3J5S | pdb_00003j5s

EttA binds to ribosome exit site and regulates translation by restricting ribosome and tRNA dynamics


ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3R8O 
experimental modelPDB 3R8T 
experimental modelPDB 2WDG 
experimental modelPDB 4FIN 
Sample
E. coli 70S ribosome complex 70S-(EttA-EQ2)-(fMet-tRNA)-(Phe-tRNA)
Sample Components
70S ribosome
Energy-dependent Translational Throttle A (EttA)
fMet-tRNA
Phe-tRNA
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification InstrumentFEI VITROBOT MARK IV
Cryogen NameETHANE
Sample Vitrification DetailsWait time 30 sec, blot time 8 sec (4 C), plunge into liquid ethane (FEI VITROBOT MARK IV)
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles39316
Reported Resolution (Å)7.5
Resolution MethodFSC 0.143 CUT-OFF
Other DetailsSubset after RELION 3D classification
Refinement TypeHALF-MAPS REFINED INDEPENDENTLY
Symmetry TypePOINT
Point SymmetryC1
Map-Model Fitting and Refinement
IdRefinement SpaceRefinement ProtocolRefinement TargetOverall B ValueFitting ProcedureDetails
1 (3R8O)REALFLEXIBLE FITCross-correlation coefficientREFINEMENT PROTOCOL--FLEXIBLE DETAILS--Protocol- M ...REFINEMENT PROTOCOL--FLEXIBLE DETAILS--Protocol- Molecular dynamics flexible fitting
2 (3R8T)REALFLEXIBLE FITCross-correlation coefficientREFINEMENT PROTOCOL--FLEXIBLE DETAILS--Protocol- M ...REFINEMENT PROTOCOL--FLEXIBLE DETAILS--Protocol- Molecular dynamics flexible fitting
3 (2WDG, 2WDG)REALFLEXIBLE FITCross-correlation coefficientREFINEMENT PROTOCOL--FLEXIBLE DETAILS--Protocol- M ...REFINEMENT PROTOCOL--FLEXIBLE DETAILS--Protocol- Molecular dynamics flexible fitting
4 (4FIN)REALFLEXIBLE FITCross-correlation coefficientREFINEMENT PROTOCOL--FLEXIBLE DETAILS--Matched the ...REFINEMENT PROTOCOL--FLEXIBLE DETAILS--Matched the apo-EttA model (derived from PDB ENTRY 4FIN) to CFTR NBD1 (PDB ENTRY 2PZE) to model the ATP-bound form of EttA. Protocol- Molecular dynamics flexible fitting
Data Acquisition
Detector TypeGATAN ULTRASCAN 4000 (4k x 4k)
Electron Dose (electrons/Å**2)17
Imaging Experiment1
Date of Experiment2013-04-05
Temperature (Kelvin)80
Microscope ModelFEI TECNAI F20
Minimum Defocus (nm)1200
Maximum Defocus (nm)2500
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS2
Imaging ModeBRIGHT FIELD
Specimen Holder ModelGATAN LIQUID NITROGEN
Nominal Magnification80000
Calibrated Magnification110637
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)200
Imaging Details
EM Software
TaskSoftware PackageVersion
MODEL FITTINGNAMD
RECONSTRUCTIONRELION
RECONSTRUCTIONSPIDER
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
Each micrograph