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

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Basic information

Entry
Database: PDB / ID: 11kh
TitleRabbit 80S with IFRD2 and LARP1, 40S head-swiveled
Components
  • (40S ribosomal protein ...) x 22
  • (60S ribosomal protein ...) x 25
  • (Large ribosomal subunit protein ...) x 13
  • (Small ribosomal subunit protein ...) x 8
  • 18S rRNA
  • 28S rRNA
  • 5.8S rRNA
  • 5S rRNA
  • 60S acidic ribosomal protein P0
  • ES27L
  • IFRD2
  • La-related protein 1
  • Proliferation-associated protein 2G4
  • Receptor of activated protein C kinase 1
  • Ribosomal protein L10
  • eL24
  • eL41
  • eL42
  • eS21
  • eS26
  • uL11
KeywordsRIBOSOME / Hibernation / In extracto Cryo EM / Rabbit
Function / homology
Function and homology information


cellular response to rapamycin / translation activator activity / eukaryotic initiation factor 4E binding / RNA cap binding / response to amino acid starvation / RNA 7-methylguanosine cap binding / TORC1 signaling / mRNA stabilization / post-transcriptional regulation of gene expression / ribosomal small subunit binding ...cellular response to rapamycin / translation activator activity / eukaryotic initiation factor 4E binding / RNA cap binding / response to amino acid starvation / RNA 7-methylguanosine cap binding / TORC1 signaling / mRNA stabilization / post-transcriptional regulation of gene expression / ribosomal small subunit binding / positive regulation of macroautophagy / TOR signaling / gastrulation / positive regulation of translational initiation / ubiquitin ligase inhibitor activity / positive regulation of signal transduction by p53 class mediator / 90S preribosome / positive regulation of viral genome replication / phagocytic cup / translation regulator activity / rough endoplasmic reticulum / ribosomal small subunit export from nucleus / positive regulation of apoptotic signaling pathway / negative regulation of translational initiation / MDM2/MDM4 family protein binding / translation initiation factor binding / 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) / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / positive regulation of cell differentiation / mRNA 3'-UTR binding / small-subunit processome / translational initiation / cell population proliferation / mRNA 5'-UTR binding / spindle / cytoplasmic ribonucleoprotein granule / cytoplasmic stress 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 / 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 / negative regulation of apoptotic process / Neutrophil degranulation / nucleolus / synapse / dendrite / perinuclear region of cytoplasm / SARS-CoV-2 activates/modulates innate and adaptive immune responses / endoplasmic reticulum / DNA binding / DNA-templated transcription / RNA binding / extracellular exosome / extracellular region / zinc ion binding / membrane / metal ion binding / nucleus
Similarity search - Function
Protein of unknown function DM15 / LARP1 HEAT repeat region / Tandem repeat in fly CG14066 (La related protein), human KIAA0731 and worm R144.7. Unknown function. / La domain containing protein / La domain / Domain in the RNA-binding Lupus La protein; unknown function / La-type HTH domain / La-type HTH domain profile. / PA2G4 family / : ...Protein of unknown function DM15 / LARP1 HEAT repeat region / Tandem repeat in fly CG14066 (La related protein), human KIAA0731 and worm R144.7. Unknown function. / La domain containing protein / La domain / Domain in the RNA-binding Lupus La protein; unknown function / La-type HTH domain / La-type HTH domain profile. / 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 / : / 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. / 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 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 S27a / Ribosomal protein S27a / Ribosomal protein S27a / 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. / Ribosomal protein S3, eukaryotic/archaeal / Ribosomal protein L34Ae / Ribosomal protein L34e / 60S ribosomal protein L4, C-terminal domain
Similarity search - Domain/homology
: / 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 ...: / 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 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 / 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 / Ubiquitin-ribosomal protein eL40 fusion protein / Large ribosomal subunit protein uL18 / La-related protein 1 / Proliferation-associated protein 2G4 / Large ribosomal subunit protein eL37
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsSeraj, Z. / Zottig, X. / Huang, C.H. / Loveland, A.B. / Diggs, S. / Sholi, E. / Grigorrieff, 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. / Grigorrieff, N. / Korostelev, A.A.
History
DepositionFeb 28, 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
BB: Small ribosomal subunit protein uS2
S2: 40S ribosomal protein S2
PP: eS21
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: large ribosomal subunit protein eL6
L7: 60S ribosomal protein L7
aa: Large ribosomal subunit protein eL8
L9: 60S ribosomal protein L9
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
23: 60S ribosomal protein L23
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
F: Proliferation-associated protein 2G4
Q: Large ribosomal subunit protein eL18
ES: ES27L
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
HH: 40S ribosomal protein S15
18: 18S rRNA
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: eL24
GG: Small ribosomal subunit protein uS11
UU: eS26
11: 60S ribosomal protein L11
IF: IFRD2
LA: La-related protein 1
t: uL11
28: 28S rRNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,342,61089
Polymers5,342,34885
Non-polymers2624
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Small ribosomal subunit protein ... , 8 types, 8 molecules BBDDS5IIMMS7S3GG

#1: Protein Small ribosomal subunit protein uS2


Mass: 32958.016 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Plasmid details: cell lysate
#4: 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
#56: 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
#58: 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
#62: 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
#72: 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
#74: 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
#79: 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 lyaste / References: UniProt: G1T1F0

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40S ribosomal protein ... , 22 types, 22 molecules S2ASFFVVZZEETTWWCCOOLLHHXXRRSSS6S4S9YYRSWXS8

#2: Protein 40S ribosomal protein S2


Mass: 31283.387 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Plasmid details: cell lysate
#46: 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
#47: 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
#48: 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
#53: 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
#54: Protein 40S ribosomal protein S12


Mass: 13048.244 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Plasmid details: cell lysate / References: UniProt: G1SFR8
#55: 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
#57: 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
#59: 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
#61: 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
#63: 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
#64: Protein 40S ribosomal protein S15


Mass: 14246.854 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Plasmid details: cell lysate / References: UniProt: G1U0Q2
#66: 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
#67: 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
#68: 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
#69: 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
#70: 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
#71: 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
#73: 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
#75: 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
#76: 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
#77: 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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Protein , 10 types, 10 molecules PP1042sFAAWUUIFt

#3: 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
#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
#43: 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
#49: 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
#50: Protein Proliferation-associated protein 2G4 / Cell cycle protein p38-2G4 homolog / hG4-1 / ErbB3-binding protein 1


Mass: 40091.848 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Plasmid details: cell lysate / References: UniProt: Q9UQ80
#60: 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
#78: Protein eL24


Mass: 17825.111 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Plasmid details: cell lysate / References: UniProt: G1SE28
#80: Protein eS26


Mass: 13047.532 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
#82: Protein IFRD2


Mass: 71172.375 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Plasmid details: cell lysate
#84: 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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RNA chain , 5 types, 5 molecules 585ES1828

#5: 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
#6: 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
#52: 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
#65: 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
#85: RNA chain 28S rRNA


Mass: 1555627.750 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 ... , 25 types, 25 molecules L8L3L4L5L7L91415171921232627dd30313435363739ffgg11

#7: 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
#8: 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
#9: 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
#10: 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 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
#14: 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
#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
#25: Protein 60S ribosomal protein L23


Mass: 13972.425 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Plasmid details: cell lysate / References: UniProt: G1T6D1
#27: 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
#28: 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
#29: 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
#31: 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
#32: 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
#35: 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
#36: 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
#37: 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
#38: 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
#40: 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
#44: 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
#45: 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
#81: 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

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Large ribosomal subunit protein ... , 13 types, 13 molecules L6aa13bb2022cc2932ee3840Q

#11: Protein large ribosomal subunit protein eL6


Mass: 39605.098 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Plasmid details: cell lysate
#13: 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
#26: 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
#30: 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
#33: 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
#34: 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
#39: 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
#41: 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

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Protein/peptide , 2 types, 2 molecules 41LA

#42: 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
#83: Protein/peptide La-related protein 1 / La ribonucleoprotein domain family member 1


Mass: 3992.367 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Plasmid details: cell lysate / References: UniProt: Q6PKG0

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Non-polymers , 1 types, 4 molecules

#86: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY
Has protein modificationN

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Experimental details

-
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-#85 / 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
IDNameVersionCategory
1cisTEM2DTMparticle selection
4CTFFIND5CTF correction
7UCSF ChimeraXmodel fitting
12cisTEM3D reconstruction
13ISOLDEmodel refinement
14PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 10932 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT
Atomic model buildingPDB-ID: 7TOR

7tor


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

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