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- PDB-8vft: Translating 80S rabbit ribosome stalled by emetine with eEF2 -

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Open data

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Basic information

Entry

Database: PDB / ID: 8vft

Title

Translating 80S rabbit ribosome stalled by emetine with eEF2

Components

18S rRNA
28S rRNA
5.8S rRNA
5S rRNA
E-site tRNA
P-site tRNA
RACK1
eEF2
eL13
eL14
eL15
eL18
eL19
eL20
eL21
eL22
eL24
eL27
eL28
eL29
eL30
eL31
eL32
eL33
eL34
eL36
eL37
eL38
eL39
eL40
eL41
eL42
eL43
eL6
eL8
eS1
eS10
eS12
eS17
eS19
eS21
eS24
eS25
eS26
eS27
eS28
eS30
eS31
eS4
eS6
eS7
eS8
mRNA
uL10
uL11
uL13
uL14
uL15
uL16
uL18
uL2
uL22
uL23
uL24
uL29
uL3
uL30
uL4
uL5
uL6
uS10
uS11
uS12
uS13
uS14
uS15
uS17
uS19
uS2
uS3
uS4
uS5
uS7
uS8
uS9

Keywords

RIBOSOME / stalled ribosome / tRNAs / eEF2

Function / homology

Function and homology information

ribosomal subunit / laminin receptor activity / translational elongation / ubiquitin ligase inhibitor activity / positive regulation of signal transduction by p53 class mediator / 90S preribosome / translation elongation factor activity / phagocytic cup / protein-RNA complex assembly / ribosomal small subunit export from nucleus ...ribosomal subunit / laminin receptor activity / translational elongation / ubiquitin ligase inhibitor activity / positive regulation of signal transduction by p53 class mediator / 90S preribosome / translation elongation factor activity / phagocytic cup / protein-RNA complex assembly / ribosomal small subunit export from nucleus / rough endoplasmic reticulum / laminin binding / translation regulator activity / gastrulation / MDM2/MDM4 family protein binding / cytosolic ribosome / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) lyase / cellular response to interleukin-4 / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / positive regulation of translation / ribosomal large subunit biogenesis / positive regulation of apoptotic signaling pathway / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / small-subunit processome / spindle / cytoplasmic ribonucleoprotein granule / rRNA processing / antimicrobial humoral immune response mediated by antimicrobial peptide / rhythmic process / positive regulation of canonical Wnt signaling pathway / heparin binding / large ribosomal subunit / regulation of translation / ribosome binding / virus receptor activity / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / 5S rRNA binding / ribosomal large subunit assembly / cytosolic small ribosomal subunit / large ribosomal subunit rRNA binding / defense response to Gram-negative bacterium / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / cytosolic large ribosomal subunit / killing of cells of another organism / perikaryon / cytoplasmic translation / cell differentiation / tRNA binding / mitochondrial inner membrane / rRNA binding / postsynaptic density / structural constituent of ribosome / ribosome / translation / ribonucleoprotein complex / cell division / DNA repair / GTPase activity / mRNA binding / apoptotic process / synapse / dendrite / centrosome / GTP binding / nucleolus / perinuclear region of cytoplasm / endoplasmic reticulum / Golgi apparatus / DNA binding / RNA binding / zinc ion binding / nucleus / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function

60s Acidic ribosomal protein / 60S acidic ribosomal protein P0 / : / 40S ribosomal protein SA / Elongation Factor G, domain II / Elongation Factor G, domain III / 40S ribosomal protein SA, C-terminal domain / 40S ribosomal protein SA C-terminus / Ribosomal protein L6, N-terminal / Ribosomal protein L6, N-terminal domain ...60s Acidic ribosomal protein / 60S acidic ribosomal protein P0 / : / 40S ribosomal protein SA / Elongation Factor G, domain II / Elongation Factor G, domain III / 40S ribosomal protein SA, C-terminal domain / 40S ribosomal protein SA C-terminus / Ribosomal protein L6, N-terminal / Ribosomal protein L6, N-terminal domain / Ubiquitin-like protein FUBI / Ribosomal protein L30e / Translation elongation factor EFG/EF2, domain IV / Elongation factor G, domain IV / Elongation factor G, domain IV / Elongation factor G C-terminus / Ribosomal protein L28e / Ribosomal L15/L27a, N-terminal / Elongation factor EFG, domain V-like / Elongation factor G C-terminus / Ribosomal protein L2, archaeal-type / 50S ribosomal protein L10, insertion domain superfamily / Ribosomal protein L23 / EF-G domain III/V-like / 60S ribosomal protein L10P, insertion domain / Insertion domain in 60S ribosomal protein L10P / Ribosomal L28e/Mak16 / Ribosomal L28e protein family / Tr-type G domain, conserved site / Translational (tr)-type guanine nucleotide-binding (G) domain signature. / Ribosomal protein L19e, C-terminal domain / metallochaperone-like domain / TRASH domain / : / Ribosomal protein S26e signature. / Ribosomal protein L41 / Ribosomal protein L41 / Ribosomal protein S21e, conserved site / Ribosomal protein S21e signature. / Ribosomal protein S26e / Ribosomal protein S26e superfamily / Ribosomal protein S26e / : / Ribosomal protein S12e signature. / Ribosomal protein S12e / Ribosomal protein L29e / Ribosomal L29e protein family / Ribosomal protein S19e, conserved site / Ribosomal protein S19e signature. / Small (40S) ribosomal subunit Asc1/RACK1 / Ribosomal protein S21e / Ribosomal protein S21e superfamily / Ribosomal protein S21e / Ribosomal protein S2, eukaryotic / Translation elongation factor EFTu-like, domain 2 / Ribosomal protein L22e / Ribosomal protein L22e superfamily / Ribosomal L22e protein family / Ribosomal protein L27e, conserved site / S27a-like superfamily / 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 / : / 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. / 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 / : / Ribosomal protein S17e, conserved site / Ribosomal protein S17e signature. / Ribosomal protein S25 / S25 ribosomal protein / Ribosomal protein L44e / Ribosomal protein S3Ae, conserved site / Ribosomal protein L44 / Ribosomal protein S3Ae signature. / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein S30 / Ribosomal protein S30 / Ribosomal protein L34e, conserved site / Ribosomal protein L34e signature. / Ribosomal protein S2, eukaryotic/archaeal
Similarity search - Domain/homology

emetine / GUANOSINE-5'-DIPHOSPHATE / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein eS32 / Ubiquitin-ribosomal protein eL40 fusion protein / Large ribosomal subunit protein uL16 ...emetine / GUANOSINE-5'-DIPHOSPHATE / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein eS32 / Ubiquitin-ribosomal protein eL40 fusion protein / Large ribosomal subunit protein uL16 / Small ribosomal subunit protein uS4 / 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 eL8 / Small ribosomal subunit protein eS7 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL6 / Large ribosomal subunit protein eL43 / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein eL14 / Small ribosomal subunit protein uS12 / Large ribosomal subunit protein eL15 / 40S ribosomal protein S24 / Large ribosomal subunit protein uL14 / Ubiquitin-like FUBI-ribosomal protein eS30 fusion protein / Small ribosomal subunit protein eS25 / Large ribosomal subunit protein eL30 / Large ribosomal subunit protein eL18 / Small ribosomal subunit protein eS26 / Small ribosomal subunit protein uS7 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein eS28 / Ribosomal protein L19 / Small ribosomal subunit protein eS8 / Small ribosomal subunit protein eS4 / Large ribosomal subunit protein uL3 / Small ribosomal subunit protein uS2 / Small ribosomal subunit protein eS6 / Small ribosomal subunit protein eS21 / Small ribosomal subunit protein eS19 / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein uS13 / Uncharacterized protein / Small ribosomal subunit protein eS10 / Small ribosomal subunit protein uS17 / Large ribosomal subunit protein eL22 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein eL39 / Large ribosomal subunit protein eL36 / Large ribosomal subunit protein eL20 / Small ribosomal subunit protein eS17 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein uL5 / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein eL27 / Large ribosomal subunit protein eL34 / Small ribosomal subunit protein eS27 / Large ribosomal subunit protein eL38 / Small ribosomal subunit protein uS19 / Large ribosomal subunit protein eL42 / Large ribosomal subunit protein eL32 / Small ribosomal subunit protein uS11 / Large ribosomal subunit protein eL28 / Small ribosomal subunit protein uS14 / Elongation factor 2 / Large ribosomal subunit protein eL37
Similarity search - Component

Biological species

Oryctolagus cuniculus (rabbit)

Method

ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å

Authors

Murray, J. / Shao, S.

Funding support

United States, 2items

Citation

Journal: To Be Published
Title: Structure of emetine-stalled ribosome
Authors: Murray, J. / Shao, S.

History

Deposition	Dec 22, 2023	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Dec 25, 2024	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	8vft.cif.gz	4.8 MB	Display	PDBx/mmCIF format
PDB format	pdb8vft.ent.gz		Display	PDB format
PDBx/mmJSON format	8vft.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8vft_validation.pdf.gz	2.1 MB	Display	wwPDB validaton report
Full document	8vft_full_validation.pdf.gz	2.4 MB	Display
Data in XML	8vft_validation.xml.gz	391.3 KB	Display
Data in CIF	8vft_validation.cif.gz	651.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/vf/8vft ftp://data.pdbj.org/pub/pdb/validation_reports/vf/8vft	HTTPS FTP

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Related structure data

Related structure data	43189MC 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 (145) #121 - Jan 2010 70S Ribosomes similarity (102) #130 - Oct 2010 Riboswitches similarity (2) #16 - Apr 2001 Aminoacyl-tRNA Synthetases similarity (1) #157 - Jan 2013 Transfer-Messenger RNA similarity (12) #10 - Oct 2000 Ribosome similarity (79) #253 - Jan 2021 Expressome similarity (8) #260 - Aug 2021 Ribonuclease P similarity (5) #181 - Jan 2015 Cascade and CRISPR similarity (1) #229 - Jan 2019 Fluorescent RNA Aptamers similarity (1) #161 - May 2013 Ricin similarity (233) #146 - Feb 2012 Aminoglycoside Antibiotics similarity (3) #15 - Mar 2001 Transfer RNA similarity (1) #249 - Sep 2020 SARS-CoV-2 RNA-dependent RNA Polymerase similarity (1) #210 - Jun 2017 Adenine Riboswitch in Action similarity (1) #87 - Mar 2007 Zinc Fingers similarity (1) #245 - May 2020 Spliceosomes similarity (14) #81 - Sep 2006 Elongation Factors similarity (17) #226 - Oct 2018 Aminoglycoside Antibiotics and Resistance similarity (3) #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) #104 - Aug 2008 Selenocysteine Synthase similarity (7) #227 - Nov 2018 Telomerase 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) #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

#266 - Feb 2022
Oligosaccharyltransferase
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#121 - Jan 2010
70S Ribosomes
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similarity (1)
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Transfer-Messenger RNA
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similarity (79)
#253 - Jan 2021
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Ribonuclease A
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Small Interfering RNA
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Telomerase
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Poly(A) Polymerase
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Toll-like Receptors
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similarity (1)

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Assembly

Deposited unit

A: uL2

B: uL3

C: uL4

D: uL18

E: eL6

F: uL30

G: eL8

H: uL6

I: uL16

J: uL5

L: eL13

M: eL14

N: eL15

O: uL13

P: uL22

Q: eL18

R: eL19

S: eL20

T: eL21

U: eL22

V: uL14

W: eL24

X: uL23

Y: uL24

Z: eL27

a: uL15

b: eL29

c: eL30

d: eL31

e: eL32

f: eL33

g: eL34

h: uL29

i: eL36

j: eL37

k: eL38

l: eL39

m: eL40

n: eL41

o: eL42

p: eL43

r: eL28

s: uL10

t: uL11

5: 28S rRNA

7: 5S rRNA

8: 5.8S rRNA

v: eEF2

9: 18S rRNA

AA: uS2

BB: eS1

CC: uS5

DD: uS3

EE: eS4

FF: uS7

GG: eS6

HH: eS7

II: eS8

JJ: uS4

KK: eS10

LL: uS17

MM: eS12

NN: uS15

OO: uS11

PP: uS19

QQ: uS9

RR: eS17

SS: uS13

TT: eS19

UU: uS10

VV: eS21

WW: uS8

XX: uS12

YY: eS24

ZZ: eS25

aa: eS26

bb: eS27

cc: eS28

dd: uS14

ee: eS30

ff: eS31

gg: RACK1

3: E-site tRNA

w: mRNA

2: P-site tRNA

hetero molecules

3.52 MDa, 85 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 , 77 types, 77 molecules ABCDEFGHIJLMNOPQRSTUVWXYZabcde...

#1: Protein	uL2 Mass: 28088.863 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TT27
#2: Protein	uL3 Mass: 46107.977 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TL06
#3: Protein	uL4 Mass: 47727.559 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SVW5
#4: Protein	uL18 Mass: 34481.828 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SYJ6
#5: Protein	eL6 Mass: 33028.336 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SKF7
#6: Protein	uL30 Mass: 29201.836 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TUB1
#7: Protein	eL8 Mass: 36221.516 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1STW0
#8: Protein	uL6 Mass: 21871.418 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SWI6
#9: Protein	uL16 Mass: 24643.057 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: B7NZQ2
#10: Protein	uL5 Mass: 20288.465 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TUB8
#11: Protein	eL13 Mass: 24331.723 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TPV0
#12: Protein	eL14 Mass: 23870.549 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SZ12
#13: Protein	eL15 Mass: 24207.285 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1T0C1
#14: Protein	uL13 Mass: 23533.299 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#15: Protein	uL22 Mass: 21444.221 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TVT6
#16: Protein	eL18 Mass: 21699.688 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TFE0
#17: Protein	eL19 Mass: 23535.281 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TJR3
#18: Protein	eL20 Mass: 20827.561 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TTY7
#19: Protein	eL21 Mass: 18609.988 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SHQ2
#20: Protein	eL22 Mass: 14813.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TSG1
#21: Protein	uL14 Mass: 14892.505 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1T6D1
#22: Protein	eL24 Mass: 17825.111 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SE28
#23: Protein	uL23 Mass: 17768.246 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SE76
#24: Protein	uL24 Mass: 17303.363 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SQH0
#25: Protein	eL27 Mass: 15835.831 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TXF6
#26: Protein	uL15 Mass: 16620.561 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SNY0
#27: Protein	eL29 Mass: 26708.707 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SGR6
#28: Protein	eL30 Mass: 12807.065 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TDL2
#29: Protein	eL31 Mass: 14494.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SHG0
#30: Protein	eL32 Mass: 15898.932 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1U437
#31: Protein	eL33 Mass: 12580.809 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SF08
#32: Protein	eL34 Mass: 13326.074 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TXG5
#33: Protein	uL29 Mass: 14566.599 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SIT5
#34: Protein	eL36 Mass: 12263.834 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TTQ5
#35: Protein	eL37 Mass: 11111.032 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: U3KPD5
#36: Protein	eL38 Mass: 8238.948 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1U001
#37: Protein	eL39 Mass: 6455.775 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TTN1
#38: Protein	eL40 / Ubiquitin-60S ribosomal protein L40 Mass: 10865.902 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: A0A2K5PSA0
#40: Protein	eL42 Mass: 12476.973 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1U344
#41: Protein	eL43 Mass: 10299.350 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SY53
#42: Protein	eL28 Mass: 15783.614 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1U7L1
#43: Protein	uL10 Mass: 34380.504 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SPK4
#44: Protein	uL11 Mass: 17847.619 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SMR7
#48: Protein	eEF2 / EF-2 Mass: 95605.406 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) References: UniProt: P55823, Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement
#50: Protein	uS2 / 40S ribosomal protein SA / 37 kDa laminin receptor precursor / 37LRP / 37/67 kDa laminin receptor / ...40S ribosomal protein SA / 37 kDa laminin receptor precursor / 37LRP / 37/67 kDa laminin receptor / LRP/LR / 67 kDa laminin receptor / 67LR / Laminin receptor 1 / LamR / Laminin-binding protein precursor p40 / LBP/p40 Mass: 32958.016 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TLT8
#51: Protein	eS1 / 40S ribosomal protein S3a Mass: 30002.061 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SS70
#52: Protein	uS5 Mass: 31327.395 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#53: Protein	uS3 Mass: 26715.344 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) References: UniProt: G1TNM3, DNA-(apurinic or apyrimidinic site) lyase
#54: Protein	eS4 / 40S ribosomal protein S4 Mass: 29654.869 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TK17
#55: Protein	uS7 / 40S ribosomal protein S5 Mass: 22913.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TFM5
#56: Protein	eS6 / 40S ribosomal protein S6 Mass: 28751.906 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TM55
#57: Protein	eS7 / 40S ribosomal protein S7 Mass: 22168.914 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SVB0
#58: Protein	eS8 / 40S ribosomal protein S8 Mass: 24263.387 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TJW1
#59: Protein	uS4 / Ribosomal protein S9 Mass: 22641.564 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: B7NZS8
#60: Protein	eS10 Mass: 18933.846 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TPV3
#61: Protein	uS17 / 40S ribosomal protein S11 Mass: 18468.826 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TRM4
#62: Protein	eS12 / 40S ribosomal protein S12 Mass: 14538.987 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SFR8
#63: Protein	uS15 / Ribosomal protein S13 Mass: 17259.389 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SP51
#64: Protein	uS11 Mass: 18133.984 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1U472
#65: Protein	uS19 / 40S ribosomal protein S15 Mass: 17049.182 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1U0Q2
#66: Protein	uS9 Mass: 16477.377 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SGX4
#67: Protein	eS17 / 40S ribosomal protein S17 Mass: 15552.119 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TU13
#68: Protein	uS13 / 40S ribosomal protein S18 Mass: 17759.777 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TPG3
#69: Protein	eS19 Mass: 16106.640 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TN62
#70: Protein	uS10 Mass: 13398.763 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SIZ2
#71: Protein	eS21 / 40S ribosomal protein S21 Mass: 9124.389 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TM82
#72: Protein	uS8 / 40S Ribosomal protein S15a Mass: 14865.555 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TG89
#73: Protein	uS12 / 40S ribosomal protein S23 Mass: 15844.666 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SZ47
#74: Protein	eS24 Mass: 15107.924 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1T3D8
#75: Protein	eS25 Mass: 13776.224 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TDB3
#76: Protein	eS26 Mass: 13047.532 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TFE8
#77: Protein	eS27 / 40S ribosomal protein S27 Mass: 9480.186 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TZ76
#78: Protein	eS28 / 40S Ribosomal protein S28 Mass: 7855.052 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TIB4
#79: Protein	uS14 / 40S ribosomal protein S29 Mass: 6690.821 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1U7M4
#80: Protein	eS30 / 40S ribosomal protein S30 Mass: 14498.884 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1T8A2
#81: Protein	eS31 / Ribosomal protein S27a Mass: 18004.041 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SK22
#82: Protein	RACK1 Mass: 35115.652 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SJB4

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Protein/peptide , 1 types, 1 molecules n

#39: 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) / References: UniProt: A0A087WNH4

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RNA chain , 7 types, 7 molecules 57893w2

#45: RNA chain	28S rRNA Mass: 1149054.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#46: RNA chain	5S rRNA Mass: 38691.914 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: GenBank: X06789.1
#47: RNA chain	5.8S rRNA Mass: 50157.676 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#49: RNA chain	18S rRNA Mass: 603376.750 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#83: RNA chain	E-site tRNA Mass: 24102.275 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#84: RNA chain	mRNA Mass: 1792.037 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#85: RNA chain	P-site tRNA Mass: 24453.535 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)

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Non-polymers , 4 types, 286 molecules

#86: Chemical	... ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 276 / Source method: obtained synthetically / Formula: Mg
#87: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 8 / 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
#89: Chemical	ChemComp-34G / emetine / (3beta,14beta)-6',7',10,11-tetramethoxyemetan Mass: 480.639 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂₉H₄₀N₂O₄

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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: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component	Name: rabbit ribosome stalled by emetine with eEF2 / Type: RIBOSOME / Entity ID: #1-#85 / Source: NATURAL
Molecular weight	Value: 4 MDa / Experimental value: NO
Source (natural)	Organism: Oryctolagus cuniculus (rabbit)
Buffer solution	pH: 7.5
Specimen	Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Vitrification	Cryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment	Model: Tecnai Polara / Image courtesy: FEI Company
Microscopy	Model: FEI POLARA 300
Electron gun	Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lens	Mode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 1000 nm
Image recording	Electron dose: 35 e/Å² / Film or detector model: FEI FALCON II (4k x 4k)

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Processing

CTF correction	Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstruction	Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 42975 / Symmetry type: POINT

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Protein , 77 types, 77 molecules ABCDEFGHIJLMNOPQRSTUVWXYZabcde...

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Protein/peptide , 1 types, 1 molecules n

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RNA chain , 7 types, 7 molecules 57893w2

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Protein , 77 types, 77 molecules ABCDEFGHIJLMNOPQRSTUVWXYZabcde...

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