3IYD | pdb_00003iyd

Three-dimensional EM structure of an intact activator-dependent transcription initiation complex

ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1LB2
experimental model	PDB	1BDF
experimental model	PDB	2AUK
experimental model	PDB	1SIG
experimental model	PDB	3DXJ

Sample
E. coli RNA polymerase holoenzyme (sigma70) and E. coli catabolite activator protein (CAP) bound to 98-mer DNA containing the lac promoter and engineered open transcription bubble
Sample Components
Catabolite Activator Protein
lac(ICAP)UP-UV5-bubble
RNA polymerase holoenzyme (sigma70)

Specimen Preparation
Sample Aggregation State	PARTICLE
Staining Type	NEGATIVE
Staining Material	Uranyl Formate
Staining Details

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	14097
Reported Resolution (Å)	19.8
Resolution Method	FSC 0.5 CUT-OFF
Other Details	EMAN interleaved with SPIDER correspondence analysis ( Details about the particle: 32816 particles were automatically selected by the Appion DoGpicker ...	EMAN interleaved with SPIDER correspondence analysis ( Details about the particle: 32816 particles were automatically selected by the Appion DoGpicker initially )
Refinement Type
Symmetry Type	POINT
Point Symmetry	C1

Map-Model Fitting and Refinement
Id	1 (1LB2, 1BDF, 2AUK, 1SIG, 3DXJ)
Refinement Space	REAL
Refinement Protocol	FLEXIBLE FIT
Refinement Target	map-derived potential energy
Overall B Value
Fitting Procedure
Details	REFINEMENT PROTOCOL--rigid body, Yup.scx simulated annealing DETAILS--A complete ternary complex model was generated using multiple PDB entries, with ...	REFINEMENT PROTOCOL--rigid body, Yup.scx simulated annealing DETAILS--A complete ternary complex model was generated using multiple PDB entries, with a homology modelling step for RNAP. The model was regularized with PHENIX and the refined against the EM map with Yup.scx using default parameters.

Data Acquisition
Detector Type	TVIPS TEMCAM-F415 (4k x 4k)
Electron Dose (electrons/Å**2)	16

Imaging Experiment	1
Date of Experiment	2008-11-04
Temperature (Kelvin)	293
Microscope Model	FEI TECNAI F20
Minimum Defocus (nm)	500
Maximum Defocus (nm)	1500
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS	2
Imaging Mode	BRIGHT FIELD
Specimen Holder Model	SIDE ENTRY, EUCENTRIC
Nominal Magnification	50000
Calibrated Magnification
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	120
Imaging Details	15 um pixel size on detector

EM Software
Task	Software Package	Version
MODEL FITTING	MODELLER
MODEL FITTING	UCSF Chimera
MODEL FITTING	Yup.scx
RECONSTRUCTION	EMAN
RECONSTRUCTION	SPIDER

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
	ACE

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.