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- PDB-11jj: Rabbit 80S with eEF2,IFRD2 and LARP1,40S-head-swiveled -

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Open data

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Basic information

Entry

Database: PDB / ID: 11jj

Title

Rabbit 80S with eEF2,IFRD2 and LARP1,40S-head-swiveled

Components

(40S ribosomal protein ...) x 21
(60S ribosomal protein ...) x 25
(Large ribosomal subunit protein ...) x 13
(Ribosomal protein ...) x 2
(Small ribosomal subunit protein ...) x 8
18S rRNA
28S rRNA
40S_SA_C domain-containing protein
5.8S rRNA
5S rRNA
60S acidic ribosomal protein P0
ES27L
Elongation factor 2
IFRD2
LARP1
Proliferation-associated protein 2G4
Receptor of activated protein C kinase 1
eL41
eL42
eS21
eS26
uL11

Keywords

RIBOSOME / Hibernation / In extracto Cryo EM / Rabbit

Function / homology

Function and homology information

gastrulation / ubiquitin ligase inhibitor activity / positive regulation of signal transduction by p53 class mediator / 90S preribosome / phagocytic cup / translation regulator activity / rough endoplasmic reticulum / ribosomal small subunit export from nucleus / positive regulation of apoptotic signaling pathway / MDM2/MDM4 family protein binding ...gastrulation / ubiquitin ligase inhibitor activity / positive regulation of signal transduction by p53 class mediator / 90S preribosome / phagocytic cup / translation regulator activity / rough endoplasmic reticulum / ribosomal small subunit export from nucleus / positive regulation of apoptotic signaling pathway / MDM2/MDM4 family protein binding / DNA-(apurinic or apyrimidinic site) lyase / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / ribosomal large subunit biogenesis / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / positive regulation of cell differentiation / small-subunit processome / spindle / cytoplasmic ribonucleoprotein granule / rRNA processing / cytosolic ribosome / azurophil granule lumen / transcription corepressor activity / regulation of translation / rhythmic process / large ribosomal subunit / ribosomal small subunit assembly / ribosome binding / ribosomal small subunit biogenesis / 5S rRNA binding / ribosomal large subunit assembly / small ribosomal subunit / cytosolic small ribosomal subunit / small ribosomal subunit rRNA binding / antimicrobial humoral immune response mediated by antimicrobial peptide / large ribosomal subunit rRNA binding / killing of cells of another organism / defense response to Gram-negative bacterium / cytosolic large ribosomal subunit / nucleic acid binding / perikaryon / cell differentiation / cytoplasmic translation / tRNA binding / postsynaptic density / negative regulation of translation / mitochondrial inner membrane / rRNA binding / ribosome / translation / structural constituent of ribosome / ribonucleoprotein complex / cell division / negative regulation of DNA-templated transcription / ubiquitin protein ligase binding / DNA repair / apoptotic process / mRNA binding / centrosome / negative regulation of apoptotic process / Neutrophil degranulation / nucleolus / synapse / dendrite / perinuclear region of cytoplasm / endoplasmic reticulum / DNA binding / DNA-templated transcription / RNA binding / extracellular exosome / extracellular region / zinc ion binding / membrane / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function

PA2G4 family / : / Peptidase M24A, methionine aminopeptidase, subfamily 2, binding site / Methionine aminopeptidase subfamily 2 signature. / 60s Acidic ribosomal protein / 60S acidic ribosomal protein P0 / Peptidase M24 / Metallopeptidase family M24 / Creatinase/aminopeptidase-like / : ...PA2G4 family / : / Peptidase M24A, methionine aminopeptidase, subfamily 2, binding site / Methionine aminopeptidase subfamily 2 signature. / 60s Acidic ribosomal protein / 60S acidic ribosomal protein P0 / Peptidase M24 / Metallopeptidase family M24 / Creatinase/aminopeptidase-like / : / 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 / 50S ribosomal protein L10, insertion domain superfamily / 60S ribosomal protein L10P, insertion domain / Insertion domain in 60S ribosomal protein L10P / Ribosomal protein L30e / Ribosomal protein L28e / Ribosomal L15/L27a, N-terminal / : / Ribosomal L28e/Mak16 / Ribosomal L28e protein family / Ribosomal protein L23 / Ribosomal protein L2, archaeal-type / metallochaperone-like domain / TRASH domain / Ribosomal protein L41 / Ribosomal protein L41 / : / Ribosomal protein S12e signature. / Ribosomal protein S12e / Ribosomal protein L29e / Ribosomal L29e protein family / Small (40S) ribosomal subunit Asc1/RACK1 / Ribosomal protein L27e, conserved site / Ribosomal protein L27e signature. / : / Ribosomal protein L6e signature. / Ribosomal protein S5, eukaryotic/archaeal / Ribosomal protein S2, eukaryotic / 40S Ribosomal protein S10 / Ribosomal protein L10e, conserved site / Ribosomal protein L10e signature. / S27a-like superfamily / Plectin/S10, N-terminal / Plectin/S10 domain / Ribosomal protein L24e, conserved site / Ribosomal protein L24e signature. / Ribosomal protein L44e signature. / Ribosomal protein L5 eukaryotic, C-terminal / Ribosomal L18 C-terminal region / Ribosomal protein L23/L25, N-terminal / Ribosomal protein L23, N-terminal domain / Ribosomal protein L10e / Ribosomal protein L34e, conserved site / Ribosomal protein L34e signature. / Ribosomal protein S30 / Ribosomal protein S30 / Ribosomal L40e family / Ribosomal protein L36e signature. / Ribosomal protein S10, eukaryotic/archaeal / Ribosomal protein L30e signature 1. / Ribosomal protein S25 / S25 ribosomal protein / Eukaryotic Ribosomal Protein L27, KOW domain / Ribosomal Protein L6, KOW domain / Ribosomal protein L27e / Ribosomal protein L27e superfamily / Ribosomal L27e protein family / Ribosomal protein L35Ae, conserved site / Ribosomal protein L35Ae signature. / : / : / : / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein L40e superfamily / Ribosomal protein L44e / Ribosomal protein L44 / Ribosomal protein S7e signature. / 60S ribosomal protein L35 / Ribosomal protein S17e, conserved site / Ribosomal protein S17e signature. / Ribosomal protein L6e / Ribosomal protein S2, eukaryotic/archaeal / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein S27a / 60S ribosomal protein L6E / Ribosomal protein L30e signature 2. / Ribosomal protein L30e, conserved site / Ribosomal protein L7, eukaryotic / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / Ribosomal protein L30, N-terminal / Ribosomal L30 N-terminal domain / : / Ribosomal protein L39e, conserved site / Ribosomal protein L39e signature.
Similarity search - Domain/homology

GUANOSINE-5'-DIPHOSPHATE / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein eS32 / Ribosomal protein L36a / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL16 ...GUANOSINE-5'-DIPHOSPHATE / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein eS32 / Ribosomal protein L36a / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL16 / Small ribosomal subunit protein uS4 / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein eL24 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein eL33 / Small ribosomal subunit protein eS12 / Large ribosomal subunit protein eL29 / Small ribosomal subunit protein uS9 / Large ribosomal subunit protein eL31 / Large ribosomal subunit protein eL21 / Large ribosomal subunit protein uL29 / Small ribosomal subunit protein uS10 / Small ribosomal subunit protein RACK1 / Ubiquitin-ribosomal protein eS31 fusion protein / Large ribosomal subunit protein eL6 / Large ribosomal subunit protein uL11 / Large ribosomal subunit protein uL15 / Small ribosomal subunit protein uS15 / Large ribosomal subunit protein uL10 / Large ribosomal subunit protein uL24 / Small ribosomal subunit protein eS1 / Large ribosomal subunit protein uL30 / Small ribosomal subunit protein eS7 / Large ribosomal subunit protein uL6 / Large ribosomal subunit protein eL43 / Large ribosomal subunit protein eL14 / Small ribosomal subunit protein uS12 / Large ribosomal subunit protein eL15 / Small ribosomal subunit protein uS11 / 40S ribosomal protein S24 / Large ribosomal subunit protein uL14 / Ubiquitin-like FUBI-ribosomal protein eS30 fusion protein / 40S ribosomal protein S4 / Small ribosomal subunit protein eS25 / Large ribosomal subunit protein eL30 / Small ribosomal subunit protein uS7 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein eS28 / Small ribosomal subunit protein uS2 / Large ribosomal subunit protein uL3 / Small ribosomal subunit protein eS6 / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein uS13 / Small ribosomal subunit protein eS10 / Small ribosomal subunit protein uS17 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein eL39 / Large ribosomal subunit protein eL36 / Small ribosomal subunit protein eS17 / Large ribosomal subunit protein uL5 / Large ribosomal subunit protein uL13 / Large ribosomal subunit protein eL27 / Large ribosomal subunit protein eL34 / Small ribosomal subunit protein eS27 / Small ribosomal subunit protein uS19 / Large ribosomal subunit protein eL28 / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS5 / Ubiquitin-ribosomal protein eL40 fusion protein / Large ribosomal subunit protein uL18 / Proliferation-associated protein 2G4 / Large ribosomal subunit protein eL37
Similarity search - Component

Biological species

Oryctolagus cuniculus (rabbit)

Method

ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.9 Å

Authors

Seraj, Z. / Zottig, X. / Huang, C.H. / Loveland, A.B. / Diggs, S. / Sholi, E. / Grigorieff, N. / Korostelev, A.A.

Funding support

United States, 1items

Citation

Journal: To Be Published
Title: In extracto cryo-EM reveals eEF2 as a major hibernation factor on 60S and 80S particles
Authors: Seraj, Z. / Zottig, X. / Huang, C.H. / Loveland, A.B. / Diggs, S. / Sholi, E. / Grigorieff, N. / Korostelev, A.A.

History

Deposition	Feb 27, 2026	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 2, 2026	Provider: repository / Type: Initial release
Revision 1.0	Sep 2, 2026	Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewer	Molecule: MolmilJmol/JSmol

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Downloads & links

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Download

PDBx/mmCIF format	11jj.cif.gz	5.2 MB	Display	PDBx/mmCIF format
PDB format	pdb11jj.ent.gz		Display	PDB format
PDBx/mmJSON format	11jj.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/1j/11jj ftp://data.pdbj.org/pub/pdb/validation_reports/1j/11jj	HTTPS FTP

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Related structure data

Related structure data	75740MC 75687C 75689C 75704C 75724C 75768C 11heC 11hgC 11hvC 11iqC 11khC 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	#266 - Feb 2022 Oligosaccharyltransferase similarity (134) #121 - Jan 2010 70S Ribosomes similarity (72) #130 - Oct 2010 Riboswitches similarity (2) #16 - Apr 2001 Aminoacyl-tRNA Synthetases similarity (1) #157 - Jan 2013 Transfer-Messenger RNA similarity (5) #10 - Oct 2000 Ribosome similarity (65) #253 - Jan 2021 Expressome similarity (8) #260 - Aug 2021 Ribonuclease P similarity (4) #181 - Jan 2015 Cascade and CRISPR similarity (1) #229 - Jan 2019 Fluorescent RNA Aptamers similarity (1) #146 - Feb 2012 Aminoglycoside Antibiotics similarity (3) #161 - May 2013 Ricin similarity (186) #15 - Mar 2001 Transfer RNA similarity (1) #249 - Sep 2020 SARS-CoV-2 RNA-dependent RNA Polymerase similarity (1) #210 - Jun 2017 Adenine Riboswitch in Action similarity (1) #87 - Mar 2007 Zinc Fingers similarity (1) #226 - Oct 2018 Aminoglycoside Antibiotics and Resistance similarity (3) #245 - May 2020 Spliceosomes similarity (2) #262 - Oct 2021 Fifty Years of Open Access to PDB Structures similarity (5) #65 - May 2005 Self-splicing RNA similarity (2) #105 - Sep 2008 Ribonuclease A similarity (1) #98 - Feb 2008 Small Interfering RNA similarity (1) #227 - Nov 2018 Telomerase similarity (2) #104 - Aug 2008 Selenocysteine Synthase similarity (2) #106 - Oct 2008 Poly(A) Polymerase similarity (1) #143 - Nov 2011 Toll-like Receptors similarity (1) #230 - Feb 2019 Initiation Factor eIF4E similarity (1) #81 - Sep 2006 Elongation Factors similarity (1) #89 - May 2007 Aconitase and Iron Regulatory Protein 1 similarity (1) #60 - Dec 2004 Ubiquitin similarity (4) #241 - Jan 2020 Twenty Years of Molecules similarity (1) #91 - Jul 2007 Thymine Dimers similarity (1)

PDB pages

PDBj /

wwPDB /

NCBI

Related items in Molecule of the Month

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Assembly

Deposited unit

IF: IFRD2

BB: 40S_SA_C domain-containing protein

S2: 40S ribosomal protein S2

PP: eS21

DD: Small ribosomal subunit protein uS17

58: 5.8S rRNA

6: 5S rRNA

L8: 60S ribosomal protein L8

L3: 60S ribosomal protein L3

L4: 60S ribosomal protein L4

L5: 60S ribosomal protein L5

L6: 60S ribosomal protein L6

L7: 60S ribosomal protein L7

aa: Large ribosomal subunit protein eL8

10: Ribosomal protein L10

13: Large ribosomal subunit protein eL13

14: 60S ribosomal protein L14

15: 60S ribosomal protein L15

bb: Large ribosomal subunit protein uL13

17: 60S ribosomal protein L17

19: 60S ribosomal protein L19

20: Large ribosomal subunit protein eL20

21: 60S ribosomal protein L21

22: Large ribosomal subunit protein eL22

cc: Large ribosomal subunit protein uL23

26: 60S ribosomal protein L26

27: 60S ribosomal protein L27

dd: 60S ribosomal protein L27a

29: Large ribosomal subunit protein eL29

30: 60S ribosomal protein L30

31: 60S ribosomal protein L31

32: Large ribosomal subunit protein eL32

ee: Large ribosomal subunit protein eL33

34: 60S ribosomal protein L34

35: 60S ribosomal protein L35

36: 60S ribosomal protein L36

37: 60S ribosomal protein L37

38: Large ribosomal subunit protein eL38

39: 60S ribosomal protein L39

40: Large ribosomal subunit protein eL40

41: eL41

42: eL42

ff: 60S ribosomal protein L37a

gg: 60S ribosomal protein L28

AS: 40S ribosomal protein S3a

FF: 40S ribosomal protein S13

VV: 40S ribosomal protein S27

s: 60S acidic ribosomal protein P0

t: uL11

F: Proliferation-associated protein 2G4

Q: Large ribosomal subunit protein eL18

ZZ: 40S ribosomal protein S27a

EE: 40S ribosomal protein S12

TT: 40S ribosomal protein S25

S5: Small ribosomal subunit protein uS7

WW: 40S ribosomal protein S28

II: Small ribosomal subunit protein uS9

CC: 40S ribosomal protein S10

AA: Receptor of activated protein C kinase 1

OO: 40S ribosomal protein S20

MM: Small ribosomal subunit protein eS19

LL: 40S ribosomal protein S18

XX: 40S ribosomal protein S29

RR: 40S ribosomal protein S23

SS: 40S ribosomal protein S24

S6: 40S ribosomal protein S6

S4: 40S ribosomal protein S4

S9: 40S ribosomal protein S9

S7: Small ribosomal subunit protein eS7

YY: 40S ribosomal protein S30

S3: Small ribosomal subunit protein uS3

RS: 40S ribosomal protein S17

WX: 40S ribosomal protein S15a

S8: 40S ribosomal protein S8

W: Ribosomal protein L24

GG: Small ribosomal subunit protein uS11

UU: eS26

11: 60S ribosomal protein L11

L9: 60S ribosomal protein L9

18: 18S rRNA

v: Elongation factor 2

LA: LARP1

A: Small ribosomal subunit protein uS19

ES: ES27L

28: 28S rRNA

23: Large ribosomal subunit protein uL14

hetero molecules

5.51 MDa, 86 polymers
Search similar-shape structures of this assembly by Omokage search (details)

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

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Components

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Protein , 11 types, 11 molecules IFBBPP42stFAAUUvLA

#1: Protein	IFRD2 Mass: 48112.852 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Plasmid details: cell lysate
#2: Protein	40S_SA_C domain-containing protein Mass: 24361.861 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Plasmid details: cell lysate / References: UniProt: G1TJH8
#4: Protein	eS21 Mass: 9124.389 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Plasmid details: cell lysate
#42: Protein	eL42 Mass: 12198.603 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Plasmid details: cell lysate / References: UniProt: A0A5F9D391
#48: Protein	60S acidic ribosomal protein P0 Mass: 21521.062 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Plasmid details: cell lysate / References: UniProt: G1SPK4
#49: Protein	uL11 Mass: 16561.117 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Plasmid details: cell lysate / References: UniProt: G1SMR7
#50: Protein	Proliferation-associated protein 2G4 / Cell cycle protein p38-2G4 homolog / hG4-1 / ErbB3-binding protein 1 Mass: 39962.668 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Plasmid details: cell lysate / References: UniProt: Q9UQ80
#59: Protein	Receptor of activated protein C kinase 1 Mass: 34669.113 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Plasmid details: cell lysate / References: UniProt: G1SJB4
#77: Protein	eS26 Mass: 11645.794 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: Author-provided sequence reference is GenBank XP_051702317.1 Source: (natural) Oryctolagus cuniculus (rabbit) / Plasmid details: cell lysate
#81: Protein	Elongation factor 2 Mass: 95474.203 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Plasmid details: cell lysate References: Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement
#82: Protein	LARP1 Mass: 123705.344 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Plasmid details: cell lysate

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40S ribosomal protein ... , 21 types, 21 molecules S2ASFFVVZZEETTWWCCOOLLXXRRSSS6S4S9YYRSWXS8

#3: Protein	40S ribosomal protein S2 Mass: 24441.846 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Plasmid details: cell lysate / References: UniProt: O18789
#45: Protein	40S ribosomal protein S3a Mass: 24759.145 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Plasmid details: cell lysate / References: UniProt: G1SS70
#46: Protein	40S ribosomal protein S13 Mass: 17057.113 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Plasmid details: cell lysate / References: UniProt: G1SP51
#47: Protein	40S ribosomal protein S27 Mass: 9348.990 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Plasmid details: cell lysate / References: UniProt: G1TZ76
#52: Protein	40S ribosomal protein S27a Mass: 7986.440 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Plasmid details: cell lysate / References: UniProt: G1SK22
#53: Protein	40S ribosomal protein S12 Mass: 14538.987 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Plasmid details: cell lysate / References: UniProt: G1SFR8
#54: Protein	40S ribosomal protein S25 Mass: 8526.119 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Plasmid details: cell lysate / References: UniProt: G1TDB3
#56: Protein	40S ribosomal protein S28 Mass: 7007.069 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Plasmid details: cell lysate / References: UniProt: G1TIB4
#58: Protein	40S ribosomal protein S10 Mass: 11529.682 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Plasmid details: cell lysate / References: UniProt: G1TPV3
#60: Protein	40S ribosomal protein S20 Mass: 11395.489 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Plasmid details: cell lysate / References: UniProt: G1SIZ2
#62: Protein	40S ribosomal protein S18 Mass: 16898.648 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Plasmid details: cell lysate / References: UniProt: G1TPG3
#63: Protein	40S ribosomal protein S29 Mass: 6559.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Plasmid details: cell lysate / References: UniProt: G1U7M4
#64: Protein	40S ribosomal protein S23 Mass: 15626.392 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Plasmid details: cell lysate / References: UniProt: G1SZ47
#65: Protein	40S ribosomal protein S24 Mass: 14432.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Plasmid details: cell lysate / References: UniProt: G1T3D8
#66: Protein	40S ribosomal protein S6 Mass: 27471.535 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Plasmid details: cell lysate / References: UniProt: G1TM55
#67: Protein	40S ribosomal protein S4 Mass: 29523.674 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Plasmid details: cell lysate / References: UniProt: G1TA47
#68: Protein	40S ribosomal protein S9 Mass: 21649.633 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Plasmid details: cell lysate / References: UniProt: B7NZS8
#70: Protein	40S ribosomal protein S30 Mass: 6317.539 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Plasmid details: cell lysate / References: UniProt: G1T8A2
#72: Protein	40S ribosomal protein S17 Mass: 15250.714 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Plasmid details: cell lysate / References: UniProt: G1TU13
#73: Protein	40S ribosomal protein S15a Mass: 14734.357 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Plasmid details: cell lysate / References: UniProt: G1TG89
#74: Protein	40S ribosomal protein S8 Mass: 24003.012 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: Author-provided sequence reference is GenBank XP_017201844.1 Source: (natural) Oryctolagus cuniculus (rabbit) / Plasmid details: cell lysate

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Small ribosomal subunit protein ... , 8 types, 8 molecules DDS5IIMMS7S3GGA

#5: Protein	Small ribosomal subunit protein uS17 / 40S ribosomal protein S11 Mass: 17586.766 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Plasmid details: cell lysate / References: UniProt: G1TRM4
#55: Protein	Small ribosomal subunit protein uS7 / 40S ribosomal protein S5 Mass: 21525.941 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Plasmid details: cell lysate / References: UniProt: G1TFM5
#57: Protein	Small ribosomal subunit protein uS9 / 40S ribosomal protein S16 Mass: 16032.804 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Plasmid details: cell lysate / References: UniProt: G1SGX4
#61: Protein	Small ribosomal subunit protein eS19 Mass: 15611.003 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: Author-provided sequence reference is GenBank XP_069928942.1 Source: (natural) Oryctolagus cuniculus (rabbit) / Plasmid details: cell lysate
#69: Protein	Small ribosomal subunit protein eS7 / 40S ribosomal protein S7 Mass: 21629.309 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Plasmid details: cell lysate / References: UniProt: G1SVB0
#71: Protein	Small ribosomal subunit protein uS3 / 40S ribosomal protein S3 Mass: 23704.916 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Plasmid details: cell lysate References: UniProt: G1TNM3, DNA-(apurinic or apyrimidinic site) lyase
#76: Protein	Small ribosomal subunit protein uS11 / 40S ribosomal protein S14 Mass: 14431.500 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Plasmid details: cell lysate / References: UniProt: G1T1F0
#83: Protein	Small ribosomal subunit protein uS19 / 40S ribosomal protein S15 Mass: 14065.574 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Plasmid details: cell lysate / References: UniProt: G1U0Q2

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RNA chain , 5 types, 5 molecules 58618ES28

#6: RNA chain	5.8S rRNA Mass: 50143.648 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Plasmid details: cell lysate / References: GenBank: 2795784436
#7: RNA chain	5S rRNA Mass: 38691.914 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Plasmid details: cell lysate
#80: RNA chain	18S rRNA Mass: 548040.188 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Plasmid details: cell lysate
#84: RNA chain	ES27L Mass: 1640122.500 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Plasmid details: cell lysate
#85: RNA chain	28S rRNA Mass: 1556560.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Plasmid details: cell lysate

+
60S ribosomal protein ... , 25 types, 25 molecules L8L3L4L5L6L714151719212627dd30313435363739ffgg11L9

#8: Protein	60S ribosomal protein L8 Mass: 26998.613 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Plasmid details: cell lysate / References: UniProt: G1TT27
#9: Protein	60S ribosomal protein L3 Mass: 45119.812 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Plasmid details: cell lysate / References: UniProt: G1TL06
#10: Protein	60S ribosomal protein L4 Mass: 41101.414 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Plasmid details: cell lysate / References: UniProt: A0A5F9DCT1
#11: Protein	60S ribosomal protein L5 / Large ribosomal subunit protein uL18 Mass: 34077.391 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Plasmid details: cell lysate / References: UniProt: P19949
#12: Protein	60S ribosomal protein L6 Mass: 33028.336 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Plasmid details: cell lysate / References: UniProt: G1SKF7
#13: Protein	60S ribosomal protein L7 Mass: 26658.754 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Plasmid details: cell lysate / References: UniProt: G1SV32
#17: Protein	60S ribosomal protein L14 / Large ribosomal subunit protein eL14 Mass: 16217.355 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Plasmid details: cell lysate / References: UniProt: G1SZ12
#18: Protein	60S ribosomal protein L15 Mass: 24076.088 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Plasmid details: cell lysate / References: UniProt: G1T0C1
#20: Protein	60S ribosomal protein L17 Mass: 17758.678 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Plasmid details: cell lysate / References: UniProt: G1SCJ6
#21: Protein	60S ribosomal protein L19 Mass: 21613.033 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Plasmid details: cell lysate
#23: Protein	60S ribosomal protein L21 Mass: 18478.791 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Plasmid details: cell lysate / References: UniProt: G1SHQ2
#26: Protein	60S ribosomal protein L26 Mass: 15891.787 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Plasmid details: cell lysate / References: UniProt: G1SQH0
#27: Protein	60S ribosomal protein L27 Mass: 15704.635 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Plasmid details: cell lysate / References: UniProt: G1TXF6
#28: Protein	60S ribosomal protein L27a Mass: 16489.363 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Plasmid details: cell lysate / References: UniProt: G1SNY0
#30: Protein	60S ribosomal protein L30 Mass: 10914.756 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Plasmid details: cell lysate / References: UniProt: G1TDL2
#31: Protein	60S ribosomal protein L31 Mass: 12635.694 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Plasmid details: cell lysate / References: UniProt: G1SHG0
#34: Protein	60S ribosomal protein L34 Mass: 12994.621 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Plasmid details: cell lysate / References: UniProt: G1TXG5
#35: Protein	60S ribosomal protein L35 Mass: 14435.403 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Plasmid details: cell lysate / References: UniProt: G1SIT5
#36: Protein	60S ribosomal protein L36 Mass: 11888.371 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Plasmid details: cell lysate / References: UniProt: G1TTQ5
#37: Protein	60S ribosomal protein L37 Mass: 10090.891 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Plasmid details: cell lysate / References: UniProt: U3KPD5
#39: Protein/peptide	60S ribosomal protein L39 Mass: 6324.579 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Plasmid details: cell lysate / References: UniProt: G1TTN1
#43: Protein	60S ribosomal protein L37a Mass: 10168.153 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Plasmid details: cell lysate / References: UniProt: G1SY53
#44: Protein	60S ribosomal protein L28 Mass: 14220.686 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Plasmid details: cell lysate / References: UniProt: G1U7L1
#78: Protein	60S ribosomal protein L11 Mass: 19399.498 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Plasmid details: cell lysate / References: UniProt: G1TUB8
#79: Protein	60S ribosomal protein L9 Mass: 21627.215 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Plasmid details: cell lysate / References: UniProt: G1SWI6

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Large ribosomal subunit protein ... , 13 types, 13 molecules aa13bb2022cc2932ee3840Q23

#14: Protein	Large ribosomal subunit protein eL8 Mass: 27351.377 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: Author-provided sequence reference is GenBank XP_069914725.1 Source: (natural) Oryctolagus cuniculus (rabbit) / Plasmid details: cell lysate
#16: Protein	Large ribosomal subunit protein eL13 Mass: 24200.525 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: Author-provided sequence reference is GenBank XP_051696694.1 Source: (natural) Oryctolagus cuniculus (rabbit) / Plasmid details: cell lysate
#19: Protein	Large ribosomal subunit protein uL13 / 60S ribosomal protein L13a Mass: 23144.859 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Plasmid details: cell lysate / References: UniProt: G1TVS8
#22: Protein	Large ribosomal subunit protein eL20 Mass: 20827.561 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Plasmid details: cell lysate
#24: Protein	Large ribosomal subunit protein eL22 Mass: 11495.275 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: Author-provided sequence reference is GenBank XP_069922515.1 Source: (natural) Oryctolagus cuniculus (rabbit) / Plasmid details: cell lysate
#25: Protein	Large ribosomal subunit protein uL23 / 60S ribosomal protein L23a Mass: 13727.181 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Plasmid details: cell lysate / References: UniProt: G1SE76
#29: Protein	Large ribosomal subunit protein eL29 / 60S ribosomal protein L29 Mass: 26708.707 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Plasmid details: cell lysate / References: UniProt: G1SGR6
#32: Protein	Large ribosomal subunit protein eL32 Mass: 15022.021 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: Author-provided sequence reference is GenBank XP_069913375.1 Source: (natural) Oryctolagus cuniculus (rabbit) / Plasmid details: cell lysate
#33: Protein	Large ribosomal subunit protein eL33 / 60S ribosomal protein L35a Mass: 12449.612 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Plasmid details: cell lysate / References: UniProt: G1SF08
#38: Protein	Large ribosomal subunit protein eL38 Mass: 8107.752 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Plasmid details: cell lysate
#40: Protein	Large ribosomal subunit protein eL40 / 60S ribosomal protein L40 Mass: 6199.574 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Plasmid details: cell lysate / References: UniProt: P0DXC2
#51: Protein	Large ribosomal subunit protein eL18 Mass: 21699.688 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: Author-provided sequence reference is GenBank XP_069919239.1 Source: (natural) Oryctolagus cuniculus (rabbit) / Plasmid details: cell lysate
#86: Protein	Large ribosomal subunit protein uL14 / 60S ribosomal protein L23 Mass: 14761.307 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Plasmid details: cell lysate / References: UniProt: G1T6D1

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Ribosomal protein ... , 2 types, 2 molecules 10W

#15: Protein	Ribosomal protein L10 / Ribosomal protein L10 (Predicted) Mass: 24511.861 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Plasmid details: cell lysate / References: UniProt: B7NZQ2
#75: Protein	Ribosomal protein L24 Mass: 14131.536 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Plasmid details: cell lysate / References: UniProt: G1SE28

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Protein/peptide , 1 types, 1 molecules 41

#41: Protein/peptide	eL41 / 60s ribosomal protein l41 Mass: 3473.451 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Plasmid details: cell lysate / References: UniProt: A0A087WNH4

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Non-polymers , 2 types, 5 molecules

#87: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#88: Chemical	ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₀H₁₅N₅O₁₁P₂ / Comment: GDP, energy-carrying molecule*YM

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Details

Has ligand of interest	N
Has protein modification	Y

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Experimental details

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Experiment

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

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Sample preparation

Component	Name: Rabbit Reticulocyte Lysate / Type: RIBOSOME / Entity ID: #1-#86 / Source: NATURAL
Source (natural)	Organism: Oryctolagus cuniculus (rabbit)
Buffer solution	pH: 7.3
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: OTHER / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lens	Mode: OTHER / Nominal defocus max: 2000 nm / Nominal defocus min: 700 nm
Image recording	Electron dose: 39 e/Å² / Film or detector model: OTHER

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Processing

EM software

ID	Name	Version	Category	Details (eV)
1	cisTEM	2D-TM	particle selection
4	CTFFIND	5	CTF correction
7	UCSF ChimeraX		model fitting	Used for rigid body fitting
12	cisTEM		3D reconstruction
13	PHENIX	2.0_5885	model refinement

CTF correction

Type: PHASE FLIPPING AND AMPLITUDE CORRECTION

3D reconstruction

Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 16727 / Symmetry type: POINT

Atomic model building

Protocol: RIGID BODY FIT

Atomic model building

PDB-ID: 7TOR

7tor

Accession code: 7TOR / Source name: PDB / Type: experimental model

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Protein , 11 types, 11 molecules IFBBPP42stFAAUUvLA

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40S ribosomal protein ... , 21 types, 21 molecules S2ASFFVVZZEETTWWCCOOLLXXRRSSS6S4S9YYRSWXS8

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Small ribosomal subunit protein ... , 8 types, 8 molecules DDS5IIMMS7S3GGA

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RNA chain , 5 types, 5 molecules 58618ES28

+
60S ribosomal protein ... , 25 types, 25 molecules L8L3L4L5L6L714151719212627dd30313435363739ffgg11L9

-
Large ribosomal subunit protein ... , 13 types, 13 molecules aa13bb2022cc2932ee3840Q23

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Ribosomal protein ... , 2 types, 2 molecules 10W

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Protein/peptide , 1 types, 1 molecules 41

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Non-polymers , 2 types, 5 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 , 11 types, 11 molecules IFBBPP42stFAAUUvLA

+40S ribosomal protein ... , 21 types, 21 molecules S2ASFFVVZZEETTWWCCOOLLXXRRSSS6S4S9YYRSWXS8

-Small ribosomal subunit protein ... , 8 types, 8 molecules DDS5IIMMS7S3GGA

-RNA chain , 5 types, 5 molecules 58618ES28

+60S ribosomal protein ... , 25 types, 25 molecules L8L3L4L5L6L714151719212627dd30313435363739ffgg11L9

-Large ribosomal subunit protein ... , 13 types, 13 molecules aa13bb2022cc2932ee3840Q23

-Ribosomal protein ... , 2 types, 2 molecules 10W

-Protein/peptide , 1 types, 1 molecules 41

-Non-polymers , 2 types, 5 molecules

-Details

-Experimental details

-Experiment

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-Electron microscopy imaging

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Protein , 11 types, 11 molecules IFBBPP42stFAAUUvLA

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40S ribosomal protein ... , 21 types, 21 molecules S2ASFFVVZZEETTWWCCOOLLXXRRSSS6S4S9YYRSWXS8

-
Small ribosomal subunit protein ... , 8 types, 8 molecules DDS5IIMMS7S3GGA

-
RNA chain , 5 types, 5 molecules 58618ES28

+
60S ribosomal protein ... , 25 types, 25 molecules L8L3L4L5L6L714151719212627dd30313435363739ffgg11L9

-
Large ribosomal subunit protein ... , 13 types, 13 molecules aa13bb2022cc2932ee3840Q23

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Ribosomal protein ... , 2 types, 2 molecules 10W

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Protein/peptide , 1 types, 1 molecules 41

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Non-polymers , 2 types, 5 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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