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

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Basic information

Database: EMDB / ID: 1884
TitleRsgA-30S ribosomal subunit-GMPPNP complex
Keywordsribosome biogenesis / RsgA / yjeq / circularly permutated GTPase / 30S subunit
SampleRsgA-30S ribosome-GMPPNP complex
SourceEscherichia coli dh5[alpha] / bacteria / image: Escherichia coli
Escherichia coli / bacteria / /
Map dataThis is the map of RsgA-30S-GMPPNP complex
Methodsingle particle reconstruction, at 9.8 Å resolution
AuthorsGuo Q / Yuan Y / Xu Y / Feng B / Liu L / Chen K / Lei J / Gao N
CitationProc. Natl. Acad. Sci. U.S.A., 2011, 108, 13100-13105

Proc. Natl. Acad. Sci. U.S.A., 2011, 108, 13100-13105 Yorodumi Papers
Structural basis for the function of a small GTPase RsgA on the 30S ribosomal subunit maturation revealed by cryoelectron microscopy.
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

Structure visualization

  • 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
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  • Surface view with fitted model
  • Atomic models: : PDB-2ykr
  • Surface level: 3.16
  • Imaged by UCSF CHIMERA
  • Download
3D viewer
Supplemental images

Downloads & links


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

Image control

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



Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 2.9 Å
Contour Level:3.16 (by author), 3.16 (movie #1):
Minimum - Maximum-6.45114 - 19.771
Average (Standard dev.)0.106065 (1.37118)


Space Group Number1
Map Geometry
Axis orderXYZ
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
start NX/NY/NZ-56-56-55
MAP C/R/S123
start NC/NR/NS-62-62-62
D min/max/mean-6.45119.7710.106

Supplemental data

Sample components

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

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 / image: Escherichia coli

Component #2: protein, RsgA

ProteinName: RsgA / a.k.a: RsgA / Oligomeric Details: monomer / Recombinant expression: Yes
SourceSpecies: Escherichia coli / bacteria / / / Strain: DH5a
Source (engineered)Expression System: Escherichia coli bl21 / bacteria / image: Escherichia coli
Vector: pET28b
Source (natural)Organelle: cellular

Component #3: ligand, Guanylyl Imidodiphosphate

LigandName: Guanylyl Imidodiphosphate / a.k.a: GMP-PNP / Recombinant expression: No
SourceSpecies: Unidentified

Experimental details

Sample preparation

Specimen stateparticle
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

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)

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

Atomic model buiding

Output model

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