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- PDB-8bpo: Structure of rabbit 80S ribosome translating beta-tubulin in comp... -

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Basic information

Entry
Database: PDB / ID: 8bpo
TitleStructure of rabbit 80S ribosome translating beta-tubulin in complex with tetratricopeptide protein 5 (TTC5) and S-phase Cyclin A Associated Protein residing in the ER (SCAPER)
Components
  • (60S ribosomal protein ...) x 32
  • (Ribosomal protein ...) x 8
  • 28S ribosomal RNA
  • 5.8S ribosomal RNA
  • 5S ribosomal RNA
  • 60S acidic ribosomal protein P0
  • Nascent polypeptide-associated complex subunit alpha N-terminal region
  • Ribosomal_L18_c domain-containing protein
  • Ribosomal_L23eN domain-containing protein
  • S phase cyclin A-associated protein in the endoplasmic reticulum
  • Tetratricopeptide repeat protein 5
  • Tubulin beta chain
  • Ubiquitin-60S ribosomal protein L40
KeywordsRIBOSOME / tubulin auto-regulation mRNA decay translation SCAPER
Function / homology
Function and homology information


ooplasm / odontoblast differentiation / positive regulation of mRNA catabolic process / sperm head / cytoskeleton-dependent intracellular transport / seminiferous tubule development / GTPase activating protein binding / ribosomal subunit / antral ovarian follicle growth / natural killer cell mediated cytotoxicity ...ooplasm / odontoblast differentiation / positive regulation of mRNA catabolic process / sperm head / cytoskeleton-dependent intracellular transport / seminiferous tubule development / GTPase activating protein binding / ribosomal subunit / antral ovarian follicle growth / natural killer cell mediated cytotoxicity / regulation of synapse organization / nuclear envelope lumen / MHC class I protein binding / ubiquitin ligase inhibitor activity / positive regulation of signal transduction by p53 class mediator / microtubule-based process / protein-RNA complex assembly / intercellular bridge / spindle assembly / rough endoplasmic reticulum / MDM2/MDM4 family protein binding / cytosolic ribosome / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / cellular response to starvation / ribosomal large subunit biogenesis / AURKA Activation by TPX2 / Regulation of TP53 Activity through Methylation / structural constituent of cytoskeleton / microtubule cytoskeleton organization / cytoplasmic ribonucleoprotein granule / Regulation of PLK1 Activity at G2/M Transition / antimicrobial humoral immune response mediated by antimicrobial peptide / mitotic spindle / azurophil granule lumen / mitotic cell cycle / large ribosomal subunit / regulation of translation / ribosome binding / retina development in camera-type eye / microtubule cytoskeleton / cell body / 5S rRNA binding / ribosomal large subunit assembly / cytoplasmic vesicle / large ribosomal subunit rRNA binding / spermatogenesis / defense response to Gram-negative bacterium / killing of cells of another organism / cytosolic large ribosomal subunit / Potential therapeutics for SARS / microtubule / nucleic acid binding / cytoplasmic translation / cytoskeleton / tRNA binding / postsynaptic density / rRNA binding / nuclear speck / nuclear body / structural constituent of ribosome / ribosome / translation / mitochondrial matrix / membrane raft / ribonucleoprotein complex / protein domain specific binding / cell division / DNA repair / mRNA binding / GTPase activity / ubiquitin protein ligase binding / synapse / DNA damage response / Neutrophil degranulation / chromatin binding / GTP binding / protein-containing complex binding / nucleolus / structural molecule activity / endoplasmic reticulum / positive regulation of transcription by RNA polymerase II / protein-containing complex / mitochondrion / DNA binding / RNA binding / extracellular exosome / extracellular region / zinc ion binding / nucleoplasm / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
S phase cyclin A-associated protein in the endoplasmic reticulum, N-terminal / S phase cyclin A-associated protein in the endoplasmic reticulum / Tetratricopeptide repeat protein 5, OB fold domain / TTC5, OB fold domain superfamily / Tetratricopeptide repeat protein 5 OB fold domain / Zinc-finger of C2H2 type / Matrin/U1-C-like, C2H2-type zinc finger / U1-like zinc finger / 60s Acidic ribosomal protein / 60S acidic ribosomal protein P0 ...S phase cyclin A-associated protein in the endoplasmic reticulum, N-terminal / S phase cyclin A-associated protein in the endoplasmic reticulum / Tetratricopeptide repeat protein 5, OB fold domain / TTC5, OB fold domain superfamily / Tetratricopeptide repeat protein 5 OB fold domain / Zinc-finger of C2H2 type / Matrin/U1-C-like, C2H2-type zinc finger / U1-like zinc finger / 60s Acidic ribosomal protein / 60S acidic ribosomal protein P0 / : / Ribosomal protein L6, N-terminal / Ribosomal protein L6, N-terminal domain / Ribosomal protein L30e / Ribosomal protein L28e / Ribosomal L15/L27a, N-terminal / Ribosomal protein L13e / 50S ribosomal protein L10, insertion domain superfamily / Ribosomal protein L23 / Ribosomal protein L30e signature 1. / 60S ribosomal protein L10P, insertion domain / Insertion domain in 60S ribosomal protein L10P / Ribosomal L28e/Mak16 / Ribosomal L28e protein family / Ribosomal protein L30e signature 2. / Ribosomal protein L30e, conserved site / Ribosomal protein L13e / Ribosomal protein L30/YlxQ / metallochaperone-like domain / TRASH domain / Ribosomal protein L41 / Ribosomal protein L41 / Ribosomal protein L29e / Ribosomal L29e protein family / Ribosomal protein L27e, conserved site / Ribosomal protein L27e signature. / Ribosomal protein L10e, conserved site / Ribosomal protein L10e signature. / Ribosomal protein L38e / Ribosomal protein L38e superfamily / Ribosomal L38e protein family / Ribosomal protein L10e / Ribosomal protein L44e signature. / Ribosomal protein L24e, conserved site / Ribosomal protein L24e signature. / : / Ribosomal protein L6e signature. / TPR repeat region circular profile. / : / Ribosomal protein L44e / Ribosomal protein L44 / Tubulin-beta mRNA autoregulation signal. / Beta tubulin, autoregulation binding site / Ribosomal protein L34e, conserved site / Ribosomal protein L34e signature. / Ribosomal protein L5 eukaryotic, C-terminal / Ribosomal L18 C-terminal region / Beta tubulin / Ribosomal protein L23/L25, N-terminal / : / Ribosomal protein L23, N-terminal domain / Eukaryotic Ribosomal Protein L27, KOW domain / Ribosomal Protein L6, KOW domain / Ribosomal protein L36e signature. / Ribosomal protein L35Ae, conserved site / Ribosomal protein L35Ae signature. / Ribosomal protein L27e / Ribosomal protein L27e superfamily / Ribosomal L27e protein family / Ribosomal protein L39e, conserved site / Ribosomal protein L39e signature. / : / Ribosomal protein L6e / Ribosomal protein L34Ae / Ribosomal protein L34e / Ribosomal protein L7A/L8 / 60S ribosomal protein L6E / 60S ribosomal protein L35 / TPR repeat profile. / 60S ribosomal protein L4, C-terminal domain / 60S ribosomal protein L4 C-terminal domain / Ribosomal protein L31e, conserved site / Ribosomal protein L31e signature. / Ribosomal protein L37ae / Ribosomal L37ae protein family / Ribosomal protein L36e / Ribosomal protein L36e domain superfamily / Ribosomal protein L36e / Ribosomal protein L14e domain / Ribosomal protein L14 / Ribosomal protein L35A / Ribosomal protein L35Ae / Ribosomal protein L39e / Ribosomal protein L39e domain superfamily / Ribosomal protein L35A superfamily / Ribosomal L39 protein / Ribosomal protein L32e, conserved site / Ribosomal protein L32e signature. / Ribosomal protein L5 eukaryotic/L18 archaeal / Ribosomal large subunit proteins 60S L5, and 50S L18
Similarity search - Domain/homology
: / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein eS32 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein eL24 ...: / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein eS32 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein eL24 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein eL33 / Large ribosomal subunit protein eL29 / Large ribosomal subunit protein eL31 / Large ribosomal subunit protein eL21 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein eL6 / Large ribosomal subunit protein uL11 / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein uL10 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein eL8 / Large ribosomal subunit protein uL6 / Large ribosomal subunit protein eL43 / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein eL14 / Large ribosomal subunit protein eL15 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein eL30 / Large ribosomal subunit protein eL13 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein eL39 / Large ribosomal subunit protein eL36 / Large ribosomal subunit protein uL5 / Large ribosomal subunit protein eL27 / Large ribosomal subunit protein eL38 / Large ribosomal subunit protein eL42 / Large ribosomal subunit protein eL32 / Large ribosomal subunit protein eL28 / Large ribosomal subunit protein eL34 / Tubulin beta chain / Tetratricopeptide repeat protein 5 / S phase cyclin A-associated protein in the endoplasmic reticulum / Large ribosomal subunit protein eL37
Similarity search - Component
Biological speciesHomo sapiens (human)
Oryctolagus cuniculus (rabbit)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsHopfler, M. / Absmeier, E. / Passmore, L.A. / Hegde, R.S.
Funding support United Kingdom, European Union, Germany, Switzerland, United States, 7items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MC_UP_A022_1007 United Kingdom
Medical Research Council (MRC, United Kingdom)MC_U105192715 United Kingdom
European Molecular Biology Organization (EMBO)ALTF 116-2020European Union
H2020 Marie Curie Actions of the European Commission101029853European Union
German Research Foundation (DFG)429892960 Germany
Swiss National Science FoundationPCEFP3_194312 Switzerland
Damon Runyon Cancer Research FoundationDRG:2279-16 United States
CitationJournal: Mol Cell / Year: 2023
Title: Mechanism of ribosome-associated mRNA degradation during tubulin autoregulation.
Authors: Markus Höpfler / Eva Absmeier / Sew-Yeu Peak-Chew / Evangelia Vartholomaiou / Lori A Passmore / Ivana Gasic / Ramanujan S Hegde /
Abstract: Microtubules play crucial roles in cellular architecture, intracellular transport, and mitosis. The availability of free tubulin subunits affects polymerization dynamics and microtubule function. ...Microtubules play crucial roles in cellular architecture, intracellular transport, and mitosis. The availability of free tubulin subunits affects polymerization dynamics and microtubule function. When cells sense excess free tubulin, they trigger degradation of the encoding mRNAs, which requires recognition of the nascent polypeptide by the tubulin-specific ribosome-binding factor TTC5. How TTC5 initiates the decay of tubulin mRNAs is unknown. Here, our biochemical and structural analysis reveals that TTC5 recruits the poorly studied protein SCAPER to the ribosome. SCAPER, in turn, engages the CCR4-NOT deadenylase complex through its CNOT11 subunit to trigger tubulin mRNA decay. SCAPER mutants that cause intellectual disability and retinitis pigmentosa in humans are impaired in CCR4-NOT recruitment, tubulin mRNA degradation, and microtubule-dependent chromosome segregation. Our findings demonstrate how recognition of a nascent polypeptide on the ribosome is physically linked to mRNA decay factors via a relay of protein-protein interactions, providing a paradigm for specificity in cytoplasmic gene regulation.
History
DepositionNov 17, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 5, 2023Provider: repository / Type: Initial release
Revision 1.1Jul 19, 2023Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.2Oct 23, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A1: 28S ribosomal RNA
B1: 5S ribosomal RNA
C1: 5.8S ribosomal RNA
D1: Nascent polypeptide-associated complex subunit alpha N-terminal region
A2: 60S ribosomal protein L8
B2: Ribosomal protein L3
C2: 60S ribosomal protein L4
D2: Ribosomal_L18_c domain-containing protein
E2: 60S ribosomal protein L6
F2: 60S ribosomal protein L7
G2: 60S ribosomal protein L7a
H2: 60S ribosomal protein L9
I2: Ribosomal protein L10
J2: 60S ribosomal protein L11
K2: 60S ribosomal protein L13
L2: 60S ribosomal protein L14
M2: Ribosomal protein L15
N2: 60S ribosomal protein L13a
O2: 60S ribosomal protein L17
P2: Ribosomal protein L18
Q2: 60S ribosomal protein L19
R2: 60S ribosomal protein L18a
S2: 60S ribosomal protein L21
T2: 60S ribosomal protein L22
U2: 60S ribosomal protein L23
V2: Ribosomal protein L24
W2: Ribosomal_L23eN domain-containing protein
X2: Ribosomal protein L26
Y2: 60S ribosomal protein L27
Z2: 60S ribosomal protein L27a
a2: 60S ribosomal protein L29
b2: 60S ribosomal protein L30
c2: 60S ribosomal protein L31
d2: Ribosomal protein L32
e2: 60S ribosomal protein L35a
f2: 60S ribosomal protein L34
g2: 60S ribosomal protein L35
h2: 60S ribosomal protein L36
i2: Ribosomal protein L37
j2: 60S ribosomal protein L38
k2: 60S ribosomal protein L39-like
l2: Ubiquitin-60S ribosomal protein L40
m2: 60S ribosomal protein L41
n2: 60S ribosomal protein L36a-like
o2: 60S ribosomal protein L37a
p2: 60S ribosomal protein L28
q2: 60S acidic ribosomal protein P0
r2: 60S ribosomal protein L12
s2: S phase cyclin A-associated protein in the endoplasmic reticulum
t2: Tetratricopeptide repeat protein 5
u2: Tubulin beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,627,752270
Polymers2,622,22451
Non-polymers5,528219
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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RNA chain , 3 types, 3 molecules A1B1C1

#1: RNA chain 28S ribosomal RNA


Mass: 1418701.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#2: RNA chain 5S ribosomal RNA


Mass: 38691.914 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: GenBank: 4CXE_4
#3: RNA chain 5.8S ribosomal RNA


Mass: 50143.648 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: GenBank: 4CXE_3

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Protein/peptide , 1 types, 1 molecules D1

#4: Protein/peptide Nascent polypeptide-associated complex subunit alpha N-terminal region


Mass: 2526.119 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)

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60S ribosomal protein ... , 32 types, 32 molecules A2C2E2F2G2H2J2K2L2N2O2Q2R2S2T2U2Y2Z2a2b2c2e2f2g2h2j2k2m2n2o2p2r2

#5: Protein 60S ribosomal protein L8


Mass: 28088.863 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#7: Protein 60S ribosomal protein L4 / uL4


Mass: 47727.559 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: A0A5F9C3C5
#9: Protein 60S ribosomal protein L6


Mass: 33028.336 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SKF7
#10: Protein 60S ribosomal protein L7


Mass: 29201.836 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#11: Protein 60S ribosomal protein L7a / eL8


Mass: 36221.516 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1STW0
#12: Protein 60S ribosomal protein L9 / uL6


Mass: 21871.418 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SWI6
#14: Protein 60S ribosomal protein L11


Mass: 20288.465 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TUB8
#15: Protein 60S ribosomal protein L13 / eL13


Mass: 24331.723 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TKB3
#16: Protein 60S ribosomal protein L14


Mass: 23870.549 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SZ12
#18: Protein 60S ribosomal protein L13a


Mass: 23533.299 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#19: Protein 60S ribosomal protein L17


Mass: 21444.221 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#21: Protein 60S ribosomal protein L19


Mass: 23535.281 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#22: 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)
#23: Protein 60S ribosomal protein L21 / eL21


Mass: 18609.988 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SHQ2
#24: Protein 60S ribosomal protein L22


Mass: 14813.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#25: Protein 60S ribosomal protein L23


Mass: 14892.505 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1T6D1
#29: Protein 60S ribosomal protein L27


Mass: 15835.831 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TXF6
#30: Protein 60S ribosomal protein L27a / uL15


Mass: 16620.561 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SNY0
#31: Protein 60S ribosomal protein L29 / eL29


Mass: 24931.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SGR6
#32: Protein 60S ribosomal protein L30 / eL30


Mass: 12807.065 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TDL2
#33: Protein 60S ribosomal protein L31 / eL31


Mass: 14494.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SHG0
#35: Protein 60S ribosomal protein L35a / eL33


Mass: 12580.809 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SF08
#36: Protein 60S ribosomal protein L34 / eL34


Mass: 13196.894 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1U945
#37: Protein 60S ribosomal protein L35 / uL29


Mass: 14435.403 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SIT5
#38: Protein 60S ribosomal protein L36


Mass: 12263.834 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TTQ5
#40: Protein 60S ribosomal protein L38 / eL38


Mass: 8238.948 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1U001
#41: Protein 60S ribosomal protein L39-like / eL39


Mass: 6455.775 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TTN1
#43: Protein/peptide 60S ribosomal protein L41 / eL41


Mass: 3473.451 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: A0A087WNH4
#44: Protein 60S ribosomal protein L36a-like / eL42


Mass: 12476.973 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1U344
#45: Protein 60S ribosomal protein L37a / eL43


Mass: 10299.350 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SY53
#46: Protein 60S ribosomal protein L28 / eL28


Mass: 15783.614 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1U7L1
#48: Protein 60S ribosomal protein L12


Mass: 17847.619 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SMR7

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Ribosomal protein ... , 8 types, 8 molecules B2I2M2P2V2X2d2i2

#6: Protein Ribosomal protein L3 / uL3


Mass: 46107.977 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TL06
#13: Protein Ribosomal protein L10 / Ribosomal protein L10 (Predicted)


Mass: 24643.057 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: B7NZQ2
#17: Protein Ribosomal protein L15


Mass: 24207.285 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1T0C1
#20: Protein Ribosomal protein L18


Mass: 21568.492 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#26: Protein Ribosomal protein L24 / eL24


Mass: 17825.111 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SE28
#28: Protein Ribosomal protein L26


Mass: 17303.363 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SQH0
#34: Protein Ribosomal protein L32 / eL32


Mass: 15898.932 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1U437
#39: Protein Ribosomal protein L37


Mass: 11111.032 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: U3KPD5

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Protein , 7 types, 7 molecules D2W2l2q2s2t2u2

#8: Protein Ribosomal_L18_c domain-containing protein / 60S ribosomal protein L5


Mass: 34481.828 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SYJ6
#27: Protein Ribosomal_L23eN domain-containing protein / uL23


Mass: 17768.246 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SE76
#42: Protein Ubiquitin-60S ribosomal protein L40


Mass: 11699.790 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#47: Protein 60S acidic ribosomal protein P0 / uL10


Mass: 34380.504 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SPK4
#49: Protein S phase cyclin A-associated protein in the endoplasmic reticulum / S phase cyclin A-associated protein in the ER / Zinc finger protein 291 / SCAPER


Mass: 159795.547 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: First 11 N-terminal residues correspond to a FLAG-tag
Source: (gene. exp.) Homo sapiens (human) / Gene: SCAPER, KIAA1454, ZNF291, MSTP063 / Production host: Homo sapiens (human) / References: UniProt: Q9BY12
#50: Protein Tetratricopeptide repeat protein 5 / TPR repeat protein 5 / Stress-responsive activator of p300 / Protein Strap / TTC5


Mass: 54176.863 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The first 49 N-terminal residues correspond to a 6x His and a twin strep tag.
Source: (gene. exp.) Homo sapiens (human) / Gene: TTC5 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8N0Z6
#51: Protein Tubulin beta chain / Tubulin beta-5 chain


Mass: 7163.992 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TUBB, TUBB5, OK/SW-cl.56 / Production host: Oryctolagus cuniculus (rabbit) / References: UniProt: P07437

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Non-polymers , 2 types, 219 molecules

#52: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 214 / Source method: obtained synthetically / Formula: Mg
#53: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn

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Details

Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: rabbit 80S ribosome translating beta-tubulin in complex with tetratricopeptide protein 5 (TTC5) and S-phase Cyclin A Associated Protein residing in the ER (SCAPER)
Type: RIBOSOME / Entity ID: #1-#51 / Source: MULTIPLE SOURCES
Molecular weightExperimental value: NO
Source (natural)Organism: Oryctolagus cuniculus (rabbit)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid type: UltrAuFoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 105000 X / Nominal defocus max: 2700 nm / Nominal defocus min: 1200 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 1.8 sec. / Electron dose: 44.7 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 20932

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Processing

Software
NameVersionClassification
phenix.real_space_refinedev_4620refinement
PHENIXdev_4620refinement
EM software
IDNameVersionCategory
1RELION4particle selection
2EPUimage acquisition
4CTFFINDCTF correction
10RELION4initial Euler assignment
11RELION4final Euler assignment
12RELION4classification
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 1227269
3D reconstructionResolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 18949 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 37.79 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.004153880
ELECTRON MICROSCOPYf_angle_d0.819226179
ELECTRON MICROSCOPYf_dihedral_angle_d15.70954278
ELECTRON MICROSCOPYf_chiral_restr0.04428142
ELECTRON MICROSCOPYf_plane_restr0.00714420

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