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- PDB-4a2i: Cryo-electron Microscopy Structure of the 30S Subunit in Complex ... -

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Basic information

Entry
Database: PDB / ID: 4a2i
TitleCryo-electron Microscopy Structure of the 30S Subunit in Complex with the YjeQ Biogenesis Factor
Components
  • (30S RIBOSOMAL PROTEIN ...) x 20
  • 16S RIBOSOMAL RNA
  • PUTATIVE RIBOSOME BIOGENESIS GTPASE RSGA
KeywordsRIBOSOME/HYDROLASE / RIBOSOME-HYDROLASE COMPLEX / RIBOSOME ASSEMBLY
Function / homology
Function and homology information


Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / mRNA binding involved in posttranscriptional gene silencing / ornithine decarboxylase inhibitor activity / misfolded RNA binding / transcription antitermination factor activity, RNA binding / RNA folding / Group I intron splicing / ribosomal small subunit biogenesis / transcription antitermination / negative regulation of translational initiation ...Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / mRNA binding involved in posttranscriptional gene silencing / ornithine decarboxylase inhibitor activity / misfolded RNA binding / transcription antitermination factor activity, RNA binding / RNA folding / Group I intron splicing / 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 / positive regulation of RNA splicing / ribosomal small subunit assembly / small ribosomal subunit rRNA binding / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / mRNA 5'-UTR binding / cytosolic small ribosomal subunit / regulation of translation / regulation of mRNA stability / negative regulation of translation / tRNA binding / ribosome / rRNA binding / structural constituent of ribosome / translation / mRNA binding / GTPase activity / response to antibiotic / GTP binding / RNA binding / zinc ion binding / membrane / metal ion binding / cytosol / cytoplasm
RsgA GTPase / Ribosomal protein S3, conserved site / 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 ...RsgA GTPase / Ribosomal protein S3, conserved site / 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 / 30S ribosomal protein S17 / Ribosomal protein S11, bacterial-type / Ribosomal protein S13, bacterial-type / Ribosomal protein S17, conserved site / Ribosomal protein S21, conserved site / Ribosomal protein S2, flavodoxin-like domain superfamily / Ribosomal protein S5 domain 2-type fold, subgroup / S15/NS1, RNA-binding / RsgA GTPase domain / Ribosomal protein S13-like, H2TH / Nucleic acid-binding, OB-fold / Ribosomal protein S5, N-terminal / Translation elongation factor EF1B/ribosomal protein S6 / K homology domain-like, alpha/beta / Ribosomal protein S18, conserved site / Ribosomal protein S4, conserved site / Ribosomal S11, conserved site / Ribosomal protein S5, N-terminal, conserved site / Ribosomal protein S10, conserved site / Ribosomal protein S13, conserved site / Ribosomal protein S14, conserved site / Ribosomal protein S19, superfamily / Ribosomal protein S7 domain / Ribosomal protein S12/S23 / Ribosomal protein S10p/S20e / S4 domain / Ribosomal protein S5, N-terminal domain / Ribosomal protein S5, C-terminal domain / Ribosomal protein S6 / Ribosomal protein S8 / Ribosomal protein S9/S16 / Ribosomal protein S11 / KH domain / Ribosomal protein S12/S23 / Ribosomal protein S13/S18 / Ribosomal protein S14p/S29e / Ribosomal protein S15 / Ribosomal protein S16 / Ribosomal protein S17 / Ribosomal protein S4/S9 N-terminal domain / Ribosomal protein S3, C-terminal domain / Ribosomal protein S16 domain superfamily / Ribosomal protein S3, C-terminal domain superfamily / P-loop containing nucleoside triphosphate hydrolase / 30s ribosomal protein S13, C-terminal / Ribosomal protein S10 domain / Circularly permuted (CP)-type guanine nucleotide-binding (G) domain / Ribosomal protein S6 superfamily / Ribosomal protein S8 superfamily / Ribosomal protein S20 superfamily / Ribosomal protein S2 / Ribosomal protein S7 domain superfamily / Ribosomal protein S10 domain superfamily / Ribosomal protein S18 superfamily / Ribosomal protein S11 superfamily / RNA-binding S4 domain superfamily / Ribosomal protein S21 superfamily / K homology domain superfamily, prokaryotic type / Ribosomal protein S2, conserved site / Ribosomal protein S19, bacterial-type / Ribosomal protein S4/S9, N-terminal / Ribosomal protein S16 / Ribosomal protein S6 / Ribosomal protein S15 / Ribosomal protein S8 / Ribosomal protein S9 / Ribosomal protein S5 / Ribosomal protein S14 / Ribosomal protein S3, C-terminal / Ribosomal protein S18 / Ribosomal protein S10 / Ribosomal protein S2 / Ribosomal protein S13 / Ribosomal protein S21 / Ribosomal protein S11 / Ribosomal protein S5/S7 / Ribosomal protein S19/S15 / Ribosomal protein S20 / Ribosomal protein S7, bacterial/organellar-type / RNA-binding S4 domain / K Homology domain, type 2 / K Homology domain / Ribosome biogenesis GTPase RsgA / Ribosomal protein S15, bacterial-type / Ribosomal protein S5, C-terminal / Ribosomal protein S12, bacterial-type / Ribosomal protein S3, bacterial-type / Ribosomal protein S2, bacteria/mitochondria/plastid
30S ribosomal protein S15 / 30S ribosomal protein S12 / 30S ribosomal protein S14 / 30S ribosomal protein S7 / 30S ribosomal protein S6 / 30S ribosomal protein S17 / 30S ribosomal protein S10 / 30S ribosomal protein S13 / 30S ribosomal protein S4 / 30S ribosomal protein S16 ...30S ribosomal protein S15 / 30S ribosomal protein S12 / 30S ribosomal protein S14 / 30S ribosomal protein S7 / 30S ribosomal protein S6 / 30S ribosomal protein S17 / 30S ribosomal protein S10 / 30S ribosomal protein S13 / 30S ribosomal protein S4 / 30S ribosomal protein S16 / 30S ribosomal protein S18 / 30S ribosomal protein S19 / 30S ribosomal protein S11 / 30S ribosomal protein S2 / 30S ribosomal protein S3 / 30S ribosomal protein S5 / gb:33357879: / 30S ribosomal protein S8 / 30S ribosomal protein S9 / 30S ribosomal protein S15 / 30S ribosomal protein S14 / 30S ribosomal protein S17 / 30S ribosomal protein S21 / Small ribosomal subunit biogenesis GTPase RsgA / 30S ribosomal protein S20
Biological speciesSALMONELLA ENTERICA SUBSP. ENTERICA SEROVAR TYPHIMURIUM (bacteria)
ESCHERICHIA COLI (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 16.5 Å
AuthorsJomaa, A. / Stewart, G. / Mears, J.A. / Kireeva, I. / Brown, E.D. / Ortega, J.
CitationJournal: RNA / Year: 2011
Title: Cryo-electron microscopy structure of the 30S subunit in complex with the YjeQ biogenesis factor.
Authors: Ahmad Jomaa / Geordie Stewart / Jason A Mears / Inga Kireeva / Eric D Brown / Joaquin Ortega /
Abstract: YjeQ is a protein broadly conserved in bacteria containing an N-terminal oligonucleotide/oligosaccharide fold (OB-fold) domain, a central GTPase domain, and a C-terminal zinc-finger domain. YjeQ ...YjeQ is a protein broadly conserved in bacteria containing an N-terminal oligonucleotide/oligosaccharide fold (OB-fold) domain, a central GTPase domain, and a C-terminal zinc-finger domain. YjeQ binds tightly and stoichiometrically to the 30S subunit, which stimulates its GTPase activity by 160-fold. Despite growing evidence for the involvement of the YjeQ protein in bacterial 30S subunit assembly, the specific function and mechanism of this protein remain unclear. Here, we report the costructure of YjeQ with the 30S subunit obtained by cryo-electron microscopy. The costructure revealed that YjeQ interacts simultaneously with helix 44, the head and the platform of the 30S subunit. This binding location of YjeQ in the 30S subunit suggests a chaperone role in processing of the 3' end of the rRNA as well as in mediating the correct orientation of the main domains of the 30S subunit. In addition, the YjeQ binding site partially overlaps with the interaction site of initiation factors 2 and 3, and upon binding, YjeQ covers three inter-subunit bridges that are important for the association of the 30S and 50S subunits. Hence, our structure suggests that YjeQ may assist in ribosome maturation by preventing premature formation of the translation initiation complex and association with the 50S subunit. Together, these results support a role for YjeQ in the late stages of 30S maturation.
Validation Report
SummaryFull reportAbout validation report
History
DepositionSep 27, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 2, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2013Group: Derived calculations
Revision 1.2Aug 23, 2017Group: Data collection / Derived calculations ...Data collection / Derived calculations / Refinement description / Source and taxonomy / Structure summary
Category: em_3d_fitting / em_software ...em_3d_fitting / em_software / entity / entity_src_nat / struct_conn
Item: _em_3d_fitting.target_criteria / _em_software.fitting_id ..._em_3d_fitting.target_criteria / _em_software.fitting_id / _em_software.image_processing_id / _em_software.name / _entity.src_method / _entity_src_nat.common_name
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "VA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "VA" 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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Assembly

Deposited unit
A: 16S RIBOSOMAL RNA
B: 30S RIBOSOMAL PROTEIN S2
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
U: 30S RIBOSOMAL PROTEIN S21
V: PUTATIVE RIBOSOME BIOGENESIS GTPASE RSGA


Theoretical massNumber of molelcules
Total (without water)791,44822
Polymers791,44822
Non-polymers00
Water0
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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30S RIBOSOMAL PROTEIN ... , 20 types, 20 molecules BCDEFGHIJKLMNOPQRSTU

#2: Protein 30S RIBOSOMAL PROTEIN S2 /


Mass: 24253.943 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / References: UniProt: P0A7V0
#3: Protein 30S RIBOSOMAL PROTEIN S3 /


Mass: 23078.785 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / References: UniProt: P0A7V3
#4: Protein 30S RIBOSOMAL PROTEIN S4 /


Mass: 23383.002 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / References: UniProt: P0A7V8
#5: Protein 30S RIBOSOMAL PROTEIN S5 /


Mass: 15804.282 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / References: UniProt: P0A7W1
#6: Protein 30S RIBOSOMAL PROTEIN S6 /


Mass: 11669.371 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / References: UniProt: P02358
#7: Protein 30S RIBOSOMAL PROTEIN S7 /


Mass: 16764.406 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / References: UniProt: P02359
#8: Protein 30S RIBOSOMAL PROTEIN S8 /


Mass: 14015.361 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / References: UniProt: P0A7W7
#9: Protein 30S RIBOSOMAL PROTEIN S9 /


Mass: 14554.882 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / References: UniProt: P0A7X3
#10: Protein 30S RIBOSOMAL PROTEIN S10 /


Mass: 11196.988 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / References: UniProt: P0A7R5
#11: Protein 30S RIBOSOMAL PROTEIN S11 /


Mass: 12487.200 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / References: UniProt: P0A7R9
#12: Protein 30S RIBOSOMAL PROTEIN S12 /


Mass: 13636.961 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / References: UniProt: P0A7S3
#13: Protein 30S RIBOSOMAL PROTEIN S13 /


Mass: 12625.753 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / References: UniProt: P0A7S9
#14: Protein 30S RIBOSOMAL PROTEIN S14 /


Mass: 11475.364 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / References: UniProt: P02370, UniProt: P0AG59*PLUS
#15: Protein 30S RIBOSOMAL PROTEIN S15 /


Mass: 10188.687 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / References: UniProt: P02371, UniProt: P0ADZ4*PLUS
#16: 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: P0A7T3
#17: Protein 30S RIBOSOMAL PROTEIN S17 /


Mass: 9263.946 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / References: UniProt: P02373, UniProt: P0AG63*PLUS
#18: Protein 30S RIBOSOMAL PROTEIN S18 /


Mass: 6466.477 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / References: UniProt: P0A7T7
#19: Protein 30S RIBOSOMAL PROTEIN S19 /


Mass: 9057.626 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / References: UniProt: P0A7U3
#20: Protein 30S RIBOSOMAL PROTEIN S20 /


Mass: 9506.190 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / References: UniProt: P0A7U7
#21: Protein 30S RIBOSOMAL PROTEIN S21 /


Mass: 6067.081 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / References: UniProt: P68679

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RNA chain / Protein , 2 types, 2 molecules AV

#1: RNA chain 16S RIBOSOMAL RNA /


Mass: 495927.719 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / References: GenBank: 33357879
#22: Protein PUTATIVE RIBOSOME BIOGENESIS GTPASE RSGA / YJEQ


Mass: 30816.074 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SALMONELLA ENTERICA SUBSP. ENTERICA SEROVAR TYPHIMURIUM (bacteria)
Plasmid: PDEST17 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): AI / References: UniProt: Q8ZKB0

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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: ESCHERICHIA COLI 30S RIBOSOMAL SUBUNIT WITH YJEQ PROTEIN BOUND IN THE PRESENCE OF GMP-PNP
Type: RIBOSOME
Buffer solutionName: 10 MM TRIS-HCL PH 7.5, 10 MM MAGNESIUM ACETATE, 60 MM NH4CL, 3 MM 2- MERCAPTOETHANOL AND 2 MM GMP-PNP
pH: 7.5
Details: 10 MM TRIS-HCL PH 7.5, 10 MM MAGNESIUM ACETATE, 60 MM NH4CL, 3 MM 2- MERCAPTOETHANOL AND 2 MM GMP-PNP
SpecimenConc.: 0.9 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: FORMVAR PLUS CARBON
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Details: BLOT FOR 7 SECONDS IN FEI VITROBOT III

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Electron microscopy imaging

MicroscopyModel: JEOL 2010F / Date: May 12, 2010
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 50000 X / Calibrated magnification: 50000 X / Nominal defocus max: 3900 nm / Nominal defocus min: 650 nm / Cs: 1 mm
Specimen holderTemperature: 100 K / Tilt angle min: 0 °
Image recordingElectron dose: 15 e/Å2 / Film or detector model: KODAK SO-163 FILM
Image scansNum. digital images: 150
Radiation wavelengthRelative weight: 1

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Processing

EM software
IDNameCategory
1UCSF Chimeramodel fitting
2Xmipp3D reconstruction
CTF correctionDetails: EACH MICROGRAPH
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionMethod: PROJECTION MATCHING / Resolution: 16.5 Å / Num. of particles: 16228 / Nominal pixel size: 2.54 Å / Actual pixel size: 2.54 Å
Details: THE COORDINATES IN THIS ENTRY WERE GENERATED BY MANUAL DOCKING OF THE STRUCTURE OF THE ESCHERICHIA COLI 30S RIBOSOMAL SUBUNIT (2AVY) AND SALMONELLA TYPHYMURIUM (2RCN) INTO THE DENSITY MAP OF ...Details: THE COORDINATES IN THIS ENTRY WERE GENERATED BY MANUAL DOCKING OF THE STRUCTURE OF THE ESCHERICHIA COLI 30S RIBOSOMAL SUBUNIT (2AVY) AND SALMONELLA TYPHYMURIUM (2RCN) INTO THE DENSITY MAP OF THE ESCHERICHIA COLI 30S_YJEQ COMPLEX GENERATED BY CRYO-ELECTRON MICROSCOPY. THE YEJQ PROTEIN WAS FITTED AS THREE SEPARATE DOMAINS: THE OB-FOLD, THE GTPASE DOMAIN, AND THE ZINC-FINGER DOMAIN. THE PROTEIN DATA BANK CONVENTIONS REQUIRE TO ENTER INFORMATION ABOUT THE UNIT CELL, CRYSTAL DATA AND COORDINATE SYSTEM. THESE INFORMATION IS MEANINGLESS IN THIS ENTRY. SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-1895.
Symmetry type: POINT
Atomic model buildingProtocol: OTHER / Space: REAL / Target criteria: Cross-correlation coefficient / Details: METHOD--MANUAL REFINEMENT PROTOCOL--X-RAY
Atomic model building
IDPDB-ID3D fitting-ID
12AVY

2avy
PDB Unreleased entry

1
22RCN1
RefinementHighest resolution: 16.5 Å
Refinement stepCycle: LAST / Highest resolution: 16.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20702 32831 0 0 53533

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