1Z7Z | pdb_00001z7z

Cryo-em structure of human coxsackievirus A21 complexed with five domain icam-1kilifi

ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1IAM
experimental model	PDB	1Z7S

Sample
COXSACKIEVIRUS A21/ICAM- 1KILIFI COMPLEX
Sample Components
HUMAN COXSACKIEVIRUS A21 VP1 1073-1286
human coxsackievirus A21 VP2 2010-2272
human coxsackievirus A21 VP3 3043-3234
human coxsackievirus A21 VP1 1287-1298
human coxsackievirus A21 VP3 3035-3239
ICAM-1KILIFI

Specimen Preparation
Sample Aggregation State	PARTICLE
Vitrification Instrument	REICHERT-JUNG PLUNGER
Cryogen Name	ETHANE
Sample Vitrification Details	PLUNGED INTO ETHANE AT LIQUID NITROGEN TEMPERATURE

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	4704
Reported Resolution (Å)	8
Resolution Method
Other Details	A B-FACTOR OF 589.46 WAS SET FOR ALL THE ATOMS BASED ON THE EQUATION OF -4LN(0.1RESOLUTION2) TO MIMIC A 8 ANGSTROM RESOLUTION CRYOEM STRUCTURE. OCCU ...	A B-FACTOR OF 589.46 WAS SET FOR ALL THE ATOMS BASED ON THE EQUATION OF -4LN(0.1RESOLUTION2) TO MIMIC A 8 ANGSTROM RESOLUTION CRYOEM STRUCTURE. OCCUPANCY OF 1.0 WAS SET FOR ALL ATOMS OF THE VIRAL CAPSID. OCCUPANCY OF 0.80, 0.56, 0.24, 0.16, AND 0.08 WAS SET FOR ATOMS OF ICAM-1 DOMAIN 1, 2, 3, 4, AND 5, RESPECTIVELY, BASED ON THE FITTING RESULTS. SEE DETAILS IN THE CITATION.
Refinement Type
Symmetry Type	POINT
Point Symmetry	I

Map-Model Fitting and Refinement
Id	1 (1IAM, 1Z7S)
Refinement Space	REAL
Refinement Protocol	RIGID BODY FIT
Refinement Target	BEST SUMF VALUE FIT USING THE PROGRAM EMFIT
Overall B Value
Fitting Procedure
Details	REFINEMENT PROTOCOL--RIGID BODY

Data Acquisition
Detector Type	KODAK SO-163 FILM
Electron Dose (electrons/Å**2)	26

Imaging Experiment	1
Date of Experiment	2001-03-15
Temperature (Kelvin)	100
Microscope Model	FEI/PHILIPS CM300FEG/T
Minimum Defocus (nm)	700
Maximum Defocus (nm)	3000
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS	2
Imaging Mode	BRIGHT FIELD
Specimen Holder Model
Nominal Magnification	45000
Calibrated Magnification	47000
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	300
Imaging Details	SAMPLES WERE MAINTAINED AT LIQUID NITROGEN TEMPERATURES IN THE ELECTRON MICROSCOPE.

EM Software
Task	Software Package	Version
MODEL FITTING	EMfit
RECONSTRUCTION	EM3DR
RECONSTRUCTION	PFT

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
	REVERSED CTF WITH WEINER FACTOR FOR 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.