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- PDB-11iq: Rabbit 80S with eEF2,eIF5A and SERBP1 -

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Basic information

Entry
Database: PDB / ID: 11iq
TitleRabbit 80S with eEF2,eIF5A and SERBP1
Components
  • (40S ribosomal protein ...) x 22
  • (60S ribosomal protein ...) x 23
  • (Large ribosomal subunit protein ...) x 16
  • (Small ribosomal subunit protein ...) x 7
  • 18S rRNA
  • 28S rRNA
  • 40S_SA_C domain-containing protein
  • 5.8S rRNA
  • 5S rRNA
  • 60S acidic ribosomal protein P0
  • ES27L
  • Elongation factor 2
  • Eukaryotic translation initiation factor 5A-1
  • Proliferation-associated protein 2G4
  • Receptor of activated protein C kinase 1
  • Ribosomal protein
  • Ribosomal protein L10
  • SERBP1
  • eL41
  • eL42
  • eS21
  • eS26
  • uL11
KeywordsRIBOSOME / Hibernation / In extracto Cryo EM / Rabbit
Function / homology
Function and homology information


Synthesis of diphthamide-EEF2 / translation at postsynapse / glial cell proliferation / skeletal muscle cell differentiation / response to folic acid / positive regulation of cytoplasmic translation / Uptake and function of diphtheria toxin / lncRNA binding / gastrulation / translational elongation ...Synthesis of diphthamide-EEF2 / translation at postsynapse / glial cell proliferation / skeletal muscle cell differentiation / response to folic acid / positive regulation of cytoplasmic translation / Uptake and function of diphtheria toxin / lncRNA binding / gastrulation / translational elongation / Peptide chain elongation / response to ischemia / ubiquitin ligase inhibitor activity / translation elongation factor activity / positive regulation of signal transduction by p53 class mediator / 90S preribosome / phagocytic cup / skeletal muscle contraction / Protein methylation / cellular response to brain-derived neurotrophic factor stimulus / translation regulator activity / rough endoplasmic reticulum / ribosomal small subunit export from nucleus / positive regulation of apoptotic signaling pathway / MDM2/MDM4 family protein binding / response to endoplasmic reticulum stress / DNA-(apurinic or apyrimidinic site) lyase / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / positive regulation of translation / ribosomal large subunit biogenesis / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / response to hydrogen peroxide / 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 / p53 binding / rRNA processing / actin filament binding / cytosolic ribosome / azurophil granule lumen / transcription corepressor activity / response to estradiol / 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 / secretory granule lumen / killing of cells of another organism / defense response to Gram-negative bacterium / ficolin-1-rich granule lumen / cytosolic large ribosomal subunit / nucleic acid binding / response to ethanol / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / perikaryon / cell differentiation / cytoplasmic translation / tRNA binding / postsynapse / postsynaptic density / negative regulation of translation / mitochondrial inner membrane / response to xenobiotic stimulus / rRNA binding / cadherin 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 / GTPase activity / negative regulation of apoptotic process / Neutrophil degranulation / nucleolus / synapse / dendrite / protein kinase binding / endoplasmic reticulum membrane / GTP binding / perinuclear region of cytoplasm / glutamatergic synapse / endoplasmic reticulum
Similarity search - Function
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 / PA2G4 family / Translation elongation factor, IF5A C-terminal / Eukaryotic elongation factor 5A hypusine, DNA-binding OB fold / Translation elongation factor IF5A-like / : ...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 / PA2G4 family / Translation elongation factor, IF5A C-terminal / Eukaryotic elongation factor 5A hypusine, DNA-binding OB fold / Translation elongation factor IF5A-like / : / 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 / : / Elongation Factor G, domain II / Elongation Factor G, domain III / Elongation factor G, domain IV / Translation elongation factor EFG/EF2, domain IV / Elongation factor G, domain IV / Elongation factor G C-terminus / Elongation factor EFG, domain V-like / Elongation factor G C-terminus / Ribosomal protein L6, N-terminal / Ribosomal protein L6, N-terminal domain / Ubiquitin-like protein FUBI / 50S ribosomal protein L10, insertion domain superfamily / EF-G domain III/V-like / 60S ribosomal protein L10P, insertion domain / Insertion domain in 60S ribosomal protein L10P / Ribosomal protein L30e / Ribosomal protein L28e / Ribosomal L15/L27a, N-terminal / Tr-type G domain, conserved site / Translational (tr)-type guanine nucleotide-binding (G) domain signature. / : / Ribosomal L28e/Mak16 / Ribosomal L28e protein family / Ribosomal protein L23 / Ribosomal protein L2, archaeal-type / Ribosomal protein L1, conserved site / Ribosomal protein L1 signature. / Ribosomal protein L1 / Ribosomal protein L1, 3-layer alpha/beta-sandwich / Ribosomal protein L41 / Ribosomal protein L41 / : / Ribosomal protein S12e signature. / Translation elongation factor EFTu-like, domain 2 / Ribosomal protein S12e / Ribosomal protein L29e / Ribosomal L29e protein family / Ribosomal protein L1-like / Ribosomal protein L1/ribosomal biogenesis protein / Ribosomal protein L1p/L10e 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 / Elongation factor Tu domain 2 / 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 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
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 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 uL1 / 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 / 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 / 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 / Eukaryotic translation initiation factor 5A-1 / Elongation factor 2 / Large ribosomal subunit protein uL18 / Proliferation-associated protein 2G4 / Large ribosomal subunit protein eL37
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.4 Å
AuthorsSeraj, Z. / Zottig, X. / Huang, C.H. / Loveland, A.B. / Diggs, S. / Sholi, E. / Grigorieff, N. / Korostelev, A.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM127094 United States
CitationJournal: 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
DepositionFeb 26, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 2, 2026Provider: repository / Type: Initial release
Revision 1.0Sep 2, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
17: Large ribosomal subunit protein uL22
DD: Small ribosomal subunit protein uS17
58: 5.8S rRNA
5: 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
13: Large ribosomal subunit protein eL13
14: 60S ribosomal protein L14
15: 60S ribosomal protein L15
bb: Large ribosomal subunit protein uL13
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
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
s: 60S acidic ribosomal protein P0
EB: Proliferation-associated protein 2G4
Q: Large ribosomal subunit protein eL18
10: Ribosomal protein L10
L9: 60S ribosomal protein L9
S7: Small ribosomal subunit protein eS7
S9: 40S ribosomal protein S9
S4: 40S ribosomal protein S4
S6: 40S ribosomal protein S6
SS: 40S ribosomal protein S24
RR: 40S ribosomal protein S23
YY: 40S ribosomal protein S30
LL: 40S ribosomal protein S18
11: 60S ribosomal protein L11
GG: Small ribosomal subunit protein uS11
23: Large ribosomal subunit protein uL14
19: 60S ribosomal protein L19
v: Elongation factor 2
S3: 40S ribosomal protein S3
FF: 40S ribosomal protein S13
S8: 40S ribosomal protein S8
S2: 40S ribosomal protein S2
BB: 40S_SA_C domain-containing protein
UU: eS26
PP: eS21
JJ: 40S ribosomal protein S17
AS: 40S ribosomal protein S3a
VV: 40S ribosomal protein S27
QQ: 40S ribosomal protein S15a
24: Large ribosomal subunit protein eL24
30: Large ribosomal subunit protein eL30
ZZ: 40S ribosomal protein S27a
18: 18S rRNA
MM: Small ribosomal subunit protein eS19
AA: Receptor of activated protein C kinase 1
OO: 40S ribosomal protein S20
RB: SERBP1
EE: 40S ribosomal protein S12
CC: 40S ribosomal protein S10
II: Small ribosomal subunit protein uS9
TT: 40S ribosomal protein S25
WW: 40S ribosomal protein S28
XX: 40S ribosomal protein S29
B: Eukaryotic translation initiation factor 5A-1
u: Ribosomal protein
S5: Small ribosomal subunit protein uS7
A: Small ribosomal subunit protein uS19
t: uL11
28: 28S rRNA
ES: ES27L
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,454,25693
Polymers5,453,48687
Non-polymers7706
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Large ribosomal subunit protein ... , 16 types, 16 molecules 17aa13bb2022cc2932ee3840Q232430

#1: Protein Large ribosomal subunit protein uL22 / 60S ribosomal protein L17


Mass: 21313.025 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Plasmid details: cell lysate / References: UniProt: G1SCJ6
#11: 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
#12: Protein Large ribosomal subunit protein eL13


Mass: 27716.664 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: 7TOR_16|Chain P[auth AL13]|60S ribosomal protein L13|Oryctolagus cuniculus
Source: (natural) Oryctolagus cuniculus (rabbit) / Plasmid details: cell lysate
#15: 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
#16: 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
#18: Protein Large ribosomal subunit protein eL22


Mass: 11495.275 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Plasmid details: cell lysate
#19: 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
#23: 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
#25: Protein Large ribosomal subunit protein eL32


Mass: 15022.021 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Plasmid details: cell lysate
#26: 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
#31: 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
#33: 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
#40: 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
#53: 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
#67: Protein Large ribosomal subunit protein eL24


Mass: 17825.111 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Author-provided sequence reference is GenBank XP_002716775.1
Source: (natural) Oryctolagus cuniculus (rabbit) / Plasmid details: cell lysate
#68: Protein Large ribosomal subunit protein eL30 / 60S ribosomal protein L30


Mass: 12675.868 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Plasmid details: cell lysate / References: UniProt: G1TDL2

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Small ribosomal subunit protein ... , 7 types, 7 molecules DDS7GGMMIIS5A

#2: 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
#43: 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
#52: 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
#71: 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
#77: 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
#83: 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
#84: Protein Small ribosomal subunit protein uS19 / 40S ribosomal protein S15


Mass: 15420.263 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 5851828ES

#3: 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
#4: 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
#70: 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
#86: RNA chain 28S rRNA


Mass: 1556294.250 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Plasmid details: cell lysate
#87: 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

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60S ribosomal protein ... , 23 types, 23 molecules L8L3L4L5L6L71415212627dd313435363739ffggL91119

#5: 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
#6: 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
#7: 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
#8: 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
#9: 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
#10: Protein 60S ribosomal protein L7


Mass: 29933.471 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: 7TOR_10|Chain J[auth AL07]|60S ribosomal protein L7|Oryctolagus cuniculus
Source: (natural) Oryctolagus cuniculus (rabbit) / Plasmid details: cell lysate
#13: 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
#14: 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
#17: 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
#20: 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
#21: 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
#22: 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
#24: 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
#27: 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
#28: 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
#29: 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
#30: 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
#32: 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
#36: 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
#37: 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
#42: 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
#51: 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
#54: 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

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Protein/peptide , 1 types, 1 molecules 41

#34: 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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Protein , 13 types, 13 molecules 42sEB10vBBUUPPAARBBut

#35: 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
#38: 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
#39: Protein Proliferation-associated protein 2G4 / Cell cycle protein p38-2G4 homolog / hG4-1 / ErbB3-binding protein 1


Mass: 41869.973 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Plasmid details: cell lysate / References: UniProt: Q9UQ80
#41: 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
#55: Protein Elongation factor 2 / EF-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: UniProt: P13639, Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement
#60: Protein 40S_SA_C domain-containing protein


Mass: 32913.965 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Plasmid details: cell lysate
#61: 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
#62: 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
#72: 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
#74: Protein SERBP1


Mass: 44919.344 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Plasmid details: cell lysate
#81: Protein Eukaryotic translation initiation factor 5A-1 / eIF-5A-1 / eIF-5A1 / Eukaryotic initiation factor 5A isoform 1 / eIF-5A / eIF-4D


Mass: 16378.705 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Plasmid details: cell lysate / References: UniProt: P10160
#82: Protein Ribosomal protein


Mass: 24879.422 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Plasmid details: cell lysate / References: UniProt: G1SKZ8
#85: 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

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40S ribosomal protein ... , 22 types, 22 molecules S9S4S6SSRRYYLLS3FFS8S2JJASVVQQZZOOEECCTTWWXX

#44: 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
#45: 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
#46: 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
#47: 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
#48: 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
#49: 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
#50: 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
#56: Protein 40S ribosomal protein S3


Mass: 25215.586 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
#57: 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
#58: 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
#59: 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
#63: 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
#64: 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
#65: 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
#66: 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
#69: 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
#73: 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
#75: 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
#76: 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
#78: 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
#79: 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
#80: 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

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Non-polymers , 2 types, 6 molecules

#88: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#89: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: GDP, energy-carrying molecule*YM

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Details

Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: CELL / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Rabbit Reticulocyte Lysate / Type: RIBOSOME / Entity ID: #1-#54, #56-#87 / Source: NATURAL
Source (natural)Organism: Oryctolagus cuniculus (rabbit)
Buffer solutionpH: 7.3
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: OTHER / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: OTHER / Nominal defocus max: 2000 nm / Nominal defocus min: 700 nm
Image recordingElectron dose: 39 e/Å2 / Film or detector model: OTHER

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Processing

EM software
IDNameVersionCategoryDetails (eV)
1cisTEM2DTMparticle selection
4CTFFIND5CTF correction
7UCSF ChimeraXmodel fittingUSED FOR RIGID BODY FITTING
11FREALIGNclassification
12cisTEM3D reconstruction
13PHENIX2.0_5885model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 157683 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT
Atomic model buildingPDB-ID: 7TOR

7tor


Accession code: 7TOR / Source name: PDB / Type: experimental model
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 134.45 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0023240248
ELECTRON MICROSCOPYf_angle_d0.6098350590
ELECTRON MICROSCOPYf_chiral_restr0.036843313
ELECTRON MICROSCOPYf_plane_restr0.004424098
ELECTRON MICROSCOPYf_dihedral_angle_d22.2227129267

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