3J34

Structure of HIV-1 Capsid Protein by Cryo-EM

ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3H47
experimental model	PDB	2KOD

Sample
HIV-1 capsid protein

Specimen Preparation
Sample Aggregation State	HELICAL ARRAY
Vitrification Instrument	HOMEMADE PLUNGER
Cryogen Name	ETHANE
Sample Vitrification Details	With 2.5 uL sample on carbon side, add 3 uL dilution buffer (100 mM NaCl, 50 mM Tris, pH 8.0) to back side. Blot 3-5 seconds from back side and plunge ...	With 2.5 uL sample on carbon side, add 3 uL dilution buffer (100 mM NaCl, 50 mM Tris, pH 8.0) to back side. Blot 3-5 seconds from back side and plunge into liquid ethane with a homemade plunger.

3D Reconstruction
Reconstruction Method	HELICAL
Number of Particles	3210
Reported Resolution (Å)	8.6
Resolution Method	FSC 0.5 CUT-OFF
Other Details	(Helical Details: The segments were aligned and reconstructed using Frealign. Twofold symmetry was imposed using IHRSR++.)
Refinement Type
Symmetry Type	HELICAL
Axial Symmetry	C1
Axial Rise	7.247
Angular Rotation	31.13

Map-Model Fitting and Refinement
Id	1 (3H47)	2 (2KOD)
Refinement Space	REAL	REAL
Refinement Protocol	FLEXIBLE FIT	FLEXIBLE FIT
Refinement Target
Overall B Value
Fitting Procedure
Details	METHOD--The MDFF-derived HOH structure was equilibrated in 1 M NaCl FOR 425 ns using MD without applying restraints. PDB entries 3H47 AND 2KOD were t ...	METHOD--The MDFF-derived HOH structure was equilibrated in 1 M NaCl FOR 425 ns using MD without applying restraints. PDB entries 3H47 AND 2KOD were the starting structures. REFINEMENT PROTOCOL--flexible	METHOD--The MDFF-derived HOH structure was equilibrated in 1 M NaCl FOR 425 ns using MD without applying restraints. PDB entries 3H47 AND 2KOD were t ...	METHOD--The MDFF-derived HOH structure was equilibrated in 1 M NaCl FOR 425 ns using MD without applying restraints. PDB entries 3H47 AND 2KOD were the starting structures. REFINEMENT PROTOCOL--flexible

Data Acquisition
Detector Type	KODAK SO-163 FILM
Electron Dose (electrons/Å**2)	15

Imaging Experiment	1
Date of Experiment	2010-12-11
Temperature (Kelvin)	82
Microscope Model	FEI POLARA 300
Minimum Defocus (nm)	1000
Maximum Defocus (nm)	3500
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS	2
Imaging Mode	BRIGHT FIELD
Specimen Holder Model	OTHER
Nominal Magnification	59000
Calibrated Magnification	58257
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	200
Imaging Details

EM Software
Task	Software Package	Version
MODEL FITTING	MDFF
RECONSTRUCTION	FREALIGN

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

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.