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- EMDB-8627: Structure of the 30S subunit, subclass I -

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Basic information

Entry
Database: EMDB / ID: 8627
TitleStructure of the 30S subunit, subclass I
Map data
Sample30S Consensus subunit, subclass I:
Function / homologyRibosomal protein S14, bacterial/plastid / Ribosomal protein S14, conserved site / Ribosomal protein S19 conserved site / Ribosomal protein S6, conserved site / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein S7, conserved site / Ribosomal protein S16, conserved site / Ribosomal protein S9, conserved site / Ribosomal protein S5 domain 2-type fold / 30S ribosomal protein S17 ...Ribosomal protein S14, bacterial/plastid / Ribosomal protein S14, conserved site / Ribosomal protein S19 conserved site / Ribosomal protein S6, conserved site / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein S7, conserved site / Ribosomal protein S16, conserved site / Ribosomal protein S9, 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 S18, conserved site / Ribosomal protein S13, conserved site / Ribosomal protein S9, bacterial/plastid / Ribosomal protein S10, conserved site / Ribosomal protein S5, N-terminal, conserved site / Ribosomal protein S2, conserved site / Ribosomal S11, conserved site / Ribosomal protein S4, 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 / Ribosomal protein S4/S9 / Ribosomal protein S16 / Ribosomal protein S12/S23 / RNA-binding S4 domain superfamily / Ribosomal protein S8 / Ribosomal protein S9/S16 / Ribosomal protein S17 / Ribosomal protein S10p/S20e / Ribosomal protein S5, N-terminal domain / Ribosomal protein S2 / 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 S11 superfamily / Ribosomal protein S19, superfamily / Ribosomal protein S18 superfamily / Ribosomal protein S10 domain superfamily / Ribosomal protein S7 domain superfamily / Ribosomal protein S20 superfamily / Ribosomal protein S3, C-terminal domain superfamily / Ribosomal protein S8 superfamily / 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 S2, flavodoxin-like domain superfamily / K homology domain superfamily, prokaryotic type / Ribosomal protein S19, bacterial-type / Ribosomal protein S13/S18 / Ribosomal protein S14 signature. / 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. / S4 domain / 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 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. / Ribosomal protein S20 / Ribosomal protein S6 / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein S11 / Ribosomal protein S5, bacterial-type
Function and homology information
SourceEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / 6.5 Å resolution
AuthorsRazi A / Guarne A / Ortega J
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: The cryo-EM structure of YjeQ bound to the 30S subunit suggests a fidelity checkpoint function for this protein in ribosome assembly.
Authors: Aida Razi / Alba Guarné / Joaquin Ortega
DateDeposition: Feb 27, 2017 / Header (metadata) release: Mar 15, 2017 / Map release: Apr 19, 2017 / Last update: Jul 18, 2018

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0197
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.0197
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_8627.map.gz (map file in CCP4 format, 42593 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
220 pix
1.45 Å/pix.
= 319. Å
220 pix
1.45 Å/pix.
= 319. Å
220 pix
1.45 Å/pix.
= 319. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.45 Å
Density
Contour Level:0.0197 (by author), 0.0197 (movie #1):
Minimum - Maximum-0.028605198 - 0.096635744
Average (Standard dev.)0.0010826479 (0.00562188)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions220220220
Origin0.0.0.
Limit219.219.219.
Spacing220220220
CellA=B=C: 319.0 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.451.451.45
M x/y/z220220220
origin x/y/z0.0000.0000.000
length x/y/z319.000319.000319.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-152-37
NX/NY/NZ998271
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS220220220
D min/max/mean-0.0290.0970.001

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Supplemental data

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Sample components

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Entire 30S Consensus subunit, subclass I

EntireName: 30S Consensus subunit, subclass I / Number of components: 1

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Component #1: protein, 30S Consensus subunit, subclass I

ProteinName: 30S Consensus subunit, subclass I / Recombinant expression: No
SourceSpecies: Escherichia coli (E. coli)

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionBuffer solution: 10 mM Tris-HCl at pH 7.5, 10 mM magnesium acetate, 150 mM NH4Cl, 3mM 2-mercaptoethanol and 2 mM GMP-PNP
pH: 7.5
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Temperature: 298 K / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
ImagingMicroscope: FEI TECNAI F20
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 2 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 25000. X (nominal), 34482. X (calibrated) / Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 500.0 - 3000.0 nm
Specimen HolderModel: GATAN LIQUID NITROGEN
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 78440
3D reconstructionResolution: 6.5 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot
(resolution estimation)

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Atomic model buiding

Modeling #1Refinement protocol: rigid body

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