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- EMDB-3146: Mechanism of eIF6 release from the nascent 60S ribosomal subunit -

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Entry
Database: EMDB / ID: EMD-3146
TitleMechanism of eIF6 release from the nascent 60S ribosomal subunit
Map dataReconstruction of 60S-eIF6-SBDS-EFL1 complex
Sample
  • Sample: Dictyostelium 60S carrying endogenous eIF6 with recombinant human SBDS and human EFL1
  • Complex: 60S ribosomal subunit
  • Protein or peptide: Eukaryotic translation initiation factor 6
  • Protein or peptide: Shwachman-Bodian-Diamond syndrome protein
  • Protein or peptide: Elongation factor-like 1
Keywordsribosome / ribosomopathy / SBDS / cryo-EM / eIF6 / Dictyostelium / EFL1 / GTPase / ribosome biogenesis
Function / homology
Function and homology information


L13a-mediated translational silencing of Ceruloplasmin expression / APC/C:Cdc20 mediated degradation of Cyclin B / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / APC-Cdc20 mediated degradation of Nek2A / SRP-dependent cotranslational protein targeting to membrane / Separation of Sister Chromatids / Senescence-Associated Secretory Phenotype (SASP) ...L13a-mediated translational silencing of Ceruloplasmin expression / APC/C:Cdc20 mediated degradation of Cyclin B / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / APC-Cdc20 mediated degradation of Nek2A / SRP-dependent cotranslational protein targeting to membrane / Separation of Sister Chromatids / Senescence-Associated Secretory Phenotype (SASP) / Autodegradation of the E3 ubiquitin ligase COP1 / activated TAK1 mediates p38 MAPK activation / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Hedgehog ligand biogenesis / Negative regulation of MAPK pathway / Regulation of necroptotic cell death / MAPK6/MAPK4 signaling / UCH proteinases / Josephin domain DUBs / Ub-specific processing proteases / Metalloprotease DUBs / DNA Damage Recognition in GG-NER / Formation of Incision Complex in GG-NER / Formation of TC-NER Pre-Incision Complex / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / Major pathway of rRNA processing in the nucleolus and cytosol / CDK-mediated phosphorylation and removal of Cdc6 / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Formation of a pool of free 40S subunits / Formation of the ternary complex, and subsequently, the 43S complex / Ribosomal scanning and start codon recognition / GTP hydrolysis and joining of the 60S ribosomal subunit / : / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / E3 ubiquitin ligases ubiquitinate target proteins / Regulation of PTEN localization / Regulation of PTEN stability and activity / ER Quality Control Compartment (ERQC) / Interleukin-1 signaling / Peroxisomal protein import / Endosomal Sorting Complex Required For Transport (ESCRT) / Negative regulators of DDX58/IFIH1 signaling / : / : / Aggrephagy / Pexophagy / : / KEAP1-NFE2L2 pathway / Regulation of NF-kappa B signaling / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / : / Orc1 removal from chromatin / Cyclin D associated events in G1 / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / Neddylation / Iron uptake and transport / Antigen processing: Ubiquitination & Proteasome degradation / leukocyte chemotaxis / GTP metabolic process / bone marrow development / inner cell mass cell proliferation / maturation of 5.8S rRNA / ribosomal subunit export from nucleus / bone mineralization / ribosomal large subunit binding / preribosome, large subunit precursor / hematopoietic progenitor cell differentiation / phagocytic vesicle / maturation of LSU-rRNA / translation elongation factor activity / extracellular matrix / translation initiation factor activity / ribosomal large subunit biogenesis / assembly of large subunit precursor of preribosome / lipid droplet / mitotic spindle organization / cytosolic ribosome assembly / modification-dependent protein catabolic process / protein tag activity / spindle pole / rRNA processing / large ribosomal subunit rRNA binding / ribosome binding / ribosomal large subunit assembly / cytosolic large ribosomal subunit / cytoplasmic translation / microtubule binding / ribosome / rRNA binding / protein ubiquitination / structural constituent of ribosome / translation / ribonucleoprotein complex / GTPase activity / mRNA binding / ubiquitin protein ligase binding / GTP binding
Similarity search - Function
Ribosome maturation protein SDO1/SBDS, C-terminal domain / SBDS protein, C-terminal domain / Ribosome maturation protein Sdo1/SBDS / Ribosome maturation protein SBDS, conserved site / Ribosome maturation protein SDO1/SBDS, central domain / Ribosome maturation protein Sdo1/SBDS, central domain superfamily / SBDS protein, domain II / Uncharacterized protein family UPF0023 signature. / Ribosome maturation protein SDO1/SBDS, N-terminal / Ribosome maturation protein SBDS, N-terminal domain superfamily ...Ribosome maturation protein SDO1/SBDS, C-terminal domain / SBDS protein, C-terminal domain / Ribosome maturation protein Sdo1/SBDS / Ribosome maturation protein SBDS, conserved site / Ribosome maturation protein SDO1/SBDS, central domain / Ribosome maturation protein Sdo1/SBDS, central domain superfamily / SBDS protein, domain II / Uncharacterized protein family UPF0023 signature. / Ribosome maturation protein SDO1/SBDS, N-terminal / Ribosome maturation protein SBDS, N-terminal domain superfamily / Ribosome maturation protein Sdo1/SBDS-like / Shwachman-Bodian-Diamond syndrome (SBDS) protein / 60s Acidic ribosomal protein / 60S acidic ribosomal protein P0 / Translation initiation factor IF6 / eIF-6 family / translation initiation factor 6 / Elongation Factor G, domain II / Elongation Factor G, domain III / Elongation factor G C-terminus / Elongation factor EFG, domain V-like / Elongation factor G C-terminus / EF-G domain III/V-like / 50S ribosomal protein L10, insertion domain superfamily / 60S ribosomal protein L10P, insertion domain / Insertion domain in 60S ribosomal protein L10P / Ribosomal L40e family / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein L40e superfamily / Ribosomal protein L10e, conserved site / Ribosomal protein L10e signature. / Ribosomal protein L10e / Ribosomal protein L24e, conserved site / Ribosomal protein L24e signature. / Ribosomal protein L6, conserved site-2 / Ribosomal protein L6 signature 2. / Ribosomal protein L3, domain 3, archaeal type superfamily / Ribosomal protein L3, archaeal/eukaryotic type / Ribosomal protein L24e-related / Ribosomal protein L24e/L24 superfamily / Ribosomal protein L24e / Translational (tr)-type GTP-binding domain / Elongation factor Tu GTP binding domain / Translational (tr)-type guanine nucleotide-binding (G) domain profile. / Ribosomal protein L10-like domain superfamily / Ribosomal protein L10 / Ribosomal protein L10P / Ribosomal protein L11, N-terminal / Ribosomal protein L11, N-terminal domain / Ribosomal protein L11/L12 / Ribosomal protein L11, C-terminal / Ribosomal protein L11, C-terminal domain superfamily / Ribosomal protein L11/L12, N-terminal domain superfamily / Ribosomal protein L11, RNA binding domain / Ribosomal protein L11/L12 / Ubiquitin conserved site / Ubiquitin domain signature. / Ubiquitin domain / Ubiquitin family / : / Ribosomal protein L10e/L16 / Ribosomal protein L10e/L16 superfamily / Ribosomal protein L16p/L10e / Ribosomal protein L6, alpha-beta domain / Ribosomal protein L6 / Ribosomal protein L6 / Ribosomal protein L6, alpha-beta domain superfamily / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Small GTP-binding protein domain / Ribosomal protein L14p/L23e / Ribosomal protein L14P / Ribosomal protein L14 superfamily / Ribosomal protein L14p/L23e / Ribosomal protein L3, conserved site / Ribosomal protein L3 signature. / Ribosomal protein L3 / Ribosomal protein L3 / Zinc-binding ribosomal protein / Translation protein, beta-barrel domain superfamily / Ribosomal protein S5 domain 2-type fold, subgroup / Ubiquitin-like domain superfamily / Ribosomal protein S5 domain 2-type fold / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Ubiquitin-ribosomal protein eL40 fusion protein / Large ribosomal subunit protein uL10 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein uL11 / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein eL24 / Large ribosomal subunit protein uL6 / Eukaryotic translation initiation factor 6 / Elongation factor-like GTPase 1 / Ribosome maturation protein SBDS
Similarity search - Component
Biological speciesDictyostelium discoideum (eukaryote) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.1 Å
AuthorsWeis F / Giudice E / Churcher M / Jin L / Hilcenko C / Wong CC / Traynor D / Kay RR / Warren AJ
CitationJournal: Nat Struct Mol Biol / Year: 2015
Title: Mechanism of eIF6 release from the nascent 60S ribosomal subunit.
Authors: Félix Weis / Emmanuel Giudice / Mark Churcher / Li Jin / Christine Hilcenko / Chi C Wong / David Traynor / Robert R Kay / Alan J Warren /
Abstract: SBDS protein (deficient in the inherited leukemia-predisposition disorder Shwachman-Diamond syndrome) and the GTPase EFL1 (an EF-G homolog) activate nascent 60S ribosomal subunits for translation by ...SBDS protein (deficient in the inherited leukemia-predisposition disorder Shwachman-Diamond syndrome) and the GTPase EFL1 (an EF-G homolog) activate nascent 60S ribosomal subunits for translation by catalyzing eviction of the antiassociation factor eIF6 from nascent 60S ribosomal subunits. However, the mechanism is completely unknown. Here, we present cryo-EM structures of human SBDS and SBDS-EFL1 bound to Dictyostelium discoideum 60S ribosomal subunits with and without endogenous eIF6. SBDS assesses the integrity of the peptidyl (P) site, bridging uL16 (mutated in T-cell acute lymphoblastic leukemia) with uL11 at the P-stalk base and the sarcin-ricin loop. Upon EFL1 binding, SBDS is repositioned around helix 69, thus facilitating a conformational switch in EFL1 that displaces eIF6 by competing for an overlapping binding site on the 60S ribosomal subunit. Our data reveal the conserved mechanism of eIF6 release, which is corrupted in both inherited and sporadic leukemias.
History
DepositionSep 6, 2015-
Header (metadata) releaseSep 23, 2015-
Map releaseOct 21, 2015-
UpdateDec 2, 2015-
Current statusDec 2, 2015Processing site: PDBe / Status: Released

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Structure visualization

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  • Surface view with section colored by density value
  • Surface level: 0.06
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  • Surface level: 0.06
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  • Surface view with fitted model
  • Atomic models: PDB-5anb
  • Surface level: 0.06
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-5anb
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Structure viewerEM map:
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Supplemental images

Downloads & links

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Map

FileDownload / File: emd_3146.map.gz / Format: CCP4 / Size: 100.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of 60S-eIF6-SBDS-EFL1 complex
Voxel sizeX=Y=Z: 1.33 Å
Density
Contour LevelBy AUTHOR: 0.06 / Movie #1: 0.06
Minimum - Maximum-0.44422188 - 0.64644915
Average (Standard dev.)0.00301982 (±0.02805543)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 399.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.331.331.33
M x/y/z300300300
origin x/y/z0.0000.0000.000
length x/y/z399.000399.000399.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS300300300
D min/max/mean-0.4440.6460.003

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Supplemental data

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Sample components

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Entire : Dictyostelium 60S carrying endogenous eIF6 with recombinant human...

EntireName: Dictyostelium 60S carrying endogenous eIF6 with recombinant human SBDS and human EFL1
Components
  • Sample: Dictyostelium 60S carrying endogenous eIF6 with recombinant human SBDS and human EFL1
  • Complex: 60S ribosomal subunit
  • Protein or peptide: Eukaryotic translation initiation factor 6
  • Protein or peptide: Shwachman-Bodian-Diamond syndrome protein
  • Protein or peptide: Elongation factor-like 1

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Supramolecule #1000: Dictyostelium 60S carrying endogenous eIF6 with recombinant human...

SupramoleculeName: Dictyostelium 60S carrying endogenous eIF6 with recombinant human SBDS and human EFL1
type: sample / ID: 1000 / Number unique components: 4

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Supramolecule #1: 60S ribosomal subunit

SupramoleculeName: 60S ribosomal subunit / type: complex / ID: 1 / Recombinant expression: No / Ribosome-details: ribosome-eukaryote: LSU 60S
Source (natural)Organism: Dictyostelium discoideum (eukaryote) / Strain: HM2917 / synonym: Slime Mold
Molecular weightExperimental: 3 MDa / Theoretical: 3 MDa

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Macromolecule #1: Eukaryotic translation initiation factor 6

MacromoleculeName: Eukaryotic translation initiation factor 6 / type: protein_or_peptide / ID: 1 / Name.synonym: eIF6
Details: endogenous dictyostelium protein purified bound the 60S ribosomal subunit
Number of copies: 1 / Recombinant expression: No
Source (natural)Organism: Dictyostelium discoideum (eukaryote) / Strain: HM2917 / synonym: Slime Mold
Molecular weightExperimental: 26 KDa / Theoretical: 26 KDa
SequenceUniProtKB: Eukaryotic translation initiation factor 6

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Macromolecule #2: Shwachman-Bodian-Diamond syndrome protein

MacromoleculeName: Shwachman-Bodian-Diamond syndrome protein / type: protein_or_peptide / ID: 2 / Name.synonym: SBDS / Number of copies: 1 / Recombinant expression: Yes
Source (natural)Organism: Homo sapiens (human) / synonym: Human
Molecular weightExperimental: 29 KDa / Theoretical: 29 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria) / Recombinant strain: C41 / Recombinant plasmid: pRSETA
SequenceUniProtKB: Ribosome maturation protein SBDS

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Macromolecule #3: Elongation factor-like 1

MacromoleculeName: Elongation factor-like 1 / type: protein_or_peptide / ID: 3 / Name.synonym: EFL1 / Number of copies: 1 / Recombinant expression: Yes
Source (natural)Organism: Homo sapiens (human) / synonym: Human
Molecular weightExperimental: 125 KDa / Theoretical: 125 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast) / Recombinant strain: BCY123 / Recombinant plasmid: pYES2
SequenceUniProtKB: Elongation factor-like GTPase 1

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
Details: 50 mM HEPES-KOH, 100 mM K(CH3COO), 10 mM Mg(CH3COO)2, 6 mM beta-mercaptoethanol
GridDetails: quantifoil R2/2 glow discharged
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 120 K / Instrument: FEI VITROBOT MARK III / Method: 6.5s blot

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Electron microscopy #1

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 105263 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.2 mm / Nominal defocus max: 2.8 µm / Nominal defocus min: 2.2 µm / Nominal magnification: 59000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Microscopy ID1
Alignment procedureLegacy - Astigmatism: Objective lens astigmatism was corrected at 59,000 times magnification
DateSep 3, 2013
Image recordingCategory: CCD / Film or detector model: FEI FALCON II (4k x 4k) / Number real images: 3844 / Average electron dose: 30 e/Å2
Details: Every image is the average of 16 frames recorded by the direct electron detector
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Electron microscopy #2

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 105263 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.2 mm / Nominal defocus max: 2.8 µm / Nominal defocus min: 2.2 µm / Nominal magnification: 59000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Microscopy ID2
Alignment procedureLegacy - Astigmatism: Objective lens astigmatism was corrected at 59,000 times magnification
DateSep 6, 2013
Image recordingCategory: CCD / Film or detector model: FEI FALCON II (4k x 4k) / Number real images: 3844 / Average electron dose: 30 e/Å2
Details: Every image is the average of 16 frames recorded by the direct electron detector
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionDetails: Each particle
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.1 Å / Resolution method: OTHER / Software - Name: RELION / Number images used: 11970

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