PDB-9m0p: Cryo-EM structure of human 80S ribosome in complex with montanine

ID or keywords:

Entry

Database: PDB / ID: 9m0p

Title

Cryo-EM structure of human 80S ribosome in complex with montanine

Components

(40S ribosomal protein ...) x 28
(60S ribosomal protein ...) x 41
18S ribosomal RNA|HOMO SAPIENS
28S ribosomal RNA|HOMO SAPIENS
5.8S ribosomal RNA|HOMO SAPIENS
5S ribosomal RNA|HOMO SAPIENS
Elongation factor 2
HUMAN INITIATOR MET-TRNA-I|HOMO SAPIENS
Receptor of activated protein C kinase 1
Small ribosomal subunit protein uS2
Ubiquitin-60S ribosomal protein L40

Keywords

RIBOSOME

Function / homology

Function and homology information

Synthesis of diphthamide-EEF2 / translation at postsynapse / response to folic acid / translation at presynapse / exit from mitosis / optic nerve development / response to insecticide / eukaryotic 80S initiation complex / negative regulation of protein neddylation / regulation of translation involved in cellular response to UV ...Synthesis of diphthamide-EEF2 / translation at postsynapse / response to folic acid / translation at presynapse / exit from mitosis / optic nerve development / response to insecticide / eukaryotic 80S initiation complex / negative regulation of protein neddylation / regulation of translation involved in cellular response to UV / positive regulation of cytoplasmic translation / axial mesoderm development / negative regulation of formation of translation preinitiation complex / regulation of G1 to G0 transition / retinal ganglion cell axon guidance / oxidized pyrimidine DNA binding / response to TNF agonist / negative regulation of endoplasmic reticulum unfolded protein response / positive regulation of base-excision repair / ribosomal protein import into nucleus / protein-DNA complex disassembly / positive regulation of respiratory burst involved in inflammatory response / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of gastrulation / 90S preribosome assembly / protein tyrosine kinase inhibitor activity / positive regulation of endodeoxyribonuclease activity / nucleolus organization / IRE1-RACK1-PP2A complex / positive regulation of Golgi to plasma membrane protein transport / TNFR1-mediated ceramide production / alpha-beta T cell differentiation / negative regulation of DNA repair / negative regulation of RNA splicing / GAIT complex / positive regulation of DNA damage response, signal transduction by p53 class mediator / aggresome / TORC2 complex binding / G1 to G0 transition / supercoiled DNA binding / NF-kappaB complex / neural crest cell differentiation / oxidized purine DNA binding / cysteine-type endopeptidase activator activity involved in apoptotic process / middle ear morphogenesis / positive regulation of ubiquitin-protein transferase activity / negative regulation of intrinsic apoptotic signaling pathway in response to hydrogen peroxide / negative regulation of bicellular tight junction assembly / regulation of establishment of cell polarity / ubiquitin-like protein conjugating enzyme binding / rRNA modification in the nucleus and cytosol / negative regulation of phagocytosis / erythrocyte homeostasis / Formation of the ternary complex, and subsequently, the 43S complex / cytoplasmic side of rough endoplasmic reticulum membrane / negative regulation of ubiquitin protein ligase activity / protein kinase A binding / laminin receptor activity / homeostatic process / ion channel inhibitor activity / lncRNA binding / Uptake and function of diphtheria toxin / Ribosomal scanning and start codon recognition / pigmentation / Translation initiation complex formation / positive regulation of mitochondrial depolarization / macrophage chemotaxis / lung morphogenesis / positive regulation of T cell receptor signaling pathway / fibroblast growth factor binding / negative regulation of Wnt signaling pathway / positive regulation of natural killer cell proliferation / male meiosis I / monocyte chemotaxis / TOR signaling / negative regulation of translational frameshifting / BH3 domain binding / Protein hydroxylation / positive regulation of activated T cell proliferation / SARS-CoV-1 modulates host translation machinery / iron-sulfur cluster binding / regulation of adenylate cyclase-activating G protein-coupled receptor signaling pathway / regulation of cell division / cellular response to ethanol / mTORC1-mediated signalling / Peptide chain elongation / skeletal muscle cell differentiation / Selenocysteine synthesis / Formation of a pool of free 40S subunits / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / cellular response to actinomycin D / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / translational elongation / Eukaryotic Translation Termination / blastocyst development / positive regulation of GTPase activity / negative regulation of ubiquitin-dependent protein catabolic process / protein serine/threonine kinase inhibitor activity / SRP-dependent cotranslational protein targeting to membrane
Similarity search - Function

Elongation Factor G, domain II / Elongation Factor G, domain III / 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 / Translation elongation factor EFG/EF2, domain IV / Elongation factor G, domain IV ...Elongation Factor G, domain II / Elongation Factor G, domain III / 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 / Translation elongation factor EFG/EF2, domain IV / Elongation factor G, domain IV / Elongation factor G, domain IV / Elongation factor G C-terminus / Elongation factor EFG, domain V-like / Elongation factor G C-terminus / Ribosomal protein L30e / Ribosomal protein L28e / Ribosomal L15/L27a, N-terminal / EF-G domain III/V-like / Ribosomal protein L23 / Ribosomal protein L2, archaeal-type / Tr-type G domain, conserved site / Ribosomal L28e/Mak16 / Ribosomal L28e protein family / Translational (tr)-type guanine nucleotide-binding (G) domain signature. / 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 L13e, conserved site / Ribosomal protein L13e signature. / Ribosomal protein S26e / Ribosomal protein S26e superfamily / Ribosomal protein S26e / Ribosomal protein L29e / Ribosomal L29e protein family / Ribosomal protein L27e, conserved site / Small (40S) ribosomal subunit Asc1/RACK1 / Ribosomal protein L27e signature. / Ribosomal protein S5, eukaryotic/archaeal / Ribosomal protein L22e / Translation elongation factor EFTu-like, domain 2 / 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. / 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
Similarity search - Domain/homology

: / : / : / : / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) ...: / : / : / : / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein eS17 / Small ribosomal subunit protein uS2 / Elongation factor 2 / 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 / 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 eL29 / 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 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 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 / Ribosomal protein uL16-like / Large ribosomal subunit protein eL36
Similarity search - Component

Biological species

Homo sapiens (human)

Method

ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.78 Å

Authors

Sakai, R. / Tanaka, Y. / Sato, K. / Tsugita, A. / Matumoto, K. / Thaveepornkul, L. / Chimnaronk, S. / Takada, A. / Miyamoto, H. / Kurokawa, R. ...

Funding support

Japan, 2items

Citation

Journal: Biorxiv / Year: 2025
Title: Modulation of translational elongation by montanine alkaloids preferentially inhibits RNA viruses.
Authors: Sakai, R. / Sato, K. / Tsugita, A. / Thaveepornkul, L. / Takada, A. / Miyamoto, H. / Kurokawa, R. / Yoshida, M. / Yokoyama, T. / Evidente, A. / Tsuge, Y. / Watari, H. / Sumiya, T. / ...

History

Deposition	Feb 25, 2025	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Jan 14, 2026	Provider: repository / Type: Initial release
Revision 1.0	Jan 14, 2026	Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0	Jan 14, 2026	Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0	Jan 14, 2026	Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0	Jan 14, 2026	Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0	Jan 14, 2026	Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0	Jan 14, 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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Related structure data

Related structure data	63560MC 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
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Deposited unit

SL: 40S ribosomal protein S11

SR: 40S ribosomal protein S17

SP: 40S ribosomal protein S15

SQ: 40S ribosomal protein S16

SV: 40S ribosomal protein S21

SX: 40S ribosomal protein S23

Sa: 40S ribosomal protein S26

SU: 40S ribosomal protein S20

Sc: 40S ribosomal protein S28

ST: 40S ribosomal protein S19

Sg: Receptor of activated protein C kinase 1

SC: 40S ribosomal protein S2

Sd: 40S ribosomal protein S29

SJ: 40S ribosomal protein S9

SN: 40S ribosomal protein S13

SO: 40S ribosomal protein S14

SG: 40S ribosomal protein S6

SW: 40S ribosomal protein S15a

SY: 40S ribosomal protein S24

Se: 40S ribosomal protein S30

Sb: 40S ribosomal protein S27

SZ: 40S ribosomal protein S25

SA: Small ribosomal subunit protein uS2

SB: 40S ribosomal protein S3a

SE: 40S ribosomal protein S4, X isoform

SD: 40S ribosomal protein S3

SH: 40S ribosomal protein S7

SI: 40S ribosomal protein S8

SK: 40S ribosomal protein S10

SF: 40S ribosomal protein S5

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: 60S ribosomal protein L26

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: 60S 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

L5: 28S ribosomal RNA|HOMO SAPIENS

L7: 5S ribosomal RNA|HOMO SAPIENS

L8: 5.8S ribosomal RNA|HOMO SAPIENS

S2: 18S ribosomal RNA|HOMO SAPIENS

S6: HUMAN INITIATOR MET-TRNA-I|HOMO SAPIENS

CA: Elongation factor 2

hetero molecules

3.86 MDa, 78 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

+
40S ribosomal protein ... , 28 types, 28 molecules SLSRSPSQSVSXSaSUScSTSCSdSJSNSOSGSWSYSeSbSZSBSESDSHSISKSF

#1: Protein	40S ribosomal protein S11 / Small ribosomal subunit protein uS17 Mass: 18468.826 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62280
#2: Protein	40S ribosomal protein S17 / Small ribosomal subunit protein eS17 Mass: 15578.156 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P08708
#3: Protein	40S ribosomal protein S15 / RIG protein / Small ribosomal subunit protein uS19 Mass: 17076.207 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62841
#4: Protein	40S ribosomal protein S16 / Small ribosomal subunit protein uS9 Mass: 16477.377 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62249
#5: Protein	40S ribosomal protein S21 / Small ribosomal subunit protein eS21 Mass: 9124.389 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P63220
#6: Protein	40S ribosomal protein S23 / Small ribosomal subunit protein uS12 Mass: 15844.666 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62266
#7: Protein	40S ribosomal protein S26 / Small ribosomal subunit protein eS26 Mass: 13047.532 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62854
#8: Protein	40S ribosomal protein S20 / Small ribosomal subunit protein uS10 Mass: 13398.763 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P60866
#9: Protein	40S ribosomal protein S28 / Small ribosomal subunit protein eS28 Mass: 7855.052 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62857
#10: Protein	40S ribosomal protein S19 / Small ribosomal subunit protein eS19 Mass: 16091.562 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P39019
#12: Protein	40S ribosomal protein S2 / 40S ribosomal protein S4 / Protein LLRep3 / Small ribosomal subunit protein uS5 Mass: 31376.516 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P15880
#13: Protein	40S ribosomal protein S29 / Small ribosomal subunit protein uS14 Mass: 6690.821 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62273
#14: Protein	40S ribosomal protein S9 / Small ribosomal subunit protein uS4 Mass: 22641.564 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P46781
#15: Protein	40S ribosomal protein S13 / Small ribosomal subunit protein uS15 Mass: 17259.389 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62277
#16: Protein	40S ribosomal protein S14 / Small ribosomal subunit protein uS11 Mass: 16302.772 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62263
#17: Protein	40S ribosomal protein S6 / Phosphoprotein NP33 / Small ribosomal subunit protein eS6 Mass: 28751.906 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62753
#18: Protein	40S ribosomal protein S15a / Small ribosomal subunit protein uS8 Mass: 14865.555 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62244
#19: Protein	40S ribosomal protein S24 / Small ribosomal subunit protein eS24 Mass: 15463.333 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62847
#20: Protein	40S ribosomal protein S30 / Small ribosomal subunit protein eS30 Mass: 6668.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62861
#21: Protein	40S ribosomal protein S27 / Metallopan-stimulin 1 / MPS-1 / Small ribosomal subunit protein eS27 Mass: 9480.186 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P42677
#22: Protein	40S ribosomal protein S25 / Small ribosomal subunit protein eS25 Mass: 13776.224 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62851
#24: Protein	40S ribosomal protein S3a / Small ribosomal subunit protein eS1 / 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
#25: 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.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62701
#26: Protein	40S ribosomal protein S3 / Small ribosomal subunit protein uS3 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
#27: Protein	40S ribosomal protein S7 / Small ribosomal subunit protein eS7 Mass: 22168.914 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62081
#28: Protein	40S ribosomal protein S8 / Small ribosomal subunit protein eS8 Mass: 24263.387 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62241
#29: Protein	40S ribosomal protein S10 / Small ribosomal subunit protein eS10 Mass: 18933.846 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P46783
#30: Protein	40S ribosomal protein S5 / Small ribosomal subunit protein uS7 Mass: 22913.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P46782

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Protein , 4 types, 4 molecules SgSALmCA

#11: 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
#23: 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: 32883.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P08865
#68: Protein	Ubiquitin-60S ribosomal protein L40 / CEP52 / Ubiquitin A-52 residue ribosomal protein fusion product 1 Mass: 14758.394 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62987
#78: Protein	Elongation factor 2 / EF-2 Mass: 95463.211 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) References: UniProt: P13639, Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement

+
60S ribosomal protein ... , 41 types, 41 molecules LALBLCLDLELFLGLHLILJLLLMLNLOLPLQLRLSLTLULVLWLXLYLZLaLbLcLdLe...

#31: Protein	60S ribosomal protein L8 / Large ribosomal subunit protein uL2 Mass: 28088.863 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62917
#32: Protein	60S ribosomal protein L3 / Large ribosomal subunit protein uL3 Mass: 46211.113 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P39023
#33: Protein	60S ribosomal protein L4 / Large ribosomal subunit protein uL4 Mass: 47804.621 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P36578
#34: Protein	60S ribosomal protein L5 / Large ribosomal subunit protein uL18 Mass: 34426.789 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P46777
#35: Protein	60S ribosomal protein L6 / Large ribosomal subunit protein eL6 Mass: 32810.176 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q02878
#36: Protein	60S ribosomal protein L7 / Large ribosomal subunit protein uL30 Mass: 29290.973 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P18124
#37: Protein	60S ribosomal protein L7a / Large ribosomal subunit protein eL8 Mass: 30061.785 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62424
#38: Protein	60S ribosomal protein L9 / Large ribosomal subunit protein uL6 Mass: 21899.471 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P32969
#39: Protein	60S ribosomal protein L10-like / Large ribosomal subunit protein uL16-like Mass: 24570.949 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q96L21
#40: Protein	60S ribosomal protein L11 / Large ribosomal subunit protein uL5 Mass: 20288.465 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62913
#41: Protein	60S ribosomal protein L13 / Large ribosomal subunit protein eL13 Mass: 24321.682 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P26373
#42: Protein	60S ribosomal protein L14 / Large ribosomal subunit protein eL14 Mass: 23485.016 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P50914
#43: Protein	60S ribosomal protein L15 / Large ribosomal subunit protein eL15 Mass: 24207.285 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P61313
#44: Protein	60S ribosomal protein L13a / Large ribosomal subunit protein uL13 Mass: 23633.412 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P40429
#45: Protein	60S ribosomal protein L17 / Large ribosomal subunit protein uL22 Mass: 21443.170 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P18621
#46: Protein	60S ribosomal protein L18 / Large ribosomal subunit protein eL18 Mass: 21687.676 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q07020
#47: Protein	60S ribosomal protein L19 / Large ribosomal subunit protein eL19 Mass: 23535.281 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P84098
#48: Protein	60S ribosomal protein L18a / Large ribosomal subunit protein eL20 Mass: 20808.514 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q02543
#49: Protein	60S ribosomal protein L21 / Large ribosomal subunit protein eL21 Mass: 18609.988 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P46778
#50: Protein	60S ribosomal protein L22 / Large ribosomal subunit protein eL22 Mass: 14813.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P35268
#51: Protein	60S ribosomal protein L23 / Large ribosomal subunit protein uL14 Mass: 14892.505 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62829
#52: Protein	60S ribosomal protein L24 / Large ribosomal subunit protein eL24 Mass: 17825.111 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P83731
#53: Protein	60S ribosomal protein L23a / Large ribosomal subunit protein uL23 Mass: 17740.193 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62750
#54: Protein	60S ribosomal protein L26 / Large ribosomal subunit protein uL24 Mass: 17303.363 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P61254
#55: Protein	60S ribosomal protein L27 / Large ribosomal subunit protein eL27 Mass: 15835.831 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P61353
#56: Protein	60S ribosomal protein L27a / Large ribosomal subunit protein uL15 Mass: 16604.535 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P46776
#57: Protein	60S ribosomal protein L29 / Large ribosomal subunit protein eL29 Mass: 17804.275 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P47914
#58: Protein	60S ribosomal protein L30 / Large ribosomal subunit protein eL30 Mass: 12805.092 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62888
#59: Protein	60S ribosomal protein L31 / Large ribosomal subunit protein eL31 Mass: 14494.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62899
#60: Protein	60S ribosomal protein L32 / Large ribosomal subunit protein eL32 Mass: 15898.932 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62910
#61: Protein	60S ribosomal protein L35a / Large ribosomal subunit protein eL33 Mass: 12564.743 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P18077
#62: Protein	60S ribosomal protein L34 / Large ribosomal subunit protein eL34 Mass: 13326.074 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P49207
#63: Protein	60S ribosomal protein L35 / Large ribosomal subunit protein uL29 Mass: 14593.624 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P42766
#64: Protein	60S ribosomal protein L36 / Large ribosomal subunit protein eL36 Mass: 12290.859 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9Y3U8
#65: Protein	60S ribosomal protein L37 / Large ribosomal subunit protein eL37 Mass: 11111.032 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P61927
#66: Protein	60S ribosomal protein L38 / Large ribosomal subunit protein eL38 Mass: 8238.948 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P63173
#67: Protein	60S ribosomal protein L39 / Large ribosomal subunit protein eL39 Mass: 6426.759 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62891
#69: Protein/peptide	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
#70: Protein	60S ribosomal protein L36a / Large ribosomal subunit protein eL42 Mass: 12476.973 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P83881
#71: Protein	60S ribosomal protein L37a / Large ribosomal subunit protein eL43 Mass: 10299.350 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P61513
#72: Protein	60S ribosomal protein L28 / Large ribosomal subunit protein eL28 Mass: 15784.622 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: MSAHLQWMVVRNCSSFLIKRNKQTYSTEPNNLKARNSFRYNGLIHRKTVGVEPAADGKGVVVVIKRRSGQRKPATSYVRTTINKNARATLSSIRHMIRKNKYRPDLRMAAIRRASAILRSQKPVMVKRKRTRPTKSS Source: (natural) Homo sapiens (human) / References: UniProt: P46779

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RNA chain , 5 types, 5 molecules L5L7L8S2S6

#73: RNA chain	28S ribosomal RNA\|HOMO SAPIENS Mass: 1640238.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: GenBank: 86475748
#74: RNA chain	5S ribosomal RNA\|HOMO SAPIENS Mass: 38998.078 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: GenBank: 23898
#75: RNA chain	5.8S ribosomal RNA\|HOMO SAPIENS / Human ribosomal DNA complete repeating unit Mass: 50449.812 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: GenBank: 555853
#76: RNA chain	18S ribosomal RNA\|HOMO SAPIENS Mass: 602752.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: GenBank: 36162
#77: RNA chain	HUMAN INITIATOR MET-TRNA-I\|HOMO SAPIENS Mass: 24231.510 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: GenBank: 174924

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Non-polymers , 3 types, 298 molecules

#79: Chemical	... ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 291 / Source method: obtained synthetically / Formula: Mg
#80: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#81: Chemical	ChemComp-A1L8F / (1S,13S,15S,16S)-16-methoxy-5,7-dioxa-12-azapentacyclo[10.6.1.02,10.04,8.013,18]nonadeca-2,4(8),9,17-tetraen-15-ol / Montanine Mass: 301.337 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₇H₁₉NO₄ / Feature type: SUBJECT OF INVESTIGATION

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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: human 80S ribosome in complex with montanine / Type: RIBOSOME / Entity ID: #1-#78 / Source: NATURAL
Source (natural)	Organism: Homo sapiens (human)
Buffer solution	pH: 7.4
Specimen	Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Vitrification	Cryogen name: ETHANE

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Electron microscopy imaging

Microscopy	Model: JEOL CRYO ARM 300
Electron gun	Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lens	Mode: BRIGHT FIELD / Nominal defocus max: 2400 nm / Nominal defocus min: 1200 nm
Image recording	Electron dose: 40 e/Å² / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software

ID	Name	Version	Category
1	cryoSPARC	4.1.2	particle selection
2	PHENIX	1.21_5207	model refinement
13	cryoSPARC	4.1.2	3D reconstruction

CTF correction

Type: PHASE FLIPPING AND AMPLITUDE CORRECTION

3D reconstruction

Resolution: 2.78 Å / Resolution method: FSC 0.143 CUT-OFF / Symmetry type: POINT

Refinement

Highest resolution: 2.78 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
ELECTRON MICROSCOPY	f_bond_d	0.004	216624
ELECTRON MICROSCOPY	f_angle_d	0.681	317803
ELECTRON MICROSCOPY	f_dihedral_angle_d	23.614	91847
ELECTRON MICROSCOPY	f_chiral_restr	0.04	39483
ELECTRON MICROSCOPY	f_plane_restr	0.006	20658

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40S ribosomal protein ... , 28 types, 28 molecules SLSRSPSQSVSXSaSUScSTSCSdSJSNSOSGSWSYSeSbSZSBSESDSHSISKSF

-
Protein , 4 types, 4 molecules SgSALmCA

+
60S ribosomal protein ... , 41 types, 41 molecules LALBLCLDLELFLGLHLILJLLLMLNLOLPLQLRLSLTLULVLWLXLYLZLaLbLcLdLe...

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RNA chain , 5 types, 5 molecules L5L7L8S2S6

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Non-polymers , 3 types, 298 molecules

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Experiment

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Sample preparation

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+40S ribosomal protein ... , 28 types, 28 molecules SLSRSPSQSVSXSaSUScSTSCSdSJSNSOSGSWSYSeSbSZSBSESDSHSISKSF

-Protein , 4 types, 4 molecules SgSALmCA

+60S ribosomal protein ... , 41 types, 41 molecules LALBLCLDLELFLGLHLILJLLLMLNLOLPLQLRLSLTLULVLWLXLYLZLaLbLcLdLe...

-RNA chain , 5 types, 5 molecules L5L7L8S2S6

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40S ribosomal protein ... , 28 types, 28 molecules SLSRSPSQSVSXSaSUScSTSCSdSJSNSOSGSWSYSeSbSZSBSESDSHSISKSF

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Protein , 4 types, 4 molecules SgSALmCA

+
60S ribosomal protein ... , 41 types, 41 molecules LALBLCLDLELFLGLHLILJLLLMLNLOLPLQLRLSLTLULVLWLXLYLZLaLbLcLdLe...

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RNA chain , 5 types, 5 molecules L5L7L8S2S6

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Non-polymers , 3 types, 298 molecules

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Details

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Experimental details

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Experiment

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