[English] 日本語
Yorodumi
- PDB-6qkl: Mechanism of eIF6 release from the nascent 60S ribosomal subunit -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: PDB / ID: 6qkl
TitleMechanism of eIF6 release from the nascent 60S ribosomal subunit
Components
  • (60S ribosomal protein ...) x 6
  • 26S RIBOSOMAL RNA
  • 60S acidic ribosomal protein P0
  • Eukaryotic translation initiation factor 6
  • Ribosome maturation protein SBDS
  • Ubiquitin-60S ribosomal protein L40
KeywordsRIBOSOME / 60S subunit / eIF6 / SBDS / uL16
Function / homologyRibosome maturation protein Sdo1/SBDS-like / Ribosomal protein L16p/L10e / Ubiquitin domain signature. / Insertion domain in 60S ribosomal protein L10P / SBDS protein C-terminal domain / Ribosomal protein L11, N-terminal domain / eIF-6 family / Ribosomal protein L24e / Shwachman-Bodian-Diamond syndrome (SBDS) protein / Ribosomal L40e family ...Ribosome maturation protein Sdo1/SBDS-like / Ribosomal protein L16p/L10e / Ubiquitin domain signature. / Insertion domain in 60S ribosomal protein L10P / SBDS protein C-terminal domain / Ribosomal protein L11, N-terminal domain / eIF-6 family / Ribosomal protein L24e / Shwachman-Bodian-Diamond syndrome (SBDS) protein / Ribosomal L40e family / Ribosomal protein L10 / Ribosomal protein L6 / Ribosomal protein L11, RNA binding domain / Ribosomal protein L3 / Ubiquitin family / Ribosomal protein L6 signature 2. / Ribosomal protein L14p/L23e / 60S ribosomal protein L10P, insertion domain / Ribosomal protein L24e/L24 superfamily / Ribosomal protein L40e superfamily / Ribosome maturation protein Sdo1/SBDS, central domain superfamily / Ribosomal protein L10e/L16 superfamily / Ribosomal protein L14 superfamily / Ribosomal protein L11/L12, N-terminal domain superfamily / Ribosomal protein L6, alpha-beta domain superfamily / Ribosome maturation protein SBDS, N-terminal domain superfamily / Ribosomal protein L11, C-terminal domain superfamily / 60S acidic ribosomal protein P0 / Ubiquitin-like domain superfamily / Ribosomal protein L3 signature. / Ribosomal protein L24e signature. / Formation of a pool of free 40S subunits / Translesion synthesis by POLK / Cyclin D associated events in G1 / Orc1 removal from chromatin / Gap-filling DNA repair synthesis and ligation in TC-NER / Dual incision in TC-NER / Formation of TC-NER Pre-Incision Complex / Formation of Incision Complex in GG-NER / DNA Damage Recognition in GG-NER / Metalloprotease DUBs / Ub-specific processing proteases / Josephin domain DUBs / UCH proteinases / Negative regulation of MAPK pathway / Termination of translesion DNA synthesis / Hedgehog 'on' state / Ribosomal protein L10e signature. / Hedgehog ligand biogenesis / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Autodegradation of the E3 ubiquitin ligase COP1 / SRP-dependent cotranslational protein targeting to membrane / APC-Cdc20 mediated degradation of Nek2A / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Cyclin B / L13a-mediated translational silencing of Ceruloplasmin expression / Downregulation of ERBB2:ERBB3 signaling / Ubiquitin domain profile. / Uncharacterized protein family UPF0023 signature. / Ribosomal protein L24e, conserved site / Ribosomal protein L11, N-terminal / Ribosomal protein L11, C-terminal / E3 ubiquitin ligases ubiquitinate target proteins / Ribosomal protein L14P / Formation of the ternary complex, and subsequently, the 43S complex / Ribosomal protein L6, alpha-beta domain / Ribosomal scanning and start codon recognition / GTP hydrolysis and joining of the 60S ribosomal subunit / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Regulation of PTEN localization / Ubiquitin domain / Regulation of PTEN stability and activity / ER Quality Control Compartment (ERQC) / Peroxisomal protein import / Endosomal Sorting Complex Required For Transport (ESCRT) / Iron uptake and transport / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Antigen processing: Ubiquitination & Proteasome degradation / Ribosomal protein L3 / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Ribosomal protein L6 / Translation initiation factor IF6 / Ribosomal protein L6, conserved site-2 / Translation protein, beta-barrel domain superfamily / Zinc-binding ribosomal protein / Ribosomal protein L10e/L16 / Ribosome maturation protein SBDS, conserved site / Ribosomal protein L10e, conserved site / Ribosome maturation protein SBDS, C-terminal / Ribosome maturation protein Sdo1/SBDS / Ribosome maturation protein SBDS, N-terminal / Ribosomal protein L40e / Ribosomal protein L10P / Ribosomal protein L3, conserved site / Ubiquitin conserved site / Ubiquitin
Function and homology information
Specimen sourceHomo sapiens (human)
Dictyostelium discoideum (eukaryote)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsKargas, V. / Warren, A.J.
Funding supportUnited Kingdom , 3 items
OrganizationGrant numberCountry
Bloodwise12048United Kingdom
Medical Research Council (United Kingdom)MC_U105161083United Kingdom
Wellcome Trust100140United Kingdom
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.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jan 29, 2019 / Release: Mar 20, 2019

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Simplified surface model + fitted atomic model
  • EMDB-3145
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-3145
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
N: 26S RIBOSOMAL RNA
A: 60S ribosomal protein L3
B: 60S ribosomal protein L9
E: 60S ribosomal protein L23
F: 60S ribosomal protein L10
G: 60S ribosomal protein L24
H: Ubiquitin-60S ribosomal protein L40
I: Eukaryotic translation initiation factor 6
J: Ribosome maturation protein SBDS
C: 60S acidic ribosomal protein P0
D: 60S ribosomal protein L12


Theoretical massNumber of molelcules
Total (without water)1,419,23811
Polyers1,419,23811
Non-polymers00
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)48660
ΔGint (kcal/M)-428
Surface area (Å2)230990
MethodPISA

-
Components

-
RNA chain , 1 types, 1 molecules N

#1: RNA chain 26S RIBOSOMAL RNA /


Mass: 1205997.750 Da / Num. of mol.: 1 / Source: (natural) Dictyostelium discoideum (eukaryote)

-
60S ribosomal protein ... , 6 types, 6 molecules ABEFGD

#2: Protein/peptide 60S ribosomal protein L3 /


Mass: 45158.758 Da / Num. of mol.: 1 / Source: (natural) Dictyostelium discoideum (eukaryote) / References: UniProt: P34113
#3: Protein/peptide 60S ribosomal protein L9 /


Mass: 21250.656 Da / Num. of mol.: 1 / Source: (natural) Dictyostelium discoideum (eukaryote) / References: UniProt: Q54XI5
#4: Protein/peptide 60S ribosomal protein L23 /


Mass: 14567.147 Da / Num. of mol.: 1 / Source: (natural) Dictyostelium discoideum (eukaryote) / References: UniProt: Q54G86
#5: Protein/peptide 60S ribosomal protein L10 /


Mass: 24591.754 Da / Num. of mol.: 1 / Source: (natural) Dictyostelium discoideum (eukaryote) / References: UniProt: Q54J69
#6: Protein/peptide 60S ribosomal protein L24 /


Mass: 8334.771 Da / Num. of mol.: 1 / Source: (natural) Dictyostelium discoideum (eukaryote) / References: UniProt: Q54VN6
#11: Protein/peptide 60S ribosomal protein L12 /


Mass: 17811.031 Da / Num. of mol.: 1 / Source: (natural) Dictyostelium discoideum (eukaryote) / References: UniProt: Q54J50

-
Protein/peptide , 4 types, 4 molecules HIJC

#7: Protein/peptide Ubiquitin-60S ribosomal protein L40 / Ubiquitin A-52 residue ribosomal protein fusion product 1


Mass: 6170.682 Da / Num. of mol.: 1 / Source: (natural) Dictyostelium discoideum (eukaryote) / References: UniProt: P14794
#8: Protein/peptide Eukaryotic translation initiation factor 6 / eIF-6


Mass: 24107.266 Da / Num. of mol.: 1 / Source: (natural) Dictyostelium discoideum (eukaryote) / References: UniProt: Q551M2
#9: Protein/peptide Ribosome maturation protein SBDS / Shwachman-Bodian-Diamond syndrome protein


Mass: 28813.602 Da / Num. of mol.: 1 / Source: (gene. exp.) Homo sapiens (human) / Gene: SBDS, CGI-97 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y3A5
#10: Protein/peptide 60S acidic ribosomal protein P0


Mass: 22434.189 Da / Num. of mol.: 1 / Source: (natural) Dictyostelium discoideum (eukaryote) / References: UniProt: P22685

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: DICTYOSTELIUM 60S CARRYING ENDOGENOUS EIF6 WITH RECOMBINANT HUMAN SBDS
Type: RIBOSOME / Entity ID: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 / Source: MULTIPLE SOURCES
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 120 kelvins / Details: 1 BLOT 6.5S

-
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 FIELDBright-field microscopy / Nominal magnification: 59000 / Nominal defocus max: 2800 nm / Nominal defocus min: 2200 nm
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 30 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k)

-
Processing

EM software
IDNameVersionCategory
4CTFFIND3CTF correction
13RELION3D reconstruction
CTF correctionType: NONE
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 43063 / Symmetry type: POINT

+
About Yorodumi

-
News

-
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. (see PDBe EMDB page)
  • 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 at PDBe / 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. See below links for details.
  • 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

+
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

+
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi

+
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi

Read more

-
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.

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