PDB-8y0w: dormant ribosome with eIF5A, eEF2 and SERBP1

ID or keywords:

Entry

Database: PDB / ID: 8y0w

Title

dormant ribosome with eIF5A, eEF2 and SERBP1

Components

(40S ribosomal protein ...) x 30
(60S ribosomal protein ...) x 42
18S rRNA
28S rRNA
5.8S rRNA
5S rRNA
Elongation factor 2
Eukaryotic translation initiation factor 5A-1
Isoform 2 of SERPINE1 mRNA-binding protein 1
Receptor of activated protein C kinase 1
Ubiquitin-60S ribosomal protein L40

Keywords

RIBOSOME / dormant ribosome / SERBP1

Function / homology

Function and homology information

Synthesis of diphthamide-EEF2 / Hypusine synthesis from eIF5A-lysine / translation at postsynapse / positive regulation of translational termination / annulate lamellae / ribosome hibernation / translation elongation factor binding / PML body organization / positive regulation of translational elongation / SUMO binding ...Synthesis of diphthamide-EEF2 / Hypusine synthesis from eIF5A-lysine / translation at postsynapse / positive regulation of translational termination / annulate lamellae / ribosome hibernation / translation elongation factor binding / PML body organization / positive regulation of translational elongation / SUMO binding / response to folic acid / translation at presynapse / exit from mitosis / male meiosis I / eukaryotic 80S initiation complex / negative regulation of protein neddylation / optic nerve development / response to insecticide / regulation of translation involved in cellular response to UV / negative regulation of endoplasmic reticulum unfolded protein response / oxidized pyrimidine DNA binding / response to TNF agonist / positive regulation of base-excision repair / axial mesoderm development / negative regulation of formation of translation preinitiation complex / regulation of G1 to G0 transition / ribosomal protein import into nucleus / positive regulation of respiratory burst involved in inflammatory response / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of cytoplasmic translation / positive regulation of gastrulation / 90S preribosome assembly / protein tyrosine kinase inhibitor activity / protein-DNA complex disassembly / IRE1-RACK1-PP2A complex / positive regulation of endodeoxyribonuclease activity / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / nucleolus organization / positive regulation of Golgi to plasma membrane protein transport / retinal ganglion cell axon guidance / TNFR1-mediated ceramide production / negative regulation of DNA repair / negative regulation of RNA splicing / GAIT complex / positive regulation of DNA damage response, signal transduction by p53 class mediator / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / supercoiled DNA binding / TORC2 complex binding / alpha-beta T cell differentiation / neural crest cell differentiation / G1 to G0 transition / NF-kappaB complex / positive regulation of ubiquitin-protein transferase activity / cysteine-type endopeptidase activator activity involved in apoptotic process / oxidized purine DNA binding / aggresome / negative regulation of intrinsic apoptotic signaling pathway in response to hydrogen peroxide / ubiquitin-like protein conjugating enzyme binding / negative regulation of bicellular tight junction assembly / regulation of establishment of cell polarity / middle ear morphogenesis / negative regulation of phagocytosis / rRNA modification in the nucleus and cytosol / Formation of the ternary complex, and subsequently, the 43S complex / erythrocyte homeostasis / cytoplasmic side of rough endoplasmic reticulum membrane / laminin receptor activity / negative regulation of ubiquitin protein ligase activity / protein kinase A binding / ion channel inhibitor activity / pigmentation / Ribosomal scanning and start codon recognition / homeostatic process / lncRNA binding / Translation initiation complex formation / positive regulation of mitochondrial depolarization / Uptake and function of diphtheria toxin / positive regulation of T cell receptor signaling pathway / macrophage chemotaxis / fibroblast growth factor binding / negative regulation of Wnt signaling pathway / lung morphogenesis / monocyte chemotaxis / positive regulation of natural killer cell proliferation / positive regulation of activated T cell proliferation / negative regulation of translational frameshifting / Protein hydroxylation / TOR signaling / BH3 domain binding / SARS-CoV-1 modulates host translation machinery / regulation of cell division / cellular response to ethanol / mTORC1-mediated signalling / regulation of adenylate cyclase-activating G protein-coupled receptor signaling pathway / iron-sulfur cluster binding / Peptide chain elongation / skeletal muscle cell differentiation / Selenocysteine synthesis / 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)
Similarity search - Function

Intracellular hyaluronan-binding protein 4, N-terminal domain / Intracellular hyaluronan-binding protein 4 N-terminal / Hyaluronan / mRNA binding family / RNA binding protein HABP4/SERBP1 / Translation elongation factor, IF5A, hypusine site / Eukaryotic initiation factor 5A hypusine signature. / Eukaryotic elongation factor 5A hypusine, DNA-binding OB fold / : / Translation initiation factor 5A-like, N-terminal / Translation elongation factor, IF5A C-terminal ...Intracellular hyaluronan-binding protein 4, N-terminal domain / Intracellular hyaluronan-binding protein 4 N-terminal / Hyaluronan / mRNA binding family / RNA binding protein HABP4/SERBP1 / Translation elongation factor, IF5A, hypusine site / Eukaryotic initiation factor 5A hypusine signature. / Eukaryotic elongation factor 5A hypusine, DNA-binding OB fold / : / Translation initiation factor 5A-like, N-terminal / Translation elongation factor, IF5A C-terminal / Eukaryotic elongation factor 5A hypusine, DNA-binding OB fold / Translation elongation factor IF5A-like / Hyaluronan/mRNA-binding protein / Hyaluronan / mRNA binding family / 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 / Elongation Factor G, domain II / Elongation Factor G, domain III / Ubiquitin-like protein FUBI / Ribosomal protein L13e, conserved site / Ribosomal protein L13e signature. / Ribosomal protein L30e / Ribosomal protein L28e / Translation elongation factor EFG/EF2, domain IV / Ribosomal L15/L27a, N-terminal / Elongation factor G, domain IV / Elongation factor G, domain IV / Elongation factor G C-terminus / Ribosomal protein L13e / Elongation factor EFG, domain V-like / Elongation factor G C-terminus / Ribosomal protein L23 / Ribosomal protein L2, archaeal-type / Ribosomal protein L30e signature 1. / EF-G domain III/V-like / Ribosomal L28e/Mak16 / Ribosomal L28e protein family / Ribosomal protein L30e signature 2. / Ribosomal protein L30e, conserved site / Tr-type G domain, conserved site / Translational (tr)-type guanine nucleotide-binding (G) domain signature. / Ribosomal protein L13e / Ribosomal protein L30/YlxQ / 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 L1, conserved site / Ribosomal protein L1 signature. / Ribosomal protein L1 / Ribosomal protein L29e / Ribosomal L29e protein family / Ribosomal protein S19e, conserved site / Ribosomal protein S19e signature. / Ribosomal protein S5, eukaryotic/archaeal / Small (40S) ribosomal subunit Asc1/RACK1 / Ribosomal protein S21e / Ribosomal protein S21e superfamily / Ribosomal protein S21e / Ribosomal protein S2, eukaryotic / Ribosomal protein L22e / Ribosomal protein L22e superfamily / Ribosomal L22e protein family / Ribosomal protein L27e, conserved site / Ribosomal protein L27e signature. / Ribosomal protein L10e, conserved site / Ribosomal protein L10e signature. / Ribosomal protein L38e / Ribosomal protein L38e superfamily / Ribosomal L38e protein family / Ribosomal protein L10e / 40S Ribosomal protein S10 / Translation elongation factor EFTu-like, domain 2 / : / Ribosomal protein L44e signature. / Ribosomal protein S7e signature. / Ribosomal protein L24e, conserved site / Ribosomal protein L24e signature. / Ribosomal protein L19/L19e conserved site / Ribosomal protein L19, eukaryotic / Ribosomal protein L19e signature. / Ribosomal protein L1, 3-layer alpha/beta-sandwich / Plectin/S10, N-terminal / Plectin/S10 domain / : / 60S ribosomal protein L18a/ L20, eukaryotes / Ribosomal protein L6e signature. / Ribosomal protein S10, eukaryotic/archaeal / Ribosomal protein S8e subdomain, eukaryotes / :
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 / 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 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 uL1 / 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 / Eukaryotic translation initiation factor 5A-1 / 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 / SERPINE1 mRNA-binding protein 1 / 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: 3.4 Å

Authors

Du, M. / Zeng, F.

Funding support

China, 3items

Organization	Grant number	Country
National Natural Science Foundation of China (NSFC)	92169111	China
National Natural Science Foundation of China (NSFC)	32100977	China
National Natural Science Foundation of China (NSFC)	32171200	China

Citation

Journal: Front Mol Biosci / Year: 2024
Title: Implication of Stm1 in the protection of eIF5A, eEF2 and tRNA through dormant ribosomes.
Authors: Mengtan Du / Xin Li / Wanlin Dong / Fuxing Zeng /

Abstract: Dormant ribosomes are typically associated with preservation factors to protect themselves from degradation under stress conditions. Stm1/SERBP1 is one such protein that anchors the 40S and 60S ...

History

Deposition	Jan 23, 2024	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Feb 7, 2024	Provider: repository / Type: Initial release
Revision 1.1	Aug 21, 2024	Group: 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
Revision 1.2	Nov 13, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

Structure viewer	Molecule: MolmilJmol/JSmol

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Related structure data

Related structure data	37991MC 37992C 37993C 37994C 37995C 8y0uC 8y0xC 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

5: Eukaryotic translation initiation factor 5A-1

CB: Elongation factor 2

L5: 28S rRNA

L7: 5S rRNA

L8: 5.8S rRNA

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

Lz: 60S ribosomal protein L10a

S: Isoform 2 of SERPINE1 mRNA-binding protein 1

S2: 18S rRNA

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

hetero molecules

3.94 MDa, 81 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

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

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Protein , 5 types, 5 molecules 5CBLmSSg

#1: Protein	Eukaryotic translation initiation factor 5A-1 / eIF-5A-1 / eIF-5A1 / Eukaryotic initiation factor 5A isoform 1 / eIF-5A / Rev-binding factor / eIF-4D Mass: 16854.264 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P63241
#2: 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
#43: 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
#49: Protein	Isoform 2 of SERPINE1 mRNA-binding protein 1 / PAI1 RNA-binding protein 1 / PAI-RBP1 / Plasminogen activator inhibitor 1 RNA-binding protein Mass: 44341.781 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q8NC51
#81: 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

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RNA chain , 4 types, 4 molecules L5L7L8S2

#3: RNA chain	28S rRNA Mass: 1640222.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: GenBank: 86475748
#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
#5: RNA chain	5.8S rRNA / 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
#50: RNA chain	18S rRNA / Human 18S ribosomal RNA Mass: 602776.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: GenBank: 36162

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60S ribosomal protein ... , 42 types, 42 molecules LALBLCLDLELFLGLHLILJLLLMLNLOLPLQLRLSLTLULVLWLXLYLZLaLbLcLdLe...

#6: 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
#7: 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
#8: 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
#9: 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
#10: 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
#11: 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
#12: 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
#13: 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
#14: 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
#15: 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
#16: 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
#17: 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
#18: 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
#19: 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
#20: 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
#21: 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
#22: 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
#23: 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
#24: 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
#25: 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
#26: 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
#27: 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
#28: 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
#29: 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
#30: 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
#31: 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
#32: 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
#33: 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
#34: 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
#35: 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
#36: 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
#37: 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
#38: 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
#39: 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
#40: 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
#41: 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
#42: 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
#44: 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
#45: 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
#46: 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
#47: 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 / Source: (natural) Homo sapiens (human) / References: UniProt: P46779
#48: Protein	60S ribosomal protein L10a / Large ribosomal subunit protein uL1 Mass: 24879.422 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62906

+
40S ribosomal protein ... , 30 types, 30 molecules SASBSCSDSESFSGSHSISJSKSLSNSOSPSQSRSSSTSUSVSWSXSYSZSaSbScSdSe

#51: 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.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P08865
#52: 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
#53: 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
#54: 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
#55: 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
#56: 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
#57: 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
#58: 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
#59: 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
#60: 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
#61: 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
#62: 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
#63: 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
#64: 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
#65: 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
#66: 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
#67: 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
#68: Protein	40S ribosomal protein S18 / Ke-3 / Ke3 / Small ribosomal subunit protein uS13 Mass: 17759.777 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62269
#69: 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
#70: 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
#71: 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
#72: 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
#73: 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
#74: 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
#75: 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
#76: 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
#77: 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
#78: 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
#79: 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
#80: 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

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Non-polymers , 2 types, 231 molecules

#82: Chemical	... ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 226 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#83: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn / 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: dormant ribosome / Type: RIBOSOME / Details: dormant ribosome with SERBP1, eEF2 and eIF5A / Entity ID: #1-#81 / Source: NATURAL
Source (natural)	Organism: Homo sapiens (human)
Buffer solution	pH: 7.5 Details: 50mM HEPES, pH7.5, 100mM KOAc, 5mM Mg(OAc)2, 1mM DTT
Specimen	Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen support	Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
Vitrification	Instrument: FEI VITROBOT MARK II / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment	Model: Titan Krios / Image courtesy: FEI Company
Microscopy	Model: FEI TITAN KRIOS
Electron gun	Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lens	Mode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1500 nm
Image recording	Electron dose: 30 e/Å² / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software

ID	Name	Version	Category
10	RELION	3.1.0	initial Euler assignment
11	RELION	3.1.0	final Euler assignment
12	RELION	3.1.0	classification

CTF correction

Type: PHASE FLIPPING AND AMPLITUDE CORRECTION

3D reconstruction

Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 74020 / Algorithm: FOURIER SPACE / Symmetry type: POINT

Refinement

Cross valid method: NONE

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Protein , 5 types, 5 molecules 5CBLmSSg

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RNA chain , 4 types, 4 molecules L5L7L8S2

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60S ribosomal protein ... , 42 types, 42 molecules LALBLCLDLELFLGLHLILJLLLMLNLOLPLQLRLSLTLULVLWLXLYLZLaLbLcLdLe...

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40S ribosomal protein ... , 30 types, 30 molecules SASBSCSDSESFSGSHSISJSKSLSNSOSPSQSRSSSTSUSVSWSXSYSZSaSbScSdSe

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Non-polymers , 2 types, 231 molecules

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Details

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Experimental details

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Experiment

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Sample preparation

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Electron microscopy imaging

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-Protein , 5 types, 5 molecules 5CBLmSSg

-RNA chain , 4 types, 4 molecules L5L7L8S2

+60S ribosomal protein ... , 42 types, 42 molecules LALBLCLDLELFLGLHLILJLLLMLNLOLPLQLRLSLTLULVLWLXLYLZLaLbLcLdLe...

+40S ribosomal protein ... , 30 types, 30 molecules SASBSCSDSESFSGSHSISJSKSLSNSOSPSQSRSSSTSUSVSWSXSYSZSaSbScSdSe

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Protein , 5 types, 5 molecules 5CBLmSSg

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RNA chain , 4 types, 4 molecules L5L7L8S2

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60S ribosomal protein ... , 42 types, 42 molecules LALBLCLDLELFLGLHLILJLLLMLNLOLPLQLRLSLTLULVLWLXLYLZLaLbLcLdLe...

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40S ribosomal protein ... , 30 types, 30 molecules SASBSCSDSESFSGSHSISJSKSLSNSOSPSQSRSSSTSUSVSWSXSYSZSaSbScSdSe

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Non-polymers , 2 types, 231 molecules

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Details

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