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- EMDB-1895: Cryo-electron Microscopy Structure of the 30S Subunit in Complex ... -

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Basic information

Entry
Database: EMDB / ID: 1895
TitleCryo-electron Microscopy Structure of the 30S Subunit in Complex with the YjeQ Biogenesis Factor
KeywordsRibosome assembly / 30S subunit / YjeQ protein / RsgA protein / GTPase
SampleEscherichia coli 30S ribosomal subunit in complex with the YjeQ protein
SourceEscherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
Map dataYjeQ in complex with the 30S ribosomal subunit
Methodsingle particle reconstruction, at 16.5 A resolution
AuthorsJomaa A / Stewart G / Mears JA / Kireeva I / Brown ED / Ortega J
CitationRNA, 2011, 17, 2026-2038

RNA, 2011, 17, 2026-2038 StrPapers
Cryo-electron microscopy structure of the 30S subunit in complex with the YjeQ biogenesis factor.
Ahmad Jomaa / Geordie Stewart / Jason A Mears / Inga Kireeva / Eric D Brown / Joaquin Ortega

DateDeposition: Apr 18, 2011 / Header (metadata) release: May 27, 2011 / Map release: Oct 28, 2011 / Last update: Apr 18, 2011

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0088
  • Imaged by UCSF CHIMERA
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  • Surface view colored by height
  • Surface level: 0.0088
  • Imaged by UCSF CHIMERA
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  • Surface view with fitted model
  • Atomic models: : PDB-4a2i
  • Surface level: 0.0088
  • Imaged by UCSF CHIMERA
  • Download
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Supplemental images

Downloads & links

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Map

Fileemd_1895.map.gz (map file in CCP4 format, 8193 KB)
Projections & slicesSize of images:
AxesZ (Sec.)Y (Row.)X (Col.)
128 pix
2.54 A/pix
= 325.12 A
128 pix
2.54 A/pix
= 325.12 A
128 pix
2.54 A/pix
= 325.12 A

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 2.54 A
Density
Contour Level:0.0088 (by author), 0.0088 (movie #1):
Minimum - Maximum-0.0217409 - 0.0623605
Average (Standard dev.)0.000295723 (0.00440148)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions128128128
Origin000
Limit127127127
Spacing128128128
CellA=B=C: 325.12 A
Alpha=beta=gamma: 90 deg.

CCP4 map header:

modeImage stored as Reals
A/pix X/Y/Z2.542.542.54
M x/y/z128128128
origin x/y/z0.0000.0000.000
length x/y/z325.120325.120325.120
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ-56-56-55
NX/NY/NZ112112112
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS128128128
D min/max/mean-0.0220.0620.000

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Supplemental data

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Sample components

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Entire Escherichia coli 30S ribosomal subunit in complex with the YjeQ p...

EntireName: Escherichia coli 30S ribosomal subunit in complex with the YjeQ protein
Details: 30S was mixed with YjeQ in 1-to-5 molar ratio / Number of components: 2
MassTheoretical: 900 kDa

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Component #1: ribosome-prokaryote, 30S ribosomal subunit

Ribosome-prokaryoteName: 30S ribosomal subunit / a.k.a: 30S subunit / Prokaryote: SSU 30S / Recombinant expression: No
MassTheoretical: 900 kDa
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

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Component #2: protein, RsgA, YjeQ

ProteinName: RsgA, YjeQ / a.k.a: Assembly factor / Oligomeric Details: Monomer / Recombinant expression: Yes
MassExperimental: 39 kDa
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
Strain: BW25113
Source (engineered)Expression System: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
Vector: pDEST17-YjeQ
Source (natural)Cell: Cytoplasm

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Experimental details

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Sample preparation

Specimen stateparticle
Sample solutionSpecimen conc.: 0.9 mg/ml
Buffer solution: 10 mM Tris-HCl pH 7.5, 10 mM magnesium acetate, 60 mM NH4Cl, 3 mM 2-mercaptoethanol.
pH: 7.5
Support film200 mesh copper grid
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Temperature: 100 K / Humidity: 100 % / Method: Blot for 7 seconds / Details: Vitrification instrument: FEI Vitrobot III

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Electron microscopy imaging

ImagingMicroscope: JEOL 2010F / Date: May 12, 2010
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 15 e/A2 / Illumination mode: FLOOD BEAM
LensMagnification: 50000 X (nominal), 50000 X (calibrated) / Astigmatism: Corrected at 200000 times magnification / Cs: 1 mm / Imaging mode: BRIGHT FIELD / Defocus: 650 - 3900 nm
Specimen HolderHolder: Side entry liquid nitrogen-cooled cryo specimen holder.This holder operates in the temperature range from -175 C to ambient
Model: GATAN LIQUID NITROGEN / Temperature: 100 K
CameraDetector: KODAK SO-163 FILM

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Image acquisition

Image acquisitionNumber of digital images: 150 / Scanner: NIKON SUPER COOLSCAN 9000 / Sampling size: 2.54 microns / Bit depth: 8

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 16228 / Details: Particles were picked with Boxer. / Applied symmetry: C1 (asymmetric)
3D reconstructionAlgorithm: Projection matching / Software: Xmipp / CTF correction: Each micrograph / Resolution: 16.5 A / Resolution method: FSC 0.5

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Atomic model buiding

Modeling #1Software: Chimera / Refinement protocol: rigid body / Target criteria: R-factor / Refinement space: REAL
Details: Protocol: Rigid Body. Each domain of YjeQ was fitted separately
Input PDB model: 2AVY
Modeling #2Software: Chimera / Refinement protocol: rigid body / Target criteria: R-factor / Refinement space: REAL
Details: Protocol: Rigid Body. Each domain of YjeQ was fitted separately
Input PDB model: 2RCN
Output model

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