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- PDB-2ykr: 30S ribosomal subunit with RsgA bound in the presence of GMPPNP -

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Basic information

Entry
Database: PDB / ID: 2ykr
Title30S ribosomal subunit with RsgA bound in the presence of GMPPNP
Components
  • (30S RIBOSOMAL PROTEIN ...) x 20
  • 16S RRNA
  • PUTATIVE RIBOSOME BIOGENESIS GTPASE RSGA
KeywordsRIBOSOME/HYDROLASE / RIBOSOME-HYDROLASE COMPLEX / RIBOSOME BIOGENESIS / YJEQ / CIRCULARLY PERMUTATED GTPASE
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 / misfolded RNA binding / transcription antitermination factor activity, RNA binding / RNA folding / Group I intron splicing / ribosomal small subunit biogenesis / transcription antitermination ...guanosine tetraphosphate binding / 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 / small ribosomal subunit / GDP binding / cytosolic small ribosomal subunit / regulation of translation / regulation of mRNA stability / tRNA binding / negative regulation of translation / ribosome / rRNA binding / structural constituent of ribosome / translation / GTPase activity / mRNA binding / response to antibiotic / GTP binding / RNA binding / zinc ion binding / membrane / metal ion binding / cytosol / cytoplasm
RsgA GTPase / Ribosomal protein S9, conserved site / Ribosomal protein S21, conserved site / Ribosomal protein S17, conserved site / Ribosomal protein S13, bacterial-type / Ribosomal protein S11, bacterial-type / 30S ribosomal protein S17 / Ribosomal protein S5 domain 2-type fold / Ribosomal protein S16, conserved site / Ribosomal protein S14, conserved site ...RsgA GTPase / Ribosomal protein S9, conserved site / Ribosomal protein S21, conserved site / Ribosomal protein S17, conserved site / Ribosomal protein S13, bacterial-type / Ribosomal protein S11, bacterial-type / 30S ribosomal protein S17 / Ribosomal protein S5 domain 2-type fold / Ribosomal protein S16, conserved site / Ribosomal protein S14, conserved site / Ribosomal protein S7, conserved site / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein S6, conserved site / Ribosomal protein S19 conserved site / Ribosomal protein S4/S9 / Ribosomal protein S9, bacterial/plastid / Ribosomal protein S18, conserved site / Ribosomal protein S13, conserved site / Ribosomal protein S19, superfamily / Ribosomal protein S5, N-terminal / Ribosomal protein S12/S23 / K homology domain superfamily, prokaryotic type / S15/NS1, RNA-binding / RsgA GTPase domain / Ribosomal protein S13-like, H2TH / Nucleic acid-binding, OB-fold / Translation elongation factor EF1B/ribosomal protein S6 / Ribosomal protein S10, conserved site / Ribosomal protein S5 domain 2-type fold, subgroup / K homology domain-like, alpha/beta / Ribosomal protein S4, conserved site / Ribosomal S11, conserved site / Ribosomal protein S2, conserved site / Ribosomal protein S5, N-terminal, conserved site / Ribosomal protein S14, bacterial/plastid / Ribosomal protein S2, flavodoxin-like domain superfamily / Ribosomal protein S7, bacterial/organellar-type / 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 S7 domain / Ribosomal protein S8 superfamily / Ribosomal protein S16 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 S3, C-terminal domain superfamily / Ribosomal protein S2 / Ribosomal protein S20 superfamily / 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 / Ribosomal protein S19, bacterial-type / Ribosomal protein S3, conserved site / Ribosomal protein S5, bacterial-type / Ribosomal protein S13 / Ribosomal protein S17/S11 / Ribosomal protein S16 / Ribosomal protein S6 / Ribosomal protein S15 / Ribosomal protein S8 / Ribosomal protein S9 / Ribosomal protein S5 / Ribosomal protein S14 / Ribosomal protein S4, bacterial-type / Ribosomal protein S3, C-terminal / Ribosomal protein S18 / Ribosomal protein S10 / Ribosomal protein S2 / Ribosomal protein S21 / Ribosomal protein S4/S9, N-terminal / Ribosomal protein S11 / Ribosomal protein S19/S15 / Ribosomal protein S20 / 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
30S ribosomal protein S17 / 30S ribosomal protein S9 / 30S ribosomal protein S15 / 30S ribosomal protein S14 / 30S ribosomal protein S9 / 30S ribosomal protein S17 / Small ribosomal subunit biogenesis GTPase RsgA / 30S ribosomal protein S21 / gb:54791136: / 30S ribosomal protein S5 ...30S ribosomal protein S17 / 30S ribosomal protein S9 / 30S ribosomal protein S15 / 30S ribosomal protein S14 / 30S ribosomal protein S9 / 30S ribosomal protein S17 / Small ribosomal subunit biogenesis GTPase RsgA / 30S ribosomal protein S21 / gb:54791136: / 30S ribosomal protein S5 / 30S ribosomal protein S8 / 30S ribosomal protein S10 / 30S ribosomal protein S4 / 30S ribosomal protein S5 / 30S ribosomal protein S4 / 30S ribosomal protein S13 / 30S ribosomal protein S3 / 30S ribosomal protein S10 / un:b3hgb0: / 30S ribosomal protein S8 / 30S ribosomal protein S19 / 30S ribosomal protein S6 / 30S ribosomal protein S20 / 30S ribosomal protein S11 / 30S ribosomal protein S14 / 30S ribosomal protein S16 / 30S ribosomal protein S2 / Small ribosomal subunit biogenesis GTPase RsgA / 30S ribosomal protein S3 / 30S ribosomal protein S18 / 30S ribosomal protein S7 / 30S ribosomal protein S6 / 30S ribosomal protein S7 / 30S ribosomal protein S11 / 30S ribosomal protein S12 / 30S ribosomal protein S12 / 30S ribosomal protein S13 / 30S ribosomal protein S16 / 30S ribosomal protein S18 / 30S ribosomal protein S19 / 30S ribosomal protein S20 / 30S ribosomal protein S2 / 30S ribosomal protein S21
Biological speciesESCHERICHIA COLI (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 9.8 Å
AuthorsGuo, Q. / Yuan, Y. / Xu, Y. / Feng, B. / Liu, L. / Chen, K. / Lei, J. / Gao, N.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2011
Title: Structural basis for the function of a small GTPase RsgA on the 30S ribosomal subunit maturation revealed by cryoelectron microscopy.
Authors: Qiang Guo / Yi Yuan / Yanji Xu / Boya Feng / Liang Liu / Kai Chen / Ming Sun / Zhixiu Yang / Jianlin Lei / Ning Gao /
Abstract: The bacterial RsgA, a circularly permutated GTPase, whose GTPase activity is dependent on the 30S ribosomal subunit, is a late-stage ribosome biogenesis factor involved in the 30S subunit maturation. ...The bacterial RsgA, a circularly permutated GTPase, whose GTPase activity is dependent on the 30S ribosomal subunit, is a late-stage ribosome biogenesis factor involved in the 30S subunit maturation. The role of RsgA is to release another 30S biogenesis factor, RbfA, from the mature 30S subunit in a GTP-dependent manner. Using cryoelectron microscopy, we have determined the structure of the 30S subunit bound with RsgA in the presence of GMPPNP at subnanometer resolution. In the structure, RsgA binds to the central part of the 30S subunit, close to the decoding center, in a position that is incompatible with multiple biogenesis factors, all three translation initiation factors, as well as A-, P-site tRNAs and the 50S subunit. Further structural analysis not only provides a structural model for the RsgA-dependent release of RbfA from the nascent 30S subunit, but also indicates RsgA's role in the ribosomal protein assembly, to promote some tertiary binding protein incorporation. Moreover, together with available biochemical and genetic data, our results suggest that RsgA might be a general checkpoint protein in the late stage of the 30S subunit biogenesis, whose function is not only to release biogenesis factors (e.g., RbfA) from the nascent 30S subunit, but also to block the association of initiation factors to the premature 30S subunit.
Validation Report
SummaryFull reportAbout validation report
History
DepositionMay 30, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 24, 2011Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2013Group: Other / Refinement description
Revision 1.2Aug 30, 2017Group: Data collection / Derived calculations ...Data collection / Derived calculations / Refinement description / Structure summary
Category: em_3d_fitting / em_image_scans ...em_3d_fitting / em_image_scans / em_software / entity / struct_conn
Item: _em_3d_fitting.target_criteria / _em_software.image_processing_id / _entity.src_method

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Structure visualization

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Assembly

Deposited unit
A: 16S RRNA
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
W: PUTATIVE RIBOSOME BIOGENESIS GTPASE RSGA


Theoretical massNumber of molelcules
Total (without water)800,89822
Polymers800,89822
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 / Fragment: RESIDUES 9-226 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: DH5ALPHA / References: UniProt: B7NID0, UniProt: P0A7V0*PLUS
#3: Protein 30S RIBOSOMAL PROTEIN S3 /


Mass: 23078.785 Da / Num. of mol.: 1 / Fragment: RESIDUES 2-207 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: DH5ALPHA / References: UniProt: A1AGK2, UniProt: P0A7V3*PLUS
#4: Protein 30S RIBOSOMAL PROTEIN S4 /


Mass: 23383.002 Da / Num. of mol.: 1 / Fragment: RESIDUES 2-206 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: DH5ALPHA / References: UniProt: A1AGI7, UniProt: P0A7V8*PLUS
#5: Protein 30S RIBOSOMAL PROTEIN S5 /


Mass: 15804.282 Da / Num. of mol.: 1 / Fragment: RESIDUES 10-159 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: DH5ALPHA / References: UniProt: D6JG86, UniProt: P0A7W1*PLUS
#6: Protein 30S RIBOSOMAL PROTEIN S6 /


Mass: 11669.371 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-100 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: DH5ALPHA / References: UniProt: B6I2A6, UniProt: P02358*PLUS
#7: Protein 30S RIBOSOMAL PROTEIN S7 /


Mass: 16861.523 Da / Num. of mol.: 1 / Fragment: RESIDUES 2-152 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: DH5ALPHA / References: UniProt: E3XT25, UniProt: P02359*PLUS
#8: Protein 30S RIBOSOMAL PROTEIN S8 /


Mass: 14015.361 Da / Num. of mol.: 1 / Fragment: RESIDUES 2-130 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: DH5ALPHA / References: UniProt: B6I220, UniProt: P0A7W7*PLUS
#9: Protein 30S RIBOSOMAL PROTEIN S9 /


Mass: 14554.882 Da / Num. of mol.: 1 / Fragment: RESIDUES 4-130 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: DH5ALPHA / References: UniProt: Q0TCN6, UniProt: P0A7X3*PLUS
#10: Protein 30S RIBOSOMAL PROTEIN S10 /


Mass: 11196.988 Da / Num. of mol.: 1 / Fragment: RESIDUES 5-102 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: DH5ALPHA / References: UniProt: A7ZSL0, UniProt: P0A7R5*PLUS
#11: Protein 30S RIBOSOMAL PROTEIN S11 /


Mass: 12487.200 Da / Num. of mol.: 1 / Fragment: RESIDUES 13-129 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: DH5ALPHA / References: UniProt: B7M103, UniProt: P0A7R9*PLUS
#12: Protein 30S RIBOSOMAL PROTEIN S12 /


Mass: 13636.961 Da / Num. of mol.: 1 / Fragment: RESIDUES 2-124 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: DH5ALPHA / References: UniProt: P0A7S4, UniProt: P0A7S3*PLUS
#13: Protein 30S RIBOSOMAL PROTEIN S13 /


Mass: 12625.753 Da / Num. of mol.: 1 / Fragment: RESIDUES 2-115 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: DH5ALPHA / References: UniProt: A1AGI9, UniProt: P0A7S9*PLUS
#14: Protein 30S RIBOSOMAL PROTEIN S14 /


Mass: 11475.364 Da / Num. of mol.: 1 / Fragment: RESIDUES 2-101 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: DH5ALPHA / References: UniProt: B7M1M1, UniProt: P0AG59*PLUS
#15: Protein 30S RIBOSOMAL PROTEIN S15 /


Mass: 10159.621 Da / Num. of mol.: 1 / Fragment: RESIDUES 2-89 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: DH5ALPHA / References: UniProt: B3HGB0, 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) / Strain: DH5ALPHA / References: UniProt: B7N6J5, UniProt: P0A7T3*PLUS
#17: Protein 30S RIBOSOMAL PROTEIN S17 /


Mass: 9263.946 Da / Num. of mol.: 1 / Fragment: RESIDUES 4-83 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: DH5ALPHA / References: UniProt: P0AG65, UniProt: P0AG63*PLUS
#18: Protein 30S RIBOSOMAL PROTEIN S18 /


Mass: 6466.477 Da / Num. of mol.: 1 / Fragment: RESIDUES 20-74 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: DH5ALPHA / References: UniProt: E3PE70, UniProt: P0A7T7*PLUS
#19: Protein 30S RIBOSOMAL PROTEIN S19 /


Mass: 9057.626 Da / Num. of mol.: 1 / Fragment: RESIDUES 3-81 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: DH5ALPHA / References: UniProt: B6I230, UniProt: P0A7U3*PLUS
#20: Protein 30S RIBOSOMAL PROTEIN S20 /


Mass: 9506.190 Da / Num. of mol.: 1 / Fragment: RESIDUES 3-87 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: DH5ALPHA / References: UniProt: B7L4E5, UniProt: P0A7U7*PLUS
#21: Protein 30S RIBOSOMAL PROTEIN S21 /


Mass: 6067.081 Da / Num. of mol.: 1 / Fragment: RESIDUES 4-54 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: DH5ALPHA / References: UniProt: B1LF57, UniProt: P68679*PLUS

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RNA chain / Protein , 2 types, 2 molecules AW

#1: RNA chain 16S RRNA


Mass: 496892.375 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: DH5ALPHA / References: GenBank: 54791136
#22: Protein PUTATIVE RIBOSOME BIOGENESIS GTPASE RSGA


Mass: 39233.246 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: DH5ALPHA / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: E3PE32, UniProt: P39286*PLUS, Hydrolases, Acting on acid anhydrides, In phosphorus-containing anhydrides

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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: 30S RIBOSOMAL SUBUNIT WITH RSGA BOUND IN THE PRESENCE OF GMPPNP
Type: RIBOSOME
Buffer solutionpH: 7.6
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: OTHER
VitrificationInstrument: FEI VITROBOT MARK I / Cryogen name: ETHANE

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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 X / Nominal defocus max: 3850 nm / Nominal defocus min: 2000 nm / Cs: 2.7 mm
Image recordingElectron dose: 20 e/Å2 / Film or detector model: FEI EAGLE (4k x 4k)
Radiation wavelengthRelative weight: 1

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Processing

EM softwareName: SPIDER / Category: 3D reconstruction
CTF correctionDetails: MAPS FROM EACH DEFOCUS GROUP
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionMethod: REFERENCE BASED / Resolution: 9.8 Å / Num. of particles: 77483 / Nominal pixel size: 2.9 Å / Actual pixel size: 2.9 Å
Details: SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD -1884. (DEPOSITION ID: 7882).
Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL / Target criteria: Cross-correlation coefficient / Details: METHOD--MDFF REFINEMENT PROTOCOL--X-RAY
Atomic model building
IDPDB-ID3D fitting-ID
13OFA

3ofa
PDB Unreleased entry

1
22RCN1
RefinementHighest resolution: 9.8 Å
Refinement stepCycle: LAST / Highest resolution: 9.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20741 32892 0 0 53633

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