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- EMDB-1884: RsgA-30S ribosomal subunit-GMPPNP complex -

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Basic information

Entry
Database: EMDB / ID: EMD-1884
TitleRsgA-30S ribosomal subunit-GMPPNP complex
Map dataThis is the map of RsgA-30S-GMPPNP complex
Sample
  • Sample: RsgA-30S ribosome-GMPPNP complex
  • Complex: 30S ribosome
  • Protein or peptide: RsgA
  • Ligand: Guanylyl Imidodiphosphate
Keywordsribosome biogenesis / RsgA / yjeq / circularly permutated GTPase / 30S subunit
Function / homology
Function and homology information


guanosine tetraphosphate binding / ornithine decarboxylase inhibitor activity / transcription antitermination factor activity, RNA binding / misfolded RNA binding / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / Group I intron splicing / RNA folding / four-way junction DNA binding / negative regulation of translational initiation / regulation of mRNA stability ...guanosine tetraphosphate binding / ornithine decarboxylase inhibitor activity / transcription antitermination factor activity, RNA binding / misfolded RNA binding / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / Group I intron splicing / RNA folding / four-way junction DNA binding / negative regulation of translational initiation / regulation of mRNA stability / mRNA regulatory element binding translation repressor activity / positive regulation of RNA splicing / transcription elongation factor complex / regulation of DNA-templated transcription elongation / DNA endonuclease activity / transcription antitermination / DNA-templated transcription termination / maintenance of translational fidelity / mRNA 5'-UTR binding / GDP binding / regulation of translation / ribosome biogenesis / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / cytosolic small ribosomal subunit / small ribosomal subunit rRNA binding / cytoplasmic translation / tRNA binding / negative regulation of translation / rRNA binding / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / response to antibiotic / GTPase activity / mRNA binding / GTP binding / RNA binding / zinc ion binding / metal ion binding / membrane / cytosol / cytoplasm
Similarity search - Function
Ribosome biogenesis GTPase RsgA / RsgA GTPase domain / RsgA GTPase / EngC GTPase domain profile. / Circularly permuted (CP)-type guanine nucleotide-binding (G) domain / Circularly permuted (CP)-type guanine nucleotide-binding (G) domain profile. / Ribosomal protein S21, conserved site / Ribosomal protein S21 signature. / Ribosomal protein S14, bacterial/plastid / Ribosomal protein S21 superfamily ...Ribosome biogenesis GTPase RsgA / RsgA GTPase domain / RsgA GTPase / EngC GTPase domain profile. / Circularly permuted (CP)-type guanine nucleotide-binding (G) domain / Circularly permuted (CP)-type guanine nucleotide-binding (G) domain profile. / Ribosomal protein S21, conserved site / Ribosomal protein S21 signature. / Ribosomal protein S14, bacterial/plastid / Ribosomal protein S21 superfamily / Ribosomal protein S16, conserved site / Ribosomal protein S16 signature. / Ribosomal protein S21 / Ribosomal protein S21 / Ribosomal protein S19, bacterial-type / Ribosomal protein S3, bacterial-type / Ribosomal protein S13, bacterial-type / Ribosomal protein S6, conserved site / Ribosomal protein S6 signature. / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein S9, bacterial/plastid / Ribosomal protein S11, bacterial-type / Ribosomal protein S20 / Ribosomal protein S20 superfamily / Ribosomal protein S20 / Ribosomal protein S4, bacterial-type / 30S ribosomal protein S17 / Ribosomal protein S5, bacterial-type / Ribosomal protein S2, bacteria/mitochondria/plastid / Ribosomal protein S18, conserved site / Ribosomal protein S18 signature. / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein S16 / Ribosomal protein S16 domain superfamily / Ribosomal protein S16 / Ribosomal protein S15, bacterial-type / Ribosomal protein S12, bacterial-type / Ribosomal protein S18 / Ribosomal protein S18 / Ribosomal protein S18 superfamily / K Homology domain / K homology RNA-binding domain / Ribosomal protein S6 / Ribosomal protein S6 / Ribosomal protein S6 superfamily / Ribosomal protein S2 signature 2. / Translation elongation factor EF1B/ribosomal protein S6 / Ribosomal protein S3, conserved site / Ribosomal protein S3 signature. / Ribosomal protein S10, conserved site / Ribosomal protein S10 signature. / Ribosomal protein S14, conserved site / Ribosomal protein S14 signature. / Ribosomal protein S2 signature 1. / KH domain / Type-2 KH domain profile. / K Homology domain, type 2 / Ribosomal protein S3, C-terminal / Ribosomal protein S3, C-terminal domain / Ribosomal protein S3, C-terminal domain superfamily / Ribosomal protein S15/S19, conserved site / Ribosomal protein S19 signature. / Ribosomal protein S10 / Ribosomal protein S19/S15 / Ribosomal protein S19/S15, superfamily / Ribosomal protein S19 / : / Ribosomal protein S5, N-terminal, conserved site / Ribosomal protein S5 signature. / Ribosomal protein S7, conserved site / Ribosomal protein S2, conserved site / Ribosomal protein S7 signature. / Ribosomal protein S2 / Ribosomal protein S2, flavodoxin-like domain superfamily / Ribosomal protein S2 / Ribosomal protein S17, conserved site / Ribosomal protein S17 signature. / K homology domain superfamily, prokaryotic type / Ribosomal protein S5 / Ribosomal protein S13, conserved site / Ribosomal protein S13 signature. / S5 double stranded RNA-binding domain profile. / Ribosomal protein S5, N-terminal / Ribosomal protein S13 / 30s ribosomal protein S13, C-terminal / Ribosomal protein S13/S18 / Ribosomal protein S5, C-terminal / Ribosomal protein S13 family profile. / Ribosomal protein S5, N-terminal domain / Ribosomal protein S5, C-terminal domain / Ribosomal protein S8 signature. / Ribosomal protein S4/S9 N-terminal domain / Ribosomal protein S4, conserved site / Ribosomal protein S15 signature. / Ribosomal protein S4 signature. / Ribosomal protein S4/S9 N-terminal domain / Ribosomal protein S4/S9, N-terminal / Ribosomal protein S14 / Ribosomal protein S14p/S29e / Ribosomal protein S4/S9
Similarity search - Domain/homology
Small ribosomal subunit protein uS4 / Small ribosomal subunit protein uS13 / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein uS10 / Small ribosomal subunit protein bS21 / : / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS19 / Small ribosomal subunit protein bS6 / Small ribosomal subunit protein bS20 ...Small ribosomal subunit protein uS4 / Small ribosomal subunit protein uS13 / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein uS10 / Small ribosomal subunit protein bS21 / : / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS19 / Small ribosomal subunit protein bS6 / Small ribosomal subunit protein bS20 / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein bS16 / Small ribosomal subunit protein uS2 / 30S ribosomal protein S5 / Small ribosomal subunit biogenesis GTPase RsgA / 30S ribosomal protein S18 / 30S ribosomal protein S7 / Small ribosomal subunit protein bS6 / Small ribosomal subunit protein uS7 / Small ribosomal subunit protein uS10 / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein uS13 / Small ribosomal subunit protein bS16 / Small ribosomal subunit protein bS18 / Small ribosomal subunit protein uS19 / Small ribosomal subunit protein bS20 / Small ribosomal subunit protein uS2 / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein uS5 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS9 / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS17 / Small ribosomal subunit protein uS17 / Small ribosomal subunit biogenesis GTPase RsgA / Small ribosomal subunit protein bS21 / Small ribosomal subunit protein uS9
Similarity search - Component
Biological speciesEscherichia coli DH5[alpha] (bacteria) / Escherichia coli (E. coli) / unidentified (others)
Methodsingle 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.
History
DepositionFeb 24, 2011-
Header (metadata) releaseNov 17, 2011-
Map releaseNov 17, 2011-
UpdateMar 13, 2013-
Current statusMar 13, 2013Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 3.16
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 3.16
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-2ykr
  • Surface level: 3.16
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd-1884.jpeg

Downloads & links

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Map

FileDownload / File: emd_1884.map.gz / Format: CCP4 / Size: 7.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThis is the map of RsgA-30S-GMPPNP complex
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.9 Å/pix.
x 125 pix.
= 362.5 Å		2.9 Å/pix.
x 125 pix.
= 362.5 Å		2.9 Å/pix.
x 125 pix.
= 362.5 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.9 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 3.16 / Movie #1: 3.16
Minimum - Maximum-6.45114 - 19.771000000000001
Average (Standard dev.)0.106065 (±1.37118)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-62-62-62
Dimensions125125125
Spacing125125125
CellA=B=C: 362.5 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.92.92.9
M x/y/z125125125
origin x/y/z-0.000-0.000-0.000
length x/y/z362.500362.500362.500
α/β/γ90.00090.00090.000
start NX/NY/NZ-56-56-55
NX/NY/NZ112112112
MAP C/R/S123
start NC/NR/NS-62-62-62
NC/NR/NS125125125
D min/max/mean-6.45119.7710.106

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Supplemental data

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Sample components

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Entire : RsgA-30S ribosome-GMPPNP complex

EntireName: RsgA-30S ribosome-GMPPNP complex
Components
  • Sample: RsgA-30S ribosome-GMPPNP complex
  • Complex: 30S ribosome
  • Protein or peptide: RsgA
  • Ligand: Guanylyl Imidodiphosphate

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Supramolecule #1000: RsgA-30S ribosome-GMPPNP complex

SupramoleculeName: RsgA-30S ribosome-GMPPNP complex / type: sample / ID: 1000
Oligomeric state: One RsgA binds to one 30S ribosome in the presence of one GMPPNP
Number unique components: 3
Molecular weightExperimental: 800 KDa / Theoretical: 800 KDa / Method: Sedimentation

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Supramolecule #1: 30S ribosome

SupramoleculeName: 30S ribosome / type: complex / ID: 1 / Name.synonym: 30S ribosome / Recombinant expression: No / Ribosome-details: ribosome-prokaryote: SSU 30S
Source (natural)Organism: Escherichia coli DH5[alpha] (bacteria)

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Macromolecule #1: RsgA

MacromoleculeName: RsgA / type: protein_or_peptide / ID: 1 / Name.synonym: RsgA / Oligomeric state: monomer / Recombinant expression: Yes
Source (natural)Organism: Escherichia coli (E. coli) / Strain: DH5a / Organelle: cellular
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria) / Recombinant plasmid: pET28b

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Macromolecule #2: Guanylyl Imidodiphosphate

MacromoleculeName: Guanylyl Imidodiphosphate / type: ligand / ID: 2 / Name.synonym: GMP-PNP / Recombinant expression: No
Source (natural)Organism: unidentified (others)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.6 / Details: 20 mM Tris-HCl,150 mM NH4Cl,10 mM Mg(OAc)2
GridDetails: 300 mesh Quantifoil
VitrificationCryogen name: ETHANE / Chamber temperature: 4 K / Instrument: OTHER
Details: Vitrification instrument: FEI Vitrobot. Rapid-freezing in liquid ethane

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingCategory: CCD / Film or detector model: FEI EAGLE (4k x 4k) / Average electron dose: 20 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.85 µm / Nominal defocus min: 2.0 µm / Nominal magnification: 59000
Sample stageSpecimen holder: Eucentric / Specimen holder model: OTHER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionDetails: Maps from each defocus group
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 9.8 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: SPIDER
Details: The final map is processed with an additional amplitude correction procedure.
Number images used: 77483

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