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- PDB-5anc: Mechanism of eIF6 release from the nascent 60S ribosomal subunit -

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Entry
Database: PDB / ID: 5anc
TitleMechanism of eIF6 release from the nascent 60S ribosomal subunit
Components
  • (60S RIBOSOMAL PROTEIN ...) x 6
  • 26S RIBOSOMAL RNA
  • 60S ACIDIC RIBOSOMAL PROTEIN P0
  • ELONGATION FACTOR TU GTP-BINDING DOMAIN-CONTAINING PROTEIN 1
  • RIBOSOME MATURATION PROTEIN SBDS
  • UBIQUITIN-60S RIBOSOMAL PROTEIN L40
KeywordsTRANSLATION / RIBOSOMOPATHY / EFL1 / GTPASE / RIBOSOME BIOGENESIS
Function / homology
Function and homology information


Recognition of DNA damage by PCNA-containing replication complex / Downregulation of ERBB2:ERBB3 signaling / 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 ...Recognition of DNA damage by PCNA-containing replication complex / Downregulation of ERBB2:ERBB3 signaling / 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 / ABC-family proteins mediated transport / AUF1 (hnRNP D0) binds and destabilizes mRNA / Degradation of DVL / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Hedgehog ligand biogenesis / Hedgehog 'on' state / Translesion synthesis by POLK / Regulation of RAS by GAPs / 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 / Gap-filling DNA repair synthesis and ligation 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 / CDK-mediated phosphorylation and removal of Cdc6 / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Formation of a pool of free 40S subunits / 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 / 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) / Regulation of pyruvate metabolism / 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 / Aggrephagy / Regulation of necroptotic cell death / leukocyte chemotaxis / GTP metabolic process / bone marrow development / inner cell mass cell proliferation / bone mineralization / hematopoietic progenitor cell differentiation / translation elongation factor activity / phagocytic vesicle / extracellular matrix / lipid droplet / mitotic spindle organization / cytosolic ribosome assembly / spindle pole / modification-dependent protein catabolic process / protein tag activity / rRNA processing / ribosome binding / large ribosomal subunit rRNA binding / ribosomal large subunit assembly / microtubule binding / cytoplasmic translation / cytosolic large ribosomal subunit / rRNA binding / ribosome / protein ubiquitination / structural constituent of ribosome / ribonucleoprotein complex / translation / GTPase activity / mRNA binding / ubiquitin protein ligase binding / GTP binding / nucleolus / RNA binding / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
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 / Ribosome maturation protein Sdo1/SBDS-like / Ribosome maturation protein SDO1/SBDS, C-terminal domain / SBDS protein, domain II / SBDS protein, C-terminal domain / Uncharacterized protein family UPF0023 signature. / Ribosome maturation protein SDO1/SBDS, N-terminal ...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 / Ribosome maturation protein Sdo1/SBDS-like / Ribosome maturation protein SDO1/SBDS, C-terminal domain / SBDS protein, domain II / SBDS protein, C-terminal domain / Uncharacterized protein family UPF0023 signature. / Ribosome maturation protein SDO1/SBDS, N-terminal / Ribosome maturation protein SBDS, N-terminal domain superfamily / Shwachman-Bodian-Diamond syndrome (SBDS) protein / 60s Acidic ribosomal protein / 60S acidic ribosomal protein P0 / : / 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 / 50S ribosomal protein L10, insertion domain superfamily / 60S ribosomal protein L10P, insertion domain / Insertion domain in 60S ribosomal protein L10P / EF-G domain III/V-like / Ribosomal protein L10e, conserved site / Ribosomal protein L10e signature. / Ribosomal protein L10e / Ribosomal protein L24e, conserved site / Ribosomal protein L24e signature. / Ribosomal L40e family / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein L40e superfamily / Ribosomal protein L6, conserved site-2 / Ribosomal protein L6 signature 2. / Ribosomal protein L24e-related / Ribosomal protein L24e/L24 superfamily / Ribosomal protein L24e / Ribosomal protein L3, domain 3, archaeal type superfamily / Ribosomal protein L3, archaeal/eukaryotic type / 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 L10P / Ribosomal protein L10 / 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 domain signature. / Ubiquitin conserved site / 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 / Small GTP-binding protein domain / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like 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
: / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / 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 ...: / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / 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 / Elongation factor-like GTPase 1 / Ribosome maturation protein SBDS
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
DICTYOSTELIUM DISCOIDEUM (eukaryote)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.2 Å
AuthorsWeis, F. / Giudice, E. / Churcher, M. / Jin, L. / Hilcenko, C. / Wong, C.C. / Traynor, D. / Kay, R.R. / Warren, A.J.
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, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 21, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 28, 2015Group: Database references
Revision 1.2Dec 2, 2015Group: Database references
Revision 1.3Apr 19, 2017Group: Other
Revision 2.0Aug 2, 2017Group: Atomic model / Data collection / Derived calculations
Category: atom_site / em_image_scans ...atom_site / em_image_scans / em_software / struct_conn
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _em_software.fitting_id / _em_software.image_processing_id / _em_software.name
Revision 2.1Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "EA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "EA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 5-STRANDED BARREL THIS IS REPRESENTED BY A 6-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

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  • Deposited structure unit
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  • Simplified surface model + fitted atomic model
  • EMDB-3147
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Structure viewerMolecule:
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Assembly

Deposited unit
A: 60S RIBOSOMAL PROTEIN L3
B: 60S RIBOSOMAL PROTEIN L9
C: 60S ACIDIC RIBOSOMAL PROTEIN P0
D: 60S RIBOSOMAL PROTEIN L12
E: 60S RIBOSOMAL PROTEIN L23
F: 60S RIBOSOMAL PROTEIN L10
G: 60S RIBOSOMAL PROTEIN L24
H: UBIQUITIN-60S RIBOSOMAL PROTEIN L40
J: RIBOSOME MATURATION PROTEIN SBDS
K: ELONGATION FACTOR TU GTP-BINDING DOMAIN-CONTAINING PROTEIN 1
N: 26S RIBOSOMAL RNA


Theoretical massNumber of molelcules
Total (without water)1,520,71411
Polymers1,520,71411
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA

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Components

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60S RIBOSOMAL PROTEIN ... , 6 types, 6 molecules ABDEFG

#1: Protein 60S RIBOSOMAL PROTEIN L3


Mass: 45158.758 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) DICTYOSTELIUM DISCOIDEUM (eukaryote) / Strain: HM2917 / References: UniProt: P34113
#2: Protein 60S RIBOSOMAL PROTEIN L9


Mass: 21250.656 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) DICTYOSTELIUM DISCOIDEUM (eukaryote) / Strain: HM2917 / References: UniProt: Q54XI5
#4: Protein 60S RIBOSOMAL PROTEIN L12


Mass: 17811.031 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) DICTYOSTELIUM DISCOIDEUM (eukaryote) / Strain: HM2917 / References: UniProt: Q54J50
#5: Protein 60S RIBOSOMAL PROTEIN L23


Mass: 14567.147 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) DICTYOSTELIUM DISCOIDEUM (eukaryote) / Strain: HM2917 / References: UniProt: Q54G86
#6: Protein 60S RIBOSOMAL PROTEIN L10


Mass: 24591.754 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) DICTYOSTELIUM DISCOIDEUM (eukaryote) / Strain: HM2917 / References: UniProt: Q54J69
#7: Protein 60S RIBOSOMAL PROTEIN L24


Mass: 8334.771 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 1-69 / Source method: isolated from a natural source / Source: (natural) DICTYOSTELIUM DISCOIDEUM (eukaryote) / Strain: HM2917 / References: UniProt: Q54VN6

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Protein , 4 types, 4 molecules CHJK

#3: Protein 60S ACIDIC RIBOSOMAL PROTEIN P0


Mass: 22434.189 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 1-205 / Source method: isolated from a natural source / Source: (natural) DICTYOSTELIUM DISCOIDEUM (eukaryote) / Strain: HM2917 / References: UniProt: P22685
#8: Protein UBIQUITIN-60S RIBOSOMAL PROTEIN L40 / UBIQUITIN A-52 RESIDUE RIBOSOMAL PROTEIN FUSION PRODUCT 1 / CEP52


Mass: 6170.682 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 77-128 / Source method: isolated from a natural source / Source: (natural) DICTYOSTELIUM DISCOIDEUM (eukaryote) / Strain: HM2917 / References: UniProt: P14794
#9: Protein RIBOSOME MATURATION PROTEIN SBDS / SHWACHMAN-BODIAN-DIAMOND SYNDROME PROTEIN / SBDS


Mass: 28813.602 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): C41 / References: UniProt: Q9Y3A5
#10: Protein ELONGATION FACTOR TU GTP-BINDING DOMAIN-CONTAINING PROTEIN 1 / ELONGATION FACTOR-LIKE 1 / PROTEIN FAM42A / EFL1


Mass: 125583.555 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: SACCHAROMYCES CEREVISIAE (brewer's yeast) / Strain (production host): BCY123 / References: UniProt: Q7Z2Z2

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RNA chain , 1 types, 1 molecules N

#11: RNA chain 26S RIBOSOMAL RNA


Mass: 1205997.750 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) DICTYOSTELIUM DISCOIDEUM (eukaryote) / Strain: HM2917 / References: GenBank: FR733594.1

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Details

Has protein modificationY
Sequence detailsRESIDUES 1-205 PRESENT IN THE MODEL RESIDUES 1-69 IN THE MODEL NO UBIQUITIN IN MODEL FRAGMENTS ...RESIDUES 1-205 PRESENT IN THE MODEL RESIDUES 1-69 IN THE MODEL NO UBIQUITIN IN MODEL FRAGMENTS A1221-A1270, C1356-C1602, A2392-U2700 AND A2925- C3480 IN THE MODEL

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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: DICTYOSTELIUM 60S WITH RECOMBINANT HUMAN SBDS AND HUMAN EFL1
Type: RIBOSOME
Buffer solutionName: 50 MM HEPES-KOH, 100 MM K(CH3COO), 10 MM MG(CH3COO)2, 6 MM BETA-MERCAPTOETHANOL
pH: 7.5
Details: 50 MM HEPES-KOH, 100 MM K(CH3COO), 10 MM MG(CH3COO)2, 6 MM BETA-MERCAPTOETHANOL
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: HOLEY CARBON
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE
Details: VITRIFICATION 1 -- CRYOGEN- ETHANE, HUMIDITY- 100, TEMPERATURE- 120, INSTRUMENT- FEI VITROBOT MARK III, METHOD- 6.5S BLOT,

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS / Date: Sep 3, 2013
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 59000 X / Calibrated magnification: 105263 X / Nominal defocus max: 2800 nm / Nominal defocus min: 2200 nm / Cs: 2.2 mm
Image recordingElectron dose: 30 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k)

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Processing

EM software
IDNameCategory
1REFMACmodel fitting
2RELION3D reconstruction
CTF correctionDetails: EACH PARTICLE
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 4.2 Å / Num. of particles: 9794 / Nominal pixel size: 1.33 Å / Actual pixel size: 1.33 Å
Details: SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-3147. (DEPOSITION ID: 13761).
Symmetry type: POINT
Atomic model buildingB value: 130.9 / Protocol: OTHER / Space: RECIPROCAL / Target criteria: FSCAVERAGE / Details: REFINEMENT PROTOCOL--CRYO-EM
RefinementHighest resolution: 4.2 Å
Refinement stepCycle: LAST / Highest resolution: 4.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22049 24758 0 0 46807

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