1X1L

Interaction of ERA,a GTPase protein, with the 3'minor domain of the 16S rRNA within the THERMUS THERMOPHILUS 30S subunit.


ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1FJF 
experimental modelPDB 1EGA 
Sample
THERMUS THERMOPHILUS 30S ribosomal subunit complexed with Era
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification Instrument
Cryogen Name
Sample Vitrification DetailsRapid-freezing in liquid ethane
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles
Reported Resolution (Å)13.5
Resolution Method
Other Detailsprojection matching using spider package. The coordinates for only the alpha carbons in protein and phosphoruses in rRNA are present in the structure ...projection matching using spider package. The coordinates for only the alpha carbons in protein and phosphoruses in rRNA are present in the structure. The number of missing atoms was so much that remark 470 for the missing atoms list were removed.
Refinement Type
Symmetry TypePOINT
Point SymmetryC1
Map-Model Fitting and Refinement
Id1 (1FJF, 1EGA)
Refinement SpaceREAL
Refinement ProtocolRIGID BODY FIT
Refinement TargetX-ray coordinates of the 30S ribosomal subunit and ERA were fitted into the 13.5 angstroms resolution CRYO-EM map of the T. Thermophilus 30S subunit-ERA complex. the atomic structure of ERA was fitted as 3 rigid bodies, N-terminal domain, C-terminal domain and C-terminal helix within the C-terminal domain. The resultant ERA structure was then energy minimized. The X-ray coordinates of T. Thermophilus 30S subunit was fitted as 4 rigid bodies, head, body, platform and 16S rRNA 3' minor domains. Only the coordinates of the 16S rRNA 3' minor domain and ERA are included HERE. The KH domain of ERA makes direct contact with the 3' terminus of the 16S rRNA.
Overall B Value
Fitting Procedure
DetailsMETHOD--cross-correlation based manual fitting in O REFINEMENT PROTOCOL--MULTIPLE RIGID BODY
Data Acquisition
Detector TypeKODAK SO-163 FILM
Electron Dose (electrons/Å**2)20
Imaging Experiment1
Date of Experiment2003-03-25
Temperature (Kelvin)93
Microscope ModelFEI TECNAI F20
Minimum Defocus (nm)1180
Maximum Defocus (nm)3940
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS2
Imaging ModeBRIGHT FIELD
Specimen Holder Model
Nominal Magnification50000
Calibrated Magnification49696
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)200
Imaging Details
EM Software
TaskSoftware PackageVersion
MODEL FITTINGO
RECONSTRUCTIONSPIDER
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
CTF correction of 3D-maps by wiener filtration