subunit protein uL18 / 60S ribosomal protein L5 Mass: 34426.789 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P46777
#5: Protein	Large ribosomal subunit protein uL3 / 60S ribosomal protein L3 / HIV-1 TAR RNA-binding protein B / TARBP-B Mass: 46224.133 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P39023
#6: Protein	Large ribosomal subunit protein uL4 / 60S ribosomal protein L4 / 60S ribosomal protein L1 Mass: 47804.621 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P36578
#7: Protein	Large ribosomal subunit protein uL2 / 60S ribosomal protein L8 Mass: 28103.855 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62917
#8: Protein	Large ribosomal subunit protein uL24 / 60S ribosomal protein L26 Mass: 17303.363 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P61254
#9: Protein	Large ribosomal subunit protein uL30 / 60S ribosomal protein L7 Mass: 29306.973 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P18124
#10: Protein	Large ribosomal subunit protein eL8 / 60S ribosomal protein L7a / PLA-X polypeptide / Surfeit locus protein 3 Mass: 30061.785 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62424
#11: Protein	Large ribosomal subunit protein uL6 / 60S ribosomal protein L9 Mass: 21899.471 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P32969
#12: Protein	Large ribosomal subunit protein eL32 / 60S ribosomal protein L32 Mass: 15898.932 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62910
#13: Protein	Large ribosomal subunit protein uL5 / 60S ribosomal protein L11 / CLL-associated antigen KW-12 Mass: 20288.465 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62913
#14: Protein	Large ribosomal subunit protein eL6 / 60S ribosomal protein L6 / Neoplasm-related protein C140 / Tax-responsive enhancer element-binding ...60S ribosomal protein L6 / Neoplasm-related protein C140 / Tax-responsive enhancer element-binding protein 107 / TaxREB107 Mass: 32810.176 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q02878
#15: Protein	Large ribosomal subunit protein eL14 / 60S ribosomal protein L14 / CAG-ISL 7 Mass: 23485.016 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P50914
#16: Protein	Large ribosomal subunit protein eL15 / 60S ribosomal protein L15 Mass: 24207.285 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P61313
#17: Protein	Large ribosomal subunit protein uL29 / 60S ribosomal protein L35 Mass: 14593.624 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P42766
#18: Protein	Large ribosomal subunit protein eL37 / 60S ribosomal protein L37 / G1.16 Mass: 11111.032 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P61927
#19: Protein	Large ribosomal subunit protein eL13 / 60S ribosomal protein L13 / Breast basic conserved protein 1 Mass: 24321.682 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P26373
#20: Protein	Large ribosomal subunit protein eL19 / 60S ribosomal protein L19 Mass: 23535.281 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P84098
#21: Protein	Large ribosomal subunit protein eL20 / 60S ribosomal protein L18a Mass: 20808.514 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q02543
#22: Protein	Large ribosomal subunit protein eL21 / 60S ribosomal protein L21 Mass: 18609.988 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P46778
#23: Protein	Large ribosomal subunit protein eL39 / 60S ribosomal protein L39 Mass: 6426.759 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62891
#24: Protein	Large ribosomal subunit protein uL14 / 60S ribosomal protein L23 / 60S ribosomal protein L17 Mass: 14892.505 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62829
#25: Protein	Large ribosomal subunit protein eL24 / 60S ribosomal protein L24 / 60S ribosomal protein L30 Mass: 17825.111 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P83731
#26: Protein	Large ribosomal subunit protein uL13 / 60S ribosomal protein L13a / 23 kDa highly basic protein Mass: 23633.412 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P40429
#27: Protein	Large ribosomal subunit protein eL27 / 60S ribosomal protein L27 Mass: 15835.831 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P61353
#28: Protein	Large ribosomal subunit protein uL15 / 60S ribosomal protein L27a Mass: 16619.527 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P46776
#29: Protein	Large ribosomal subunit protein eL29 Mass: 18017.555 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q6IPI1
#30: Protein	Large ribosomal subunit protein eL30 / 60S ribosomal protein L30 Mass: 12805.092 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62888
#31: Protein	Large ribosomal subunit protein eL31 / 60S ribosomal protein L31 Mass: 14494.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62899
#32: Protein	Large ribosomal subunit protein eL42 / 60S ribosomal protein L36a / 60S ribosomal protein L44 / Cell growth-inhibiting gene 15 protein / ...60S ribosomal protein L36a / 60S ribosomal protein L44 / Cell growth-inhibiting gene 15 protein / Cell migration-inducing gene 6 protein Mass: 12489.991 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P83881
#33: Protein	Large ribosomal subunit protein eL33 / 60S ribosomal protein L35a / Cell growth-inhibiting gene 33 protein Mass: 12564.743 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P18077
#34: Protein	Large ribosomal subunit protein eL34 / 60S ribosomal protein L34 Mass: 13326.074 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P49207
#35: Protein	Large ribosomal subunit protein uL22 / 60S ribosomal protein L17 / 60S ribosomal protein L23 / 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
#36: Protein	Large ribosomal subunit protein eL36 / 60S ribosomal protein L36 Mass: 12290.859 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9Y3U8
#37: Protein	Large ribosomal subunit protein eL18 / 60S ribosomal protein L18 Mass: 21687.676 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q07020
#38: Protein	Large ribosomal subunit protein eL38 / 60S ribosomal protein L38 Mass: 8238.948 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P63173
#39: Protein	Large ribosomal subunit protein eL28 / 60S ribosomal protein L28 Mass: 15679.466 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P46779
#40: Protein	Large ribosomal subunit protein eL22 / 60S ribosomal protein L22 / EBER-associated protein / EAP / Epstein-Barr virus small RNA-associated ...60S ribosomal protein L22 / EBER-associated protein / EAP / Epstein-Barr virus small RNA-associated protein / Heparin-binding protein HBp15 Mass: 14813.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P35268
#41: Protein	Large ribosomal subunit protein uL23 / 60S ribosomal protein L23a Mass: 17740.193 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62750
#42: Protein	Large ribosomal subunit protein eL40 / 60S ribosomal protein L40 Mass: 11512.793 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62987
#43: Protein	Large ribosomal subunit protein eL43 / 60S ribosomal protein L37a Mass: 10299.350 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P61513
#44: Protein	Large ribosomal subunit protein uL16 / 60S ribosomal protein L10 / Laminin receptor homolog / Protein QM / Ribosomal protein L10 / Tumor ...60S ribosomal protein L10 / Laminin receptor homolog / Protein QM / Ribosomal protein L10 / Tumor suppressor QM Mass: 24630.061 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P27635

+
Small ribosomal subunit protein ... , 30 types, 30 molecules S1SASCSDSESGSHSISJSKSLSMSNSOSPSQSSSTSUSVSWSXSZSaSbScSdSfSoSy

#45: Protein	Small ribosomal subunit protein eS1 / 40S ribosomal protein S3a / v-fos transformation effector protein / Fte-1 Mass: 30002.061 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P61247
#46: Protein	Small ribosomal subunit protein uS2 / 37 kDa laminin receptor precursor / 37LRP / 37/67 kDa laminin receptor / LRP/LR / 40S ribosomal ...37 kDa laminin receptor precursor / 37LRP / 37/67 kDa laminin receptor / LRP/LR / 40S ribosomal protein SA / 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 Mass: 32778.777 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P08865
#47: Protein	Small ribosomal subunit protein uS5 / 40S ribosomal protein S2 / 40S ribosomal protein S4 / Protein LLRep3 Mass: 31376.516 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P15880
#48: Protein	Small ribosomal subunit protein uS7 / 40S ribosomal protein S5 Mass: 22913.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P46782
#49: Protein	Small ribosomal subunit protein eS4, X isoform / 40S ribosomal protein S4 / SCR10 / Single copy abundant mRNA protein Mass: 29654.869 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62701
#50: Protein	Small ribosomal subunit protein eS6 / 40S ribosomal protein S6 / Phosphoprotein NP33 Mass: 28751.906 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62753
#51: Protein	Small ribosomal subunit protein eS7 / 40S ribosomal protein S7 Mass: 22168.914 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62081
#52: Protein	Small ribosomal subunit protein eS8 / 40S ribosomal protein S8 Mass: 24263.387 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62241
#53: Protein	Small ribosomal subunit protein uS4 / 40S ribosomal protein S9 Mass: 22641.564 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P46781
#54: Protein	Small ribosomal subunit protein uS3 / 40S ribosomal protein S3 Mass: 26729.369 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) References: UniProt: P23396, DNA-(apurinic or apyrimidinic site) lyase
#55: Protein	Small ribosomal subunit protein uS17 / 40S ribosomal protein S11 Mass: 18468.826 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62280
#56: Protein	Small ribosomal subunit protein eS10 / 40S ribosomal protein S10 Mass: 18933.846 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P46783
#57: Protein	Small ribosomal subunit protein uS15 / 40S ribosomal protein S13 Mass: 17259.389 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62277
#58: Protein	Small ribosomal subunit protein uS11 / 40S ribosomal protein S14 Mass: 16302.772 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62263
#59: Protein	Small ribosomal subunit protein uS19 / 40S ribosomal protein S15 / RIG protein Mass: 17076.207 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62841
#60: Protein	Small ribosomal subunit protein uS9 / 40S ribosomal protein S16 Mass: 16477.377 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62249
#61: Protein	Small ribosomal subunit protein eS17 / 40S ribosomal protein S17 Mass: 15578.156 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P08708
#62: Protein	Small ribosomal subunit protein uS13 / 40S ribosomal protein S18 / Ke-3 / Ke3 Mass: 17759.777 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62269
#63: Protein	Small ribosomal subunit protein eS19 / 40S ribosomal protein S19 Mass: 16091.562 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P39019
#64: Protein	Small ribosomal subunit protein eS21 / 40S ribosomal protein S21 Mass: 9124.389 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P63220
#65: Protein	Small ribosomal subunit protein uS8 / 40S ribosomal protein S15a Mass: 14865.555 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62244
#66: Protein	Small ribosomal subunit protein uS12 / 40S ribosomal protein S23 Mass: 15860.666 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62266
#68: Protein	Small ribosomal subunit protein uS10 / 40S ribosomal protein S20 Mass: 13398.763 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P60866
#69: Protein	Small ribosomal subunit protein eS26 / 40S ribosomal protein S26 Mass: 13047.532 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62854
#70: Protein	Small ribosomal subunit protein eS27 / 40S ribosomal protein S27 / Metallopan-stimulin 1 / MPS-1 Mass: 9480.186 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P42677
#71: Protein	Small ribosomal subunit protein eS25 / 40S ribosomal protein S25 Mass: 13776.224 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62851
#72: Protein	Small ribosomal subunit protein eS28 / 40S ribosomal protein S28 Mass: 7855.052 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62857
#74: Protein	Small ribosomal subunit protein uS14 / 40S ribosomal protein S29 Mass: 6690.821 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62273
#76: Protein/peptide	Small ribosomal subunit protein eS32 / 60S ribosomal protein L41 / HG12 / Large ribosomal subunit protein eL41 Mass: 3473.451 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62945
#77: Protein	Small ribosomal subunit protein eS12 / 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: P25398

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Protein , 4 types, 4 molecules SYSeSgSz

#67: Protein	Isoform 3 of Small ribosomal subunit protein eS24 / 40S ribosomal protein S24 Mass: 15366.284 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62847
#73: Protein	FAU ubiquitin-like and ribosomal protein S30 Mass: 14415.724 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62861
#75: Protein	Receptor of activated protein C kinase 1 / Cell proliferation-inducing gene 21 protein / Guanine nucleotide-binding protein subunit beta-2- ...Cell proliferation-inducing gene 21 protein / Guanine nucleotide-binding protein subunit beta-2-like 1 / Guanine nucleotide-binding protein subunit beta-like protein 12.3 / Human lung cancer oncogene 7 protein / HLC-7 / Receptor for activated C kinase / Small ribosomal subunit protein RACK1 Mass: 35115.652 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P63244
#78: 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: P62979

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Non-polymers , 6 types, 7142 molecules

#80: Chemical	... ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 321 / Source method: obtained synthetically / Formula: Mg
#81: Chemical	... ChemComp-K / POTASSIUM ION Mass: 39.098 Da / Num. of mol.: 94 / Source method: obtained synthetically / Formula: K
#82: Chemical	ChemComp-B3P / 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL Mass: 282.334 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₁H₂₆N₂O₆ / Comment: pH buffer*YM
#83: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#84: Chemical	ChemComp-A1BNL / N-[4-(5-benzamido-1-methyl-1H-pyrazol-3-yl)phenyl]-2-chlorobenzamide Mass: 430.886 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂₄H₁₉ClN₄O₂ / Feature type: SUBJECT OF INVESTIGATION
#85: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 6717 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	Y
Has protein modification	Y

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Experiment

Experiment	Method: ELECTRON MICROSCOPY
EM experiment	Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component	Name: 80S ribosome / Type: RIBOSOME / Entity ID: #1-#79 / Source: NATURAL
Source (natural)	Organism: Homo sapiens (human)
Buffer solution	pH: 7.5
Specimen	Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Vitrification	Cryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment	Model: Titan Krios / Image courtesy: FEI Company
Microscopy	Model: TFS KRIOS
Electron gun	Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lens	Mode: BRIGHT FIELD / Nominal defocus max: 2200 nm / Nominal defocus min: 900 nm
Image recording	Electron dose: 39.3 e/Å² / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software	Name: PHENIX / Version: 1.21_5207 / Category: model refinement
CTF correction	Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstruction	Resolution: 2.33 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 236566 / Symmetry type: POINT
Refinement	Cross valid method: NONE

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RNA chain , 4 types, 4 molecules L1L5L9S2

+
Large ribosomal subunit protein ... , 41 types, 41 molecules L8LBLCLDLELFLGLHLILJLKLMLNLOLPLQLRLSLTLULVLWLYLZLaLbLcLdLeLf...

+
Small ribosomal subunit protein ... , 30 types, 30 molecules S1SASCSDSESGSHSISJSKSLSMSNSOSPSQSSSTSUSVSWSXSZSaSbScSdSfSoSy

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Protein , 4 types, 4 molecules SYSeSgSz

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Non-polymers , 6 types, 7142 molecules

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-RNA chain , 4 types, 4 molecules L1L5L9S2

+Large ribosomal subunit protein ... , 41 types, 41 molecules L8LBLCLDLELFLGLHLILJLKLMLNLOLPLQLRLSLTLULVLWLYLZLaLbLcLdLeLf...

+Small ribosomal subunit protein ... , 30 types, 30 molecules S1SASCSDSESGSHSISJSKSLSMSNSOSPSQSSSTSUSVSWSXSZSaSbScSdSfSoSy

-Protein , 4 types, 4 molecules SYSeSgSz

-Non-polymers , 6 types, 7142 molecules

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RNA chain , 4 types, 4 molecules L1L5L9S2

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Large ribosomal subunit protein ... , 41 types, 41 molecules L8LBLCLDLELFLGLHLILJLKLMLNLOLPLQLRLSLTLULVLWLYLZLaLbLcLdLeLf...

+
Small ribosomal subunit protein ... , 30 types, 30 molecules S1SASCSDSESGSHSISJSKSLSMSNSOSPSQSSSTSUSVSWSXSZSaSbScSdSfSoSy

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Protein , 4 types, 4 molecules SYSeSgSz

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Non-polymers , 6 types, 7142 molecules

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Details

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Experimental details

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Experiment

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