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- PDB-11he: Rabbit 60S ribosomal subunit with eEF2 domain IV closed -

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Basic information

Entry
Database: PDB / ID: 11he
TitleRabbit 60S ribosomal subunit with eEF2 domain IV closed
Components
  • (60S ribosomal protein ...) x 26
  • (Large ribosomal subunit protein ...) x 13
  • (Ribosomal protein ...) x 2
  • 28S rRNA
  • 5.8S rRNA
  • 5S rRNA
  • 60S acidic ribosomal protein P0
  • ES27L
  • Elongation factor 2
  • Proliferation-associated protein 2G4
  • eL42
  • uL11
KeywordsRIBOSOME / Hibernation / In extracto Cryo EM / Rabbit
Function / homology
Function and homology information


translational elongation / ubiquitin ligase inhibitor activity / translation elongation factor activity / positive regulation of signal transduction by p53 class mediator / rough endoplasmic reticulum / MDM2/MDM4 family protein binding / positive regulation of translation / ribosomal large subunit biogenesis / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / positive regulation of cell differentiation ...translational elongation / ubiquitin ligase inhibitor activity / translation elongation factor activity / positive regulation of signal transduction by p53 class mediator / rough endoplasmic reticulum / MDM2/MDM4 family protein binding / positive regulation of translation / ribosomal large subunit biogenesis / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / positive regulation of cell differentiation / cytoplasmic ribonucleoprotein granule / rRNA processing / azurophil granule lumen / transcription corepressor activity / regulation of translation / large ribosomal subunit / ribosome binding / 5S rRNA binding / ribosomal large subunit assembly / 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 / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / cytoplasmic translation / postsynaptic density / negative regulation of translation / rRNA binding / ribosome / translation / structural constituent of ribosome / ribonucleoprotein complex / negative regulation of DNA-templated transcription / ubiquitin protein ligase binding / mRNA binding / GTPase activity / negative regulation of apoptotic process / Neutrophil degranulation / nucleolus / synapse / GTP binding / endoplasmic reticulum / DNA-templated transcription / RNA binding / extracellular exosome / extracellular region / zinc ion binding / membrane / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
PA2G4 family / : / Peptidase M24A, methionine aminopeptidase, subfamily 2, binding site / Methionine aminopeptidase subfamily 2 signature. / 60s Acidic ribosomal protein / 60S acidic ribosomal protein P0 / Peptidase M24 / Metallopeptidase family M24 / Creatinase/aminopeptidase-like / : ...PA2G4 family / : / Peptidase M24A, methionine aminopeptidase, subfamily 2, binding site / Methionine aminopeptidase subfamily 2 signature. / 60s Acidic ribosomal protein / 60S acidic ribosomal protein P0 / Peptidase M24 / Metallopeptidase family M24 / Creatinase/aminopeptidase-like / : / 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 / 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 L1, conserved site / Ribosomal protein L1 signature. / Ribosomal protein L1 / metallochaperone-like domain / TRASH domain / Ribosomal protein L1, 3-layer alpha/beta-sandwich / Translation elongation factor EFTu-like, domain 2 / Ribosomal protein L29e / Ribosomal L29e protein family / Ribosomal protein L1-like / Ribosomal protein L1/ribosomal biogenesis protein / Ribosomal protein L1p/L10e family / Ribosomal protein L27e, conserved site / Ribosomal protein L27e signature. / Elongation factor Tu domain 2 / Ribosomal protein L10e, conserved site / Ribosomal protein L10e signature. / 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 L40e family / Ribosomal protein L36e signature. / Ribosomal protein L30e signature 1. / Eukaryotic Ribosomal Protein L27, KOW domain / Ribosomal protein L27e / Ribosomal protein L27e superfamily / Ribosomal L27e protein family / : / : / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein L40e superfamily / Ribosomal protein L44e / Ribosomal protein L44 / 60S ribosomal protein L35 / Ribosomal protein L30e signature 2. / Ribosomal protein L30e, conserved site / Ribosomal protein L7, eukaryotic / Ribosomal protein L30, N-terminal / Ribosomal L30 N-terminal domain / : / Ribosomal protein L39e, conserved site / Ribosomal protein L39e signature. / Ribosomal protein L34Ae / Ribosomal protein L34e / 60S ribosomal protein L4, C-terminal domain / 60S ribosomal protein L4 C-terminal domain / Ribosomal protein L30/YlxQ / Ribosomal protein L13, eukaryotic/archaeal / Ribosomal protein L36e / Ribosomal protein L14e domain / Ribosomal protein L36e domain superfamily / Ribosomal protein L36e / Ribosomal protein L14 / Ribosomal protein L31e, conserved site / Ribosomal protein L31e signature. / : / Translational (tr)-type GTP-binding domain / Elongation factor Tu GTP binding domain / Translational (tr)-type guanine nucleotide-binding (G) domain profile. / Ribosomal protein L37ae / Ribosomal L37ae protein family
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Ribosomal protein L36a / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein uL22 ...GUANOSINE-5'-DIPHOSPHATE / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Ribosomal protein L36a / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein eL24 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein eL29 / Large ribosomal subunit protein eL31 / Large ribosomal subunit protein eL21 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein uL1 / Large ribosomal subunit protein uL11 / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein uL10 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein uL6 / Large ribosomal subunit protein eL43 / Large ribosomal subunit protein eL14 / Large ribosomal subunit protein eL15 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein eL30 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein eL39 / Large ribosomal subunit protein eL36 / Large ribosomal subunit protein uL5 / Large ribosomal subunit protein uL13 / Large ribosomal subunit protein eL27 / Large ribosomal subunit protein eL34 / Large ribosomal subunit protein eL28 / Ubiquitin-ribosomal protein eL40 fusion protein / Large ribosomal subunit protein uL18 / Elongation factor 2 / Proliferation-associated protein 2G4 / Large ribosomal subunit protein eL37
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.86 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 24, 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

Downloads & links

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Assembly

Deposited unit
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
11: 60S ribosomal protein L11
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
24: Ribosomal protein L24
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
42: eL42
ff: 60S ribosomal protein L37a
gg: 60S ribosomal protein L28
s: 60S acidic ribosomal protein P0
t: uL11
EB: Proliferation-associated protein 2G4
u: 60S ribosomal protein L10a
Q: Large ribosomal subunit protein eL18
ES: ES27L
28: 28S rRNA
v: Elongation factor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,271,12954
Polymers4,270,49050
Non-polymers6394
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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RNA chain , 4 types, 4 molecules 585ES28

#1: 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
#2: 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
#48: RNA chain ES27L


Mass: 1640122.500 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: 28S ribosomal RNA including ES27L-B sequence was used as the sample sequence
Source: (natural) Oryctolagus cuniculus (rabbit) / Plasmid details: cell lysate
#49: 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

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60S ribosomal protein ... , 26 types, 26 molecules L8L3L4L5L7L9111415171921232627dd30313435363739ffggu

#3: Protein 60S ribosomal protein L8


Mass: 37607.992 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Plasmid details: cell lysate
#4: 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
#5: 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
#6: 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
#8: 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
#10: 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
#12: 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
#14: 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
#15: 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 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
#18: 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
#20: 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
#22: 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
#25: 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
#26: 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
#27: 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
#29: 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
#30: 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
#33: 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
#34: 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
#35: 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
#36: 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
#38: 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
#41: 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
#42: 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
#46: Protein 60S ribosomal protein L10a


Mass: 23599.887 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Plasmid details: cell lysate / References: UniProt: G1SKZ8

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

#7: 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
#9: 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
#13: 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
#16: 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
#19: Protein Large ribosomal subunit protein eL20


Mass: 22876.947 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Plasmid details: cell lysate
#21: 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
#24: 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
#28: 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
#31: 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
#32: Protein Large ribosomal subunit protein eL33


Mass: 12449.612 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
#37: 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
#39: 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
#47: 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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Ribosomal protein ... , 2 types, 2 molecules 1024

#11: 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
#23: Protein Ribosomal protein L24


Mass: 7512.774 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Plasmid details: cell lysate / References: UniProt: G1SE28

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Protein , 5 types, 5 molecules 42stEBv

#40: 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
#43: 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
#44: 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
#45: 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
#50: Protein Elongation factor 2 / EF-2


Mass: 95406.156 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Plasmid details: cell lysate
References: UniProt: P55823, Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement

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Non-polymers , 2 types, 4 molecules

#51: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#52: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


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

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Details

Has ligand of interestN
Has protein modificationN

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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: #50, #1-#49 / 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
1cisTEM2D-TMparticle selection
4CTFFIND5CTF correction
12FREALIGN9.11classification
13cisTEM3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.86 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 22323 / Symmetry type: POINT

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  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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