[English] 日本語
Yorodumi
- PDB-5uz4: The cryo-EM structure of YjeQ bound to the 30S subunit suggests a... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5uz4
TitleThe cryo-EM structure of YjeQ bound to the 30S subunit suggests a fidelity checkpoint function for this protein in ribosome assembly
Components
  • (30S ribosomal protein ...) x 19
  • 16S RIBOSOMAL RNA
  • Small ribosomal subunit biogenesis GTPase RsgA
KeywordsRIBOSOME/Hydrolase / Ribosome assembly / 30S subunit / YjeQ protein / RsgA protein / RIBOSOME-Hydrolase complex
Function / homology
Function and homology information


guanosine tetraphosphate binding / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / mRNA binding involved in posttranscriptional gene silencing / ornithine decarboxylase inhibitor activity / transcription antitermination factor activity, RNA binding / ribosomal small subunit biogenesis / transcription antitermination / negative regulation of translational initiation / four-way junction DNA binding / DNA-templated transcription, termination ...guanosine tetraphosphate binding / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / mRNA binding involved in posttranscriptional gene silencing / ornithine decarboxylase inhibitor activity / transcription antitermination factor activity, RNA binding / ribosomal small subunit biogenesis / transcription antitermination / negative regulation of translational initiation / four-way junction DNA binding / DNA-templated transcription, termination / translation repressor activity, mRNA regulatory element binding / positive regulation of translational fidelity / endodeoxyribonuclease activity / maintenance of translational fidelity / ribosomal small subunit assembly / small ribosomal subunit rRNA binding / mRNA 5'-UTR binding / small ribosomal subunit / GDP binding / cytosolic small ribosomal subunit / regulation of translation / negative regulation of translation / tRNA binding / ribosome / rRNA binding / structural constituent of ribosome / translation / mRNA binding / GTPase activity / response to antibiotic / GTP binding / zinc ion binding / membrane / metal ion binding / cytosol
RsgA GTPase / 30S ribosomal protein S17 / Ribosomal protein S16 domain superfamily / Ribosomal protein S7 domain / Ribosomal protein S2, flavodoxin-like domain superfamily / Ribosomal protein S19, superfamily / Ribosomal protein S14, bacterial/plastid / Ribosomal protein S9, bacterial/plastid / Ribosomal protein S4/S9 / Ribosomal protein S19 conserved site ...RsgA GTPase / 30S ribosomal protein S17 / Ribosomal protein S16 domain superfamily / Ribosomal protein S7 domain / Ribosomal protein S2, flavodoxin-like domain superfamily / Ribosomal protein S19, superfamily / Ribosomal protein S14, bacterial/plastid / Ribosomal protein S9, bacterial/plastid / Ribosomal protein S4/S9 / Ribosomal protein S19 conserved site / Ribosomal protein S6, conserved site / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein S7, conserved site / Ribosomal protein S16, conserved site / Ribosomal protein S9, conserved site / Ribosomal protein S5 domain 2-type fold / Ribosomal protein S11, bacterial-type / 30s ribosomal protein S13, C-terminal / Ribosomal protein S13, bacterial-type / Ribosomal protein S3, conserved site / Ribosomal protein S18, conserved site / Ribosomal protein S14, conserved site / Ribosomal protein S13, conserved site / Ribosomal protein S10, conserved site / Ribosomal protein S5, N-terminal, conserved site / Ribosomal protein S2, conserved site / Ribosomal S11, conserved site / Ribosomal protein S4, conserved site / K homology domain-like, alpha/beta / Ribosomal protein S5 domain 2-type fold, subgroup / Translation elongation factor EF1B/ribosomal protein S6 / Ribosomal protein S5, N-terminal / P-loop containing nucleoside triphosphate hydrolase / Ribosomal protein S10 domain / Ribosomal protein S13-like, H2TH / Ribosomal protein S6 / Ribosomal protein S20 / Ribosomal protein S19 / Ribosomal protein S18 / Ribosomal protein S17 / Ribosomal protein S16 / Ribosomal protein S15 / Ribosomal protein S14p/S29e / Ribosomal protein S13/S18 / Ribosomal protein S12/S23 / Ribosomal protein S11 / Ribosomal protein S10p/S20e / Ribosomal protein S9/S16 / Ribosomal protein S8 / Ribosomal protein S7p/S5e / Ribosomal protein S5, C-terminal domain / Circularly permuted (CP)-type guanine nucleotide-binding (G) domain / Ribosomal protein S18 superfamily / Ribosomal protein S6 superfamily / Ribosomal protein S8 superfamily / Ribosomal protein S3, C-terminal domain superfamily / Ribosomal protein S20 superfamily / Ribosomal protein S7 domain superfamily / Ribosomal protein S10 domain superfamily / Ribosomal protein S11 superfamily / Ribosomal protein S5, N-terminal domain / RNA-binding S4 domain superfamily / Ribosomal protein S2 / Ribosomal protein S3, C-terminal domain / KH domain / Ribosomal protein S4/S9 N-terminal domain / S4 domain / Nucleic acid-binding, OB-fold / Ribosomal protein S17, conserved site / RsgA GTPase domain / Ribosomal protein S14 / Ribosomal protein S4/S9, N-terminal / Ribosomal protein S13 / Ribosomal protein S2 / Ribosomal protein S10 / Ribosomal protein S18 / Ribosomal protein S3, C-terminal / Ribosomal protein S5 / Ribosomal protein S19/S15 / Ribosomal protein S9 / Ribosomal protein S8 / Ribosomal protein S15 / Ribosomal protein S6 / Ribosomal protein S16 / Ribosomal protein S17/S11 / Ribosomal protein S11 / Ribosomal protein S20 / Ribosomal protein S5/S7 / Ribosomal protein S2, bacteria/mitochondria/plastid / K homology domain superfamily, prokaryotic type / Ribosomal protein S12/S23 / Ribosomal protein S19, bacterial-type / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein S5, bacterial-type / Ribosomal protein S4, bacterial-type / Ribosomal protein S3, bacterial-type / RNA-binding S4 domain / Ribosomal protein S12, bacterial-type / Ribosomal protein S5, C-terminal / Ribosomal protein S15, bacterial-type
30S ribosomal protein S14 / gb:1095872043: / 30S ribosomal protein S15 / Small ribosomal subunit biogenesis GTPase RsgA / 30S ribosomal protein S2 / 30S ribosomal protein S15 / 30S ribosomal protein S16 / 30S ribosomal protein S20 / 30S ribosomal protein S2 / 30S ribosomal protein S9 ...30S ribosomal protein S14 / gb:1095872043: / 30S ribosomal protein S15 / Small ribosomal subunit biogenesis GTPase RsgA / 30S ribosomal protein S2 / 30S ribosomal protein S15 / 30S ribosomal protein S16 / 30S ribosomal protein S20 / 30S ribosomal protein S2 / 30S ribosomal protein S9 / 30S ribosomal protein S4 / 30S ribosomal protein S8 / 30S ribosomal protein S14 / 30S ribosomal protein S17 / 30S ribosomal protein S3 / 30S ribosomal protein S19 / 30S ribosomal protein S10 / 30S ribosomal protein S12 / 30S ribosomal protein S18 / 30S ribosomal protein S5 / 30S ribosomal protein S6 / 30S ribosomal protein S7 / 30S ribosomal protein S10 / 30S ribosomal protein S13 / 30S ribosomal protein S13 / 30S ribosomal protein S16 / 30S ribosomal protein S19 / 30S ribosomal protein S20 / 30S ribosomal protein S3 / 30S ribosomal protein S4 / 30S ribosomal protein S5 / 30S ribosomal protein S11
Biological speciesEscherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 5.8 Å
AuthorsRazi, A. / Guarne, A. / Ortega, J.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)MOP-82930 Canada
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: The cryo-EM structure of YjeQ bound to the 30S subunit suggests a fidelity checkpoint function for this protein in ribosome assembly.
Authors: Aida Razi / Alba Guarné / Joaquin Ortega /
Abstract: Recent work suggests that bacterial YjeQ (RsgA) participates in the late stages of assembly of the 30S subunit and aids the assembly of the decoding center but also binds the mature 30S subunit with ...Recent work suggests that bacterial YjeQ (RsgA) participates in the late stages of assembly of the 30S subunit and aids the assembly of the decoding center but also binds the mature 30S subunit with high affinity. To determine the function and mechanisms of YjeQ in the context of the mature subunit, we determined the cryo-EM structure of the fully assembled 30S subunit in complex with YjeQ at 5.8-Å resolution. We found that binding of YjeQ stabilizes helix 44 into a conformation similar to that adopted by the subunit during proofreading. This finding indicates that, along with acting as an assembly factor, YjeQ has a role as a checkpoint protein, consisting of testing the proofreading ability of the 30S subunit. The structure also informs the mechanism by which YjeQ implements the release from the 30S subunit of a second assembly factor, called RbfA. Finally, it reveals how the 30S subunit stimulates YjeQ GTPase activity and leads to release of the protein. Checkpoint functions have been described for eukaryotic ribosome assembly factors; however, this work describes an example of a bacterial assembly factor that tests a specific translation mechanism of the 30S subunit.
Validation Report
SummaryFull reportAbout validation report
History
DepositionFeb 24, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 19, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2017Group: Database references
Revision 1.2May 10, 2017Group: Database references
Revision 1.3Sep 27, 2017Group: Author supporting evidence / Data collection / Category: em_software / pdbx_audit_support
Item: _em_software.name / _pdbx_audit_support.funding_organization
Revision 1.4Jan 15, 2020Group: Advisory / Author supporting evidence / Category: pdbx_audit_support / pdbx_unobs_or_zero_occ_atoms / Item: _pdbx_audit_support.funding_organization

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-8621
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 16S RIBOSOMAL RNA
C: 30S ribosomal protein S3
D: 30S ribosomal protein S4
E: 30S ribosomal protein S5
F: 30S ribosomal protein S6
G: 30S ribosomal protein S7
H: 30S ribosomal protein S8
I: 30S ribosomal protein S9
J: 30S ribosomal protein S10
K: 30S ribosomal protein S11
L: 30S ribosomal protein S12
M: 30S ribosomal protein S13
N: 30S ribosomal protein S14
O: 30S ribosomal protein S15
P: 30S ribosomal protein S16
Q: 30S ribosomal protein S17
R: 30S ribosomal protein S18
S: 30S ribosomal protein S19
T: 30S ribosomal protein S20
B: 30S ribosomal protein S2
Z: Small ribosomal subunit biogenesis GTPase RsgA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)813,84423
Polymers813,12321
Non-polymers7212
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

+
30S ribosomal protein ... , 19 types, 19 molecules CDEFGHIJKLMNOPQRSTB

#2: Protein 30S ribosomal protein S3 /


Mass: 26031.316 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: B7MCS9, UniProt: P0A7V3*PLUS
#3: Protein 30S ribosomal protein S4 /


Mass: 23514.199 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: B7MCR2, UniProt: P0A7V8*PLUS
#4: Protein 30S ribosomal protein S5 /


Mass: 17629.398 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7W3, UniProt: P0A7W1*PLUS
#5: Protein 30S ribosomal protein S6 / / Small ribosomal subunit protein bS6


Mass: 15211.058 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P02358
#6: Protein 30S ribosomal protein S7 / / Small ribosomal subunit protein uS7


Mass: 20055.156 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P02359
#7: Protein 30S ribosomal protein S8 /


Mass: 14146.557 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: B7MCS1
#8: Protein 30S ribosomal protein S9 /


Mass: 14886.270 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: B7MBZ1
#9: Protein 30S ribosomal protein S10 /


Mass: 11755.597 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: B7MCT6, UniProt: P0A7R5*PLUS
#10: Protein 30S ribosomal protein S11 /


Mass: 13870.975 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: B7MCR3
#11: Protein 30S ribosomal protein S12 /


Mass: 13768.157 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: B7MCV7
#12: Protein 30S ribosomal protein S13 /


Mass: 13128.467 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7T1, UniProt: P0A7S9*PLUS
#13: Protein 30S ribosomal protein S14 /


Mass: 11606.560 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: B7MCS2, UniProt: P0AG59*PLUS
#14: Protein 30S ribosomal protein S15 /


Mass: 10319.882 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: Q8X9M2, UniProt: P0ADZ4*PLUS
#15: Protein 30S ribosomal protein S16 /


Mass: 9207.572 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: B7MIU7, UniProt: P0A7T3*PLUS
#16: Protein 30S ribosomal protein S17 /


Mass: 9724.491 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: B7MCS6
#17: Protein 30S ribosomal protein S18 /


Mass: 9005.472 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: B7MLK7
#18: Protein 30S ribosomal protein S19 /


Mass: 10455.355 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: B7MCT1, UniProt: P0A7U3*PLUS
#19: Protein 30S ribosomal protein S20 /


Mass: 9708.464 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: B7MAE3, UniProt: P0A7U7*PLUS
#20: Protein 30S ribosomal protein S2 /


Mass: 26781.670 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: B7MBF0, UniProt: P0A7V0*PLUS

-
RNA chain / Protein , 2 types, 2 molecules AZ

#1: RNA chain 16S RIBOSOMAL RNA /


Mass: 494971.188 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: GenBank: 1095872043
#21: Protein Small ribosomal subunit biogenesis GTPase RsgA


Mass: 37345.172 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rsgA, engC, yjeQ, b4161, JW4122 / Production host: Escherichia coli (E. coli)
References: UniProt: P39286, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides

-
Non-polymers , 2 types, 2 molecules

#22: Chemical ChemComp-ZN / ZINC ION / Zinc


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#23: Chemical ChemComp-GGM / 3'-O-(N-methylanthraniloyl)-beta:gamma-imidoguanosine-5'-triphosphate / MANT-GMPPNP


Mass: 655.343 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H24N7O14P3

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: Structure of the 30S subunit in complex with YjeQ GTPase
Type: COMPLEX
Entity ID: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21
Source: MULTIPLE SOURCES
Source (natural)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: C-flat CFT-222C
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 298 K

-
Electron microscopy imaging

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI F20
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 25000 X / Calibrated magnification: 34482 X / Nominal defocus max: 3000 nm / Nominal defocus min: 500 nm / Cs: 2 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN
Model: GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER
Image recordingAverage exposure time: 0.5 sec. / Electron dose: 1 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)
Image scansMovie frames/image: 30 / Used frames/image: 1-20

-
Processing

EM software
IDNameVersionCategory
9RELION1.4initial Euler assignment
10RELION1.4final Euler assignment
11RELION1.4classification
13Cootmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 487018
3D reconstructionResolution: 5.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 130462 / Symmetry type: POINT
Atomic model buildingProtocol: OTHER

+
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