[English] 日本語
Yorodumi
- PDB-9bdp: 80S ribosome bound with angiogenin and complex of eEF1A and Ala-t... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9bdp
Title80S ribosome bound with angiogenin and complex of eEF1A and Ala-tRNAAla
Components
  • (40S ribosomal protein ...) x 23
  • (60S ribosomal protein ...) x 28
  • (Large ribosomal subunit protein ...) x 10
  • (Ribosomal protein ...) x 3
  • (Small ribosomal subunit protein ...) x 4
  • 18S rRNA
  • 28S rRNA
  • 40S_SA_C domain-containing protein
  • 5.8S rRNA
  • 5S rRNA
  • 60S acidic ribosomal protein P0
  • Angiogenin
  • Elongation factor 1-alpha
  • Receptor of activated protein C kinase 1
  • eL41
  • eL42
  • eS21
  • eS26
  • mRNA
  • tRNAAla
  • tRNAfMet
  • uL11
KeywordsRIBOSOME / Angiogenin / RNase
Function / homology
Function and homology information


Eukaryotic Translation Elongation / eukaryotic translation elongation factor 1 complex / activation of phospholipase A2 activity / angiogenin-PRI complex / diacylglycerol biosynthetic process / tRNA-derived small RNA (tsRNA or tRNA-related fragment, tRF) biogenesis / tRNA decay / HSF1 activation / melatonin binding / tRNA export from nucleus ...Eukaryotic Translation Elongation / eukaryotic translation elongation factor 1 complex / activation of phospholipase A2 activity / angiogenin-PRI complex / diacylglycerol biosynthetic process / tRNA-derived small RNA (tsRNA or tRNA-related fragment, tRF) biogenesis / tRNA decay / HSF1 activation / melatonin binding / tRNA export from nucleus / cell communication / sulfur compound metabolic process / ribosomal subunit / Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters / Adherens junctions interactions / Protein methylation / fungal-type vacuole membrane / oocyte maturation / regulation of G1 to G0 transition / exit from mitosis / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / regulation of translation involved in cellular response to UV / protein-DNA complex disassembly / positive regulation of DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / optic nerve development / translational elongation / mammalian oogenesis stage / retinal ganglion cell axon guidance / G1 to G0 transition / homeostatic process / activation-induced cell death of T cells / positive regulation of signal transduction by p53 class mediator / ubiquitin ligase inhibitor activity / rRNA transcription / phagocytic cup / actin filament bundle assembly / : / basement membrane / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / TOR signaling / T cell proliferation involved in immune response / protein-RNA complex assembly / RNA nuclease activity / ribosomal small subunit export from nucleus / erythrocyte development / translation regulator activity / translation elongation factor activity / cellular response to actinomycin D / cytosolic ribosome / ovarian follicle development / rough endoplasmic reticulum / positive regulation of phosphorylation / endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / gastrulation / MDM2/MDM4 family protein binding / positive regulation of endothelial cell proliferation / Neutrophil degranulation / RNA endonuclease activity / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / cellular response to amino acid starvation / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) lyase / activation of protein kinase B activity / negative regulation of ubiquitin-dependent protein catabolic process / actin filament polymerization / rescue of stalled ribosome / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / 90S preribosome / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / negative regulation of protein phosphorylation / response to hormone / maturation of LSU-rRNA / ribosomal large subunit biogenesis / cellular response to leukemia inhibitory factor / maturation of SSU-rRNA / positive regulation of translation / positive regulation of protein secretion / small-subunit processome / positive regulation of apoptotic signaling pathway / protein kinase C binding / peptide binding / negative regulation of smooth muscle cell proliferation / negative regulation of protein kinase activity / positive regulation of protein-containing complex assembly / placenta development / cellular response to gamma radiation / mRNA 5'-UTR binding / transcription coactivator binding / cytoplasmic ribonucleoprotein granule / spindle / G1/S transition of mitotic cell cycle / rRNA processing / antimicrobial humoral immune response mediated by antimicrobial peptide / large ribosomal subunit / GDP binding / actin filament binding / rhythmic process / cell migration / actin cytoskeleton / positive regulation of canonical Wnt signaling pathway
Similarity search - Function
Translation elongation factor EF1A, eukaryotic/archaeal / 60s Acidic ribosomal protein / Translation elongation factor EFTu/EF1A, C-terminal / Elongation factor Tu C-terminal domain / 60S acidic ribosomal protein P0 / 40S ribosomal protein SA, C-terminal domain / 40S ribosomal protein SA C-terminus / Ubiquitin-like protein FUBI / Ribosomal protein L6, N-terminal / Ribosomal protein L6, N-terminal domain ...Translation elongation factor EF1A, eukaryotic/archaeal / 60s Acidic ribosomal protein / Translation elongation factor EFTu/EF1A, C-terminal / Elongation factor Tu C-terminal domain / 60S acidic ribosomal protein P0 / 40S ribosomal protein SA, C-terminal domain / 40S ribosomal protein SA C-terminus / Ubiquitin-like protein FUBI / Ribosomal protein L6, N-terminal / Ribosomal protein L6, N-terminal domain / Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal / Ribosomal protein L30e / Ribosomal protein L2, archaeal-type / Ribosomal protein L28e / Ribosomal L15/L27a, N-terminal / Pancreatic ribonuclease / Ribonuclease A, active site / Ribonuclease A-domain / Ribonuclease A-like domain superfamily / Pancreatic ribonuclease / Pancreatic ribonuclease family signature. / Pancreatic ribonuclease / Ribosomal protein L23 / 50S ribosomal protein L10, insertion domain superfamily / Ribosomal L28e/Mak16 / Ribosomal L28e protein family / 60S ribosomal protein L10P, insertion domain / Insertion domain in 60S ribosomal protein L10P / : / Ribosomal protein S26e signature. / Tr-type G domain, conserved site / Translational (tr)-type guanine nucleotide-binding (G) domain signature. / : / Ribosomal protein L41 / Ribosomal protein L41 / Ribosomal protein S26e / Ribosomal protein S26e superfamily / Ribosomal protein S26e / Ribosomal protein S21e, conserved site / Ribosomal protein S21e signature. / Ribosomal protein S12e signature. / metallochaperone-like domain / Ribosomal protein S12e / TRASH domain / Ribosomal protein S5, eukaryotic/archaeal / Ribosomal protein S19e, conserved site / Ribosomal protein S19e signature. / Small (40S) ribosomal subunit Asc1/RACK1 / Ribosomal protein S2, eukaryotic / Ribosomal protein S21e / Ribosomal protein S21e superfamily / Ribosomal protein S21e / Ribosomal protein L29e / Ribosomal L29e protein family / 40S Ribosomal protein S10 / Ribosomal protein S10, eukaryotic/archaeal / Plectin/S10, N-terminal / Plectin/S10 domain / Ribosomal protein L22e / Ribosomal protein L22e superfamily / Ribosomal L22e protein family / Ribosomal protein L38e / Ribosomal protein L38e superfamily / Ribosomal L38e protein family / Ribosomal protein S2, eukaryotic/archaeal / : / Ribosomal protein S17e, conserved site / Ribosomal protein S17e signature. / Ribosomal protein S8e subdomain, eukaryotes / Ribosomal protein S30 / Ribosomal protein S30 / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / Ribosomal protein L27e, conserved site / Ribosomal protein L27e signature. / Ribosomal protein S7e signature. / Ribosomal protein L44e signature. / Ribosomal protein L10e, conserved site / Ribosomal protein L10e signature. / Ribosomal protein S3, eukaryotic/archaeal / Ribosomal protein L10e / Ribosomal protein L13e / Ribosomal protein L13e / Ribosomal protein L19, eukaryotic / Ribosomal protein S19e / Ribosomal protein S3Ae, conserved site / Ribosomal protein S19e / Ribosomal protein S3Ae signature. / Ribosomal_S19e / Ribosomal protein S27e signature. / 60S ribosomal protein L18a/ L20, eukaryotes / Ribosomal protein S4e, N-terminal, conserved site / Ribosomal protein S4e signature. / 40S ribosomal protein S4, C-terminal domain / 40S ribosomal protein S4 C-terminus / : / Ribosomal protein S19A/S15e / Ribosomal protein S8e, conserved site / Ribosomal protein S8e signature. / Ribosomal protein L24e, conserved site / Ribosomal protein L24e signature.
Similarity search - Domain/homology
: / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein eS32 / Large ribosomal subunit protein eL42 / Large ribosomal subunit protein uL4 ...: / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein eS32 / Large ribosomal subunit protein eL42 / 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 / Large ribosomal subunit protein eL6 / Large ribosomal subunit protein uL11 / Large ribosomal subunit protein uL15 / Small ribosomal subunit protein uS15 / Large ribosomal subunit protein uL10 / Large ribosomal subunit protein uL24 / Small ribosomal subunit protein eS1 / Large ribosomal subunit protein eL8 / 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 / Large ribosomal subunit protein eL30 / Large ribosomal subunit protein eL18 / Small ribosomal subunit protein eS26 / Small ribosomal subunit protein uS7 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein eS28 / 40S ribosomal protein SA / Small ribosomal subunit protein eS8 / Large ribosomal subunit protein eL13 / Large ribosomal subunit protein uL3 / Small ribosomal subunit protein eS6 / Small ribosomal subunit protein eS21 / Small ribosomal subunit protein eS19 / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein uS13 / Small ribosomal subunit protein eS10 / Small ribosomal subunit protein uS17 / Large ribosomal subunit protein eL22 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein eL39 / Large ribosomal subunit protein eL36 / Large ribosomal subunit protein eL20 / Small ribosomal subunit protein eS17 / Large ribosomal subunit protein uL5 / Large ribosomal subunit protein eL32 / Ribosomal protein L13a / Large ribosomal subunit protein eL27 / Large ribosomal subunit protein eL34 / Large ribosomal subunit protein eL19 / Small ribosomal subunit protein eS27 / Large ribosomal subunit protein eL38 / Small ribosomal subunit protein uS19 / Large ribosomal subunit protein eL28 / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS5 / Elongation factor 1-alpha / Angiogenin / Ubiquitin-ribosomal protein eL40 fusion protein / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein eL37
Similarity search - Component
Biological speciesHomo sapiens (human)
Saccharomyces cerevisiae (brewer's yeast)
Oryctolagus cuniculus (rabbit)
Escherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsLoveland, A.B. / Korostelev, A.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM127094 United States
CitationJournal: Nature / Year: 2024
Title: Structural mechanism of angiogenin activation by the ribosome.
Authors: Anna B Loveland / Cha San Koh / Robin Ganesan / Allan Jacobson / Andrei A Korostelev /
Abstract: Angiogenin, an RNase-A-family protein, promotes angiogenesis and has been implicated in cancer, neurodegenerative diseases and epigenetic inheritance. After activation during cellular stress, ...Angiogenin, an RNase-A-family protein, promotes angiogenesis and has been implicated in cancer, neurodegenerative diseases and epigenetic inheritance. After activation during cellular stress, angiogenin cleaves tRNAs at the anticodon loop, resulting in translation repression. However, the catalytic activity of isolated angiogenin is very low, and the mechanisms of the enzyme activation and tRNA specificity have remained a puzzle. Here we identify these mechanisms using biochemical assays and cryogenic electron microscopy (cryo-EM). Our study reveals that the cytosolic ribosome is the activator of angiogenin. A cryo-EM structure features angiogenin bound in the A site of the 80S ribosome. The C-terminal tail of angiogenin is rearranged by interactions with the ribosome to activate the RNase catalytic centre, making the enzyme several orders of magnitude more efficient in tRNA cleavage. Additional 80S-angiogenin structures capture how tRNA substrate is directed by the ribosome into angiogenin's active site, demonstrating that the ribosome acts as the specificity factor. Our findings therefore suggest that angiogenin is activated by ribosomes with a vacant A site, the abundance of which increases during cellular stress. These results may facilitate the development of therapeutics to treat cancer and neurodegenerative diseases.
History
DepositionApr 12, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 24, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A18S: 18S rRNA
A28S: 28S rRNA
A58S: 5.8S rRNA
A5S: 5S rRNA
AL02: 60S ribosomal protein L8
AL03: 60S ribosomal protein L3
AL04: 60S ribosomal protein L4
AL05: 60S ribosomal protein L5
AL06: 60S ribosomal protein L6
AL07: 60S ribosomal protein L7
AL08: Large ribosomal subunit protein eL8
AL09: 60S ribosomal protein L9
AL10: Ribosomal protein L10
AL11: 60S ribosomal protein L11
AL12: uL11
AL13: Large ribosomal subunit protein eL13
AL14: 60S ribosomal protein L14
AL15: 60S ribosomal protein L15
AL16: Large ribosomal subunit protein uL13
AL17: 60S ribosomal protein L17
AL18: Large ribosomal subunit protein eL18
AL19: 60S ribosomal protein L19
AL20: 60S ribosomal protein L18a
AL21: 60S ribosomal protein L21
AL22: Large ribosomal subunit protein eL22
AL23: 60S ribosomal protein L23
AL24: Ribosomal protein L24
AL25: Large ribosomal subunit protein uL23
AL26: 60S ribosomal protein L26
AL27: 60S ribosomal protein L27
AL28: 60S ribosomal protein L27a
AL29: Large ribosomal subunit protein eL29
AL30: 60S ribosomal protein L30
AL31: 60S ribosomal protein L31
AL32: Large ribosomal subunit protein eL32
AL33: 60S ribosomal protein L35a
AL34: 60S ribosomal protein L34
AL35: 60S ribosomal protein L35
AL36: 60S ribosomal protein L36
AL37: 60S ribosomal protein L37
AL38: Large ribosomal subunit protein eL38
AL39: 60S ribosomal protein L39
AL40: Large ribosomal subunit protein eL40
AL41: eL41
AL42: eL42
AL43: 60S ribosomal protein L37a
ALNW: 60S ribosomal protein L28
ALP0: 60S acidic ribosomal protein P0
ANG: Angiogenin
ARAC: Receptor of activated protein C kinase 1
AS00: 40S_SA_C domain-containing protein
AS01: 40S ribosomal protein S3a
AS02: 40S ribosomal protein S2
AS03: 40S ribosomal protein S3
AS04: 40S ribosomal protein S4
AS05: Ribosomal protein S5
AS06: 40S ribosomal protein S6
AS07: Small ribosomal subunit protein eS7
AS08: 40S ribosomal protein S8
AS09: 40S ribosomal protein S9
AS10: 40S ribosomal protein S10
AS11: 40S ribosomal protein S11
AS12: 40S ribosomal protein S12
AS13: 40S ribosomal protein S13
AS14: Small ribosomal subunit protein uS11
AS15: 40S ribosomal protein S15
AS16: Small ribosomal subunit protein uS9
AS17: 40S ribosomal protein S17
AS18: 40S ribosomal protein S18
AS19: Small ribosomal subunit protein eS19
AS20: 40S ribosomal protein S20
AS21: eS21
AS22: 40S ribosomal protein S15a
AS23: 40S ribosomal protein S23
AS24: 40S ribosomal protein S24
AS25: 40S ribosomal protein S25
AS26: eS26
AS27: 40S ribosomal protein S27
AS28: 40S ribosomal protein S28
AS29: 40S ribosomal protein S29
AS30: 40S ribosomal protein S30
EF1A: Elongation factor 1-alpha
ETRN: tRNAfMet
MRNA: mRNA
PTRN: tRNAfMet
TIRN: tRNAAla


Theoretical massNumber of molelcules
Total (without water)3,385,48186
Polymers3,385,48186
Non-polymers00
Water00
1


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

-
Components

-
RNA chain , 7 types, 8 molecules A18SA28SA58SA5SETRNPTRNMRNATIRN

#1: RNA chain 18S rRNA


Mass: 602777.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Tissue: Reticulocyte
#2: RNA chain 28S rRNA


Mass: 1166972.250 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Tissue: Reticulocyte
#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) / Tissue: Reticulocyte
#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) / Tissue: Reticulocyte / References: GenBank: X06789.1
#83: RNA chain tRNAfMet


Mass: 24802.785 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: GenBank: 1848934315
#84: RNA chain mRNA


Mass: 8591.155 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#85: RNA chain tRNAAla


Mass: 24486.477 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Production host: Escherichia coli (E. coli) / References: GenBank: 1163001469

+
60S ribosomal protein ... , 28 types, 28 molecules AL02AL03AL04AL05AL06AL07AL09AL11AL14AL15AL17AL19AL20AL21AL23AL26AL27AL28AL30AL31AL33AL34AL35AL36AL37AL39AL43ALNW

#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) / Tissue: Reticulocyte / 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) / Tissue: Reticulocyte / 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) / Tissue: Reticulocyte / 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) / Tissue: Reticulocyte / References: UniProt: P19949
#9: Protein 60S ribosomal protein L6


Mass: 28818.293 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Tissue: Reticulocyte / References: UniProt: G1SKF7
#10: 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) / Tissue: Reticulocyte / References: UniProt: G1SV32
#12: 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) / Tissue: Reticulocyte / References: UniProt: G1SWI6
#14: 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) / Tissue: Reticulocyte / References: UniProt: G1TUB8
#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) / Tissue: Reticulocyte / 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) / Tissue: Reticulocyte / 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) / Tissue: Reticulocyte / References: UniProt: G1SCJ6
#22: 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) / Tissue: Reticulocyte / References: UniProt: G1TYL6
#23: Protein 60S ribosomal protein L18a


Mass: 20827.561 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Tissue: Reticulocyte / References: UniProt: G1TTY7
#24: 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) / Tissue: Reticulocyte / References: UniProt: G1SHQ2
#26: 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) / Tissue: Reticulocyte / References: UniProt: G1T6D1
#29: 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) / Tissue: Reticulocyte / References: UniProt: G1SQH0
#30: 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) / Tissue: Reticulocyte / References: UniProt: G1TXF6
#31: 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) / Tissue: Reticulocyte / References: UniProt: G1SNY0
#33: 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) / Tissue: Reticulocyte / References: UniProt: G1TDL2
#34: 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) / Tissue: Reticulocyte / References: UniProt: G1SHG0
#36: Protein 60S ribosomal protein L35a


Mass: 12449.612 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Tissue: Reticulocyte / References: UniProt: G1SF08
#37: 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) / Tissue: Reticulocyte / References: UniProt: G1TXG5
#38: 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) / Tissue: Reticulocyte / References: UniProt: G1SIT5
#39: 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) / Tissue: Reticulocyte / References: UniProt: G1TTQ5
#40: 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) / Tissue: Reticulocyte / References: UniProt: U3KPD5
#42: 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) / Tissue: Reticulocyte / References: UniProt: G1TTN1
#46: 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) / Tissue: Reticulocyte / References: UniProt: G1SY53
#47: 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) / Tissue: Reticulocyte / References: UniProt: G1U7L1

-
Large ribosomal subunit protein ... , 10 types, 10 molecules AL08AL13AL16AL18AL22AL25AL29AL32AL38AL40

#11: Protein Large ribosomal subunit protein eL8 / 60S ribosomal protein L7a


Mass: 27351.377 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Tissue: Reticulocyte / References: UniProt: G1STW0
#16: Protein Large ribosomal subunit protein eL13 / 60S ribosomal protein L13


Mass: 24200.525 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Tissue: Reticulocyte / References: UniProt: G1TKB3
#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) / Tissue: Reticulocyte / References: UniProt: G1TVS8
#21: Protein Large ribosomal subunit protein eL18 / 60S ribosomal protein L18


Mass: 21568.492 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Tissue: Reticulocyte / References: UniProt: G1TFE0
#25: Protein Large ribosomal subunit protein eL22 / 60S ribosomal protein L22


Mass: 11495.275 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Tissue: Reticulocyte / References: UniProt: G1TSG1
#28: 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) / Tissue: Reticulocyte / References: UniProt: G1SE76
#32: 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) / Tissue: Reticulocyte / References: UniProt: G1SGR6
#35: Protein Large ribosomal subunit protein eL32 / 60S ribosomal protein L32


Mass: 15022.021 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Tissue: Reticulocyte / References: UniProt: G1TUN8
#41: Protein Large ribosomal subunit protein eL38 / 60S ribosomal protein L38


Mass: 8107.752 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Tissue: Reticulocyte / References: UniProt: G1U001
#43: 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) / Tissue: Reticulocyte / References: UniProt: P0DXC2

-
Ribosomal protein ... , 3 types, 3 molecules AL10AL24AS05

#13: 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) / Tissue: Reticulocyte / References: UniProt: B7NZQ2
#27: Protein Ribosomal protein L24


Mass: 14131.536 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Tissue: Reticulocyte / References: UniProt: G1SE28
#56: Protein Ribosomal protein S5


Mass: 21525.941 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Tissue: Reticulocyte / References: UniProt: G1TFM5

-
Protein , 9 types, 9 molecules AL12AL42ALP0ANGARACAS00AS21AS26EF1A

#15: Protein uL11


Mass: 16561.117 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Tissue: Reticulocyte / References: UniProt: G1SMR7
#45: Protein eL42


Mass: 12198.603 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Tissue: Reticulocyte / References: UniProt: A0A5F9D391
#48: Protein 60S acidic ribosomal protein P0


Mass: 21521.062 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Tissue: Reticulocyte / References: UniProt: G1SPK4
#49: Protein Angiogenin / Ribonuclease 5 / RNase 5


Mass: 16576.117 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ANG, RNASE5 / Production host: Escherichia coli (E. coli)
References: UniProt: P03950, Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters
#50: 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) / Tissue: Reticulocyte / References: UniProt: G1SJB4
#51: Protein 40S_SA_C domain-containing protein


Mass: 24361.861 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Tissue: Reticulocyte / References: UniProt: G1TJH8
#72: Protein eS21 / 40S ribosomal protein S21


Mass: 9124.389 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Tissue: Reticulocyte / References: UniProt: G1TM82
#77: Protein eS26 / 40S ribosomal protein S26


Mass: 11645.794 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Tissue: Reticulocyte / References: UniProt: G1TFE8
#82: Protein Elongation factor 1-alpha / EF-1-alpha / Eukaryotic elongation factor 1A / eEF1A / Translation elongation factor 1A


Mass: 50110.621 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: BJ2168 / References: UniProt: P02994

-
Protein/peptide , 1 types, 1 molecules AL41

#44: 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) / Tissue: Reticulocyte / References: UniProt: A0A087WNH4

+
40S ribosomal protein ... , 23 types, 23 molecules AS01AS02AS03AS04AS06AS08AS09AS10AS11AS12AS13AS15AS17AS18AS20AS22AS23AS24AS25AS27AS28AS29AS30

#52: 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) / Tissue: Reticulocyte / References: UniProt: G1SS70
#53: 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) / Tissue: Reticulocyte / References: UniProt: O18789
#54: 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) / Tissue: Reticulocyte
References: UniProt: G1TNM3, DNA-(apurinic or apyrimidinic site) lyase
#55: 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) / Tissue: Reticulocyte / References: UniProt: G1TA47
#57: 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) / Tissue: Reticulocyte / References: UniProt: G1TM55
#59: Protein 40S ribosomal protein S8


Mass: 24003.012 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Tissue: Reticulocyte / References: UniProt: G1TJW1
#60: 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) / Tissue: Reticulocyte / References: UniProt: B7NZS8
#61: 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) / Tissue: Reticulocyte / References: UniProt: G1TPV3
#62: Protein 40S ribosomal protein S11


Mass: 17586.766 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Tissue: Reticulocyte / References: UniProt: G1TRM4
#63: 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) / Tissue: Reticulocyte / References: UniProt: G1SFR8
#64: 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) / Tissue: Reticulocyte / References: UniProt: G1SP51
#66: 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) / Tissue: Reticulocyte / References: UniProt: G1U0Q2
#68: 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) / Tissue: Reticulocyte / References: UniProt: G1TU13
#69: 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) / Tissue: Reticulocyte / References: UniProt: G1TPG3
#71: 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) / Tissue: Reticulocyte / References: UniProt: G1SIZ2
#73: Protein 40S ribosomal protein S15a


Mass: 14734.357 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Tissue: Reticulocyte / References: UniProt: G1TG89
#74: 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) / Tissue: Reticulocyte / References: UniProt: G1SZ47
#75: 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) / Tissue: Reticulocyte / References: UniProt: G1T3D8
#76: Protein 40S ribosomal protein S25


Mass: 29512.916 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Tissue: Reticulocyte
#78: 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) / Tissue: Reticulocyte / References: UniProt: G1TZ76
#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) / Tissue: Reticulocyte / 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) / Tissue: Reticulocyte / References: UniProt: G1U7M4
#81: 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) / Tissue: Reticulocyte / References: UniProt: G1T8A2

-
Small ribosomal subunit protein ... , 4 types, 4 molecules AS07AS14AS16AS19

#58: 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) / Tissue: Reticulocyte / References: UniProt: G1SVB0
#65: 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) / Tissue: Reticulocyte / References: UniProt: G1T1F0
#67: 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) / Tissue: Reticulocyte / References: UniProt: G1SGX4
#70: Protein Small ribosomal subunit protein eS19 / 40S ribosomal protein S19


Mass: 15611.003 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Tissue: Reticulocyte / References: UniProt: G1TN62

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: 80S ribosome bound with angiogenin and complex of eEF1A and Ala-tRNAAla
Type: RIBOSOME / Entity ID: all / Source: MULTIPLE SOURCES
Molecular weightValue: 4.5 MDa / Experimental value: NO
Buffer solutionpH: 7
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid type: Quantifoil R2/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 278 K

-
Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1500 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm / Alignment procedure: COMA FREE
Image recordingElectron dose: 30 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

-
Processing

EM software
IDNameCategory
1cisTEMparticle selection
2SerialEMimage acquisition
4cisTEMCTF correction
10cisTEMinitial Euler assignment
11cisTEMfinal Euler assignment
12FREALIGNclassification
13FREALIGN3D reconstruction
CTF correctionType: PHASE FLIPPING ONLY
Particle selectionNum. of particles selected: 273774
3D reconstructionResolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 3604 / Num. of class averages: 1 / Symmetry type: POINT

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • 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

-
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

Read more