2YBB | pdb_00002ybb

Fitted model for bovine mitochondrial supercomplex I1III2IV1 by single particle cryo-EM (EMD-1876)

ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3IAM
experimental model	PDB	3M9C
experimental model	PDB	1PP9
experimental model	PDB	1BGY
experimental model	PDB	1OCC
experimental model	PDB	2B4Z

Sample
RESPIRATORY SUPERCOMPLEX B (I1III2IV1) COMPOSED OF COMPLEX I, DIMERIC COMPLEX III AND COMPLEX IV FROM BOVINE HEART MITOCHONDRIA

Specimen Preparation
Sample Aggregation State	PARTICLE
Vitrification Instrument	HOMEMADE PLUNGER
Cryogen Name	ETHANE
Sample Vitrification Details	VITRIFICATION 1 -- CRYOGEN- ETHANE, HUMIDITY- 70, TEMPERATURE- 95, INSTRUMENT- CUSTOM-MADE HAND PLUNGER, METHOD- ONE- SIDED BLOTTING FOR 26 - 30 SECON ...	VITRIFICATION 1 -- CRYOGEN- ETHANE, HUMIDITY- 70, TEMPERATURE- 95, INSTRUMENT- CUSTOM-MADE HAND PLUNGER, METHOD- ONE- SIDED BLOTTING FOR 26 - 30 SECONDS BEFORE PLUNGING, DETAILS- SAMPLE WAS ADSORBED TO CARBON FILM FOR 30 SECONDS BEFORE BLOTTING

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	10684
Reported Resolution (Å)	19
Resolution Method
Other Details	FINAL MAP WAS CALCULATED WITH SIRT FROM COMBINED TILTED AND UNTILTED DATASETS WITH 10684 PARTICLES EACH AND OMITTING 30 PER CENT OF IMAGES WITH LOWEST ...	FINAL MAP WAS CALCULATED WITH SIRT FROM COMBINED TILTED AND UNTILTED DATASETS WITH 10684 PARTICLES EACH AND OMITTING 30 PER CENT OF IMAGES WITH LOWEST CROSS CORRELATION. THIS ENTRY IS BASED ON PDBS 3IAM,3M9C,1PP9,1BGY,1OCC AND 2B4Z WHICH WERE FITTED MANUALLY INTO THE EM DENSITY MAP OF BOVINE SUPERCOMPLEX I1III2IV1. THE POSITION OF 2B4Z WAS INFERRED FROM PDB 3CX5. THE CHAIN NAMES ARE CASE SENSITIVE. CHAINS A-K AND a-k DENOTE IDENTICAL CHAINS WITHIN A DIMER. CHAINS L-X AND M-P BELONG TO DIFFERENT PROTEINS. SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-1876.
Refinement Type
Symmetry Type	POINT
Point Symmetry	C1

Map-Model Fitting and Refinement
Id	1 (3IAM, 3M9C, 1PP9, 1BGY, 1OCC, 2B4Z)
Refinement Space	REAL
Refinement Protocol	RIGID BODY FIT
Refinement Target
Overall B Value
Fitting Procedure
Details	METHOD--RIGID BODY REFINEMENT PROTOCOL--X-RAY

Data Acquisition
Detector Type	KODAK SO-163 FILM
Electron Dose (electrons/Å**2)	25

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)	78
Microscope Model	FEI TECNAI F30
Minimum Defocus (nm)	500
Maximum Defocus (nm)	6000
Minimum Tilt Angle (degrees)	-50
Maximum Tilt Angle (degrees)
Nominal CS	2
Imaging Mode	BRIGHT FIELD
Specimen Holder Model
Nominal Magnification	59000
Calibrated Magnification	58829
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	200
Imaging Details	LOW DOSE CONDITIONS. FOR RANDOM CONICAL TILT EACH AREA WAS IMAGED TWICE WITH THE FIRST IMAGE TAKEN AT A TILT ANGLE OF -45 OR -50 DEGREE

EM Software
Task	Software Package	Version
MODEL FITTING	UCSF Chimera
RECONSTRUCTION	IMAGIC
RECONSTRUCTION	SPIDER

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
	PHASE-FLIPPPING ON EACH PARTICLE

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.