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

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Entry
Database: EMDB / ID: 1884
TitleRsgA-30S ribosomal subunit-GMPPNP complex
Map dataThis is the map of RsgA-30S-GMPPNP complex
SampleRsgA-30S ribosome-GMPPNP complex:
ribosome-prokaryote / RsgA / ligand
Keywordsribosome biogenesis / RsgA / yjeq / circularly permutated GTPase / 30S subunit
Function / homologyRibosomal protein S2, flavodoxin-like domain superfamily / Ribosomal S11, 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 S3, conserved site / Ribosomal protein S21, conserved site / Ribosomal protein S18, conserved site ...Ribosomal protein S2, flavodoxin-like domain superfamily / Ribosomal S11, 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 S3, conserved site / Ribosomal protein S21, 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 protein S4, conserved site / Ribosomal protein S16, 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 / Nucleic acid-binding, OB-fold / Ribosomal protein S13-like, H2TH / RsgA GTPase domain / S15/NS1, RNA-binding / 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 S9, conserved site / Ribosomal protein S7, conserved site / Ribosomal protein S3, bacterial / Ribosomal protein S3, C-terminal domain superfamily / Ribosomal protein S15 / Ribosomal protein S14p/S29e / Ribosomal protein S19 / Ribosomal protein S3, C-terminal domain / Ribosomal protein S7p/S5e / Ribosomal protein S12/S23 / Ribosomal protein S4/S9 N-terminal domain / Ribosomal protein S21 superfamily / RNA-binding S4 domain superfamily / Ribosomal protein S11 superfamily / Ribosomal protein S18 superfamily / Ribosomal protein S10 domain superfamily / Ribosomal protein S7 domain superfamily / Ribosomal protein S20 superfamily / Ribosomal protein S8 superfamily / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein S6 superfamily / Circularly permuted (CP)-type guanine nucleotide-binding (G) domain / Ribosomal protein S10 domain / 30s ribosomal protein S13, C-terminal / P-loop containing nucleoside triphosphate hydrolase / Ribosomal protein S16 domain superfamily / Ribosomal protein S7 domain / Ribosomal protein S10p/S20e / 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 S2, bacteria/mitochondria/plastid / Ribosomal protein S12, bacterial-type / Ribosomal protein S5, N-terminal domain / Ribosomal protein S14 signature. / Ribosomal protein S20 / RsgA GTPase / Ribosomal protein S5, C-terminal domain / KH domain / Ribosomal protein S7 signature. / Ribosomal protein S8 signature. / Ribosomal protein S11 signature. / Ribosomal protein S12 signature. / Ribosomal protein S17 signature. / Ribosomal protein S18 signature. / Ribosomal protein S19 signature. / Ribosomal protein S9 signature. / Ribosomal protein S10 signature. / Ribosomal protein S15 signature. / Ribosomal protein S3 signature. / Ribosomal protein S6 / Ribosomal protein S5 signature. / Ribosomal protein S4 signature. / Ribosomal protein S13 signature. / Ribosomal protein S16 signature. / Ribosomal protein S2 signature 1. / Ribosomal protein S2 signature 2. / Ribosomal protein S6 signature. / Ribosomal protein S21 signature. / Ribosomal protein S13 family profile. / Type-2 KH domain profile. / S5 double stranded RNA-binding domain profile. / S4 RNA-binding domain profile. / EngC GTPase domain profile. / Circularly permuted (CP)-type guanine nucleotide-binding (G) domain profile. / S4 domain
Function and homology information
SourceEscherichia coli DH5[alpha] (bacteria) / Escherichia coli (E. coli) / unidentified (others)
Methodsingle particle reconstruction / cryo EM / 9.8 Å resolution
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
Validation ReportPDB-ID: 2ykr

SummaryFull reportAbout validation report
DateDeposition: Feb 24, 2011 / Header (metadata) release: Nov 17, 2011 / Map release: Nov 17, 2011 / Last update: Mar 13, 2013

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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
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_1884.map.gz (map file in CCP4 format, 7631 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
125 pix
2.9 Å/pix.
= 362.5 Å
125 pix
2.9 Å/pix.
= 362.5 Å
125 pix
2.9 Å/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
Contour Level:3.16 (by author), 3.16 (movie #1):
Minimum - Maximum-6.45114 - 19.771
Average (Standard dev.)0.106065 (1.37118)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions125125125
Origin-62-62-62
Limit626262
Spacing125125125
CellA=B=C: 362.5 Å
α=β=γ: 90 deg.

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 / Number of components: 3
Oligomeric State: One RsgA binds to one 30S ribosome in the presence of one GMPPNP
MassTheoretical: 800 kDa / Experimental: 800 kDa / Measured by: Sedimentation

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Component #1: ribosome-prokaryote, 30S ribosome

Ribosome-prokaryoteName: 30S ribosome / a.k.a: 30S ribosome / Prokaryote: SSU 30S / Recombinant expression: No
SourceSpecies: Escherichia coli DH5[alpha] (bacteria)

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Component #2: protein, RsgA

ProteinName: RsgA / a.k.a: RsgA / Oligomeric Details: monomer / Recombinant expression: Yes
SourceSpecies: Escherichia coli (E. coli) / Strain: DH5a
Source (engineered)Expression System: Escherichia coli BL21 (bacteria) / Vector: pET28b
Source (natural)Organelle: cellular

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Component #3: ligand, Guanylyl Imidodiphosphate

LigandName: Guanylyl Imidodiphosphate / a.k.a: GMP-PNP / Recombinant expression: No
SourceSpecies: unidentified (others)

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionBuffer solution: 20 mM Tris-HCl,150 mM NH4Cl,10 mM Mg(OAc)2 / pH: 7.6
Support film300 mesh Quantifoil
VitrificationInstrument: FEI VITROBOT / Cryogen name: ETHANE / Temperature: 4 K
Details: Vitrification instrument: FEI Vitrobot. Rapid-freezing in liquid ethane

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 20 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 59000 X (nominal) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 2000 - 3850 nm
Specimen HolderHolder: Eucentric / Model: OTHER
CameraDetector: FEI EAGLE (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 77483 / Applied symmetry: C1 (asymmetric)
3D reconstructionAlgorithm: Reference based / Software: SPIDER / CTF correction: Maps from each defocus group
Details: The final map is processed with an additional amplitude correction procedure.
Resolution: 9.8 Å / Resolution method: FSC 0.5

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Atomic model buiding

Output model

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