3DNN | pdb_00003dnn

Molecular structure for the HIV-1 gp120 trimer in the unliganded state

ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1GC1

Sample
HIV-1 BaL
Sample Components
HIV-1 Envelope Glycoprotein GP120

Specimen Preparation
Sample Aggregation State	PARTICLE
Vitrification Instrument	FEI VITROBOT MARK I
Cryogen Name	ETHANE
Sample Vitrification Details	Ethane 77K 100%RH Vitrobot

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles
Reported Resolution (Å)	20
Resolution Method
Other Details	IMOD was used for tomographic reconstruction. Programs developed in-house were used for alignment and classification of individual tomographic volumes ...	IMOD was used for tomographic reconstruction. Programs developed in-house were used for alignment and classification of individual tomographic volumes. The final map is the average of ~4000 individual spikes.
Refinement Type
Symmetry Type	POINT
Point Symmetry	C3

Map-Model Fitting and Refinement
Id	1 (1GC1)
Refinement Space	REAL
Refinement Protocol	RIGID BODY FIT
Refinement Target	correlation coefficient
Overall B Value
Fitting Procedure
Details	METHOD--Automatic. The coordinates for this entry and the two related entries 3DNL and 3DNO are based on fitting 1GC1 coordinates for the gp120 monom ...	METHOD--Automatic. The coordinates for this entry and the two related entries 3DNL and 3DNO are based on fitting 1GC1 coordinates for the gp120 monomer deposited previously by Kwong et al in 1998 into the density map for the trimer derived by electron microscopy. Therefore, authors did not deposit new structure factors, and, any features such as unusual torsion angles are the same as in the 1GC1 coordinates. REFINEMENT PROTOCOL--rigid body

Data Acquisition
Detector Type	GENERIC CCD
Electron Dose (electrons/Å**2)	80

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)	90
Microscope Model	FEI POLARA 300
Minimum Defocus (nm)	2000
Maximum Defocus (nm)	4000
Minimum Tilt Angle (degrees)	-70
Maximum Tilt Angle (degrees)	70
Nominal CS	2.2
Imaging Mode	BRIGHT FIELD
Specimen Holder Model
Nominal Magnification	34000
Calibrated Magnification
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	200
Imaging Details

EM Software
Task	Software Package	Version
MODEL FITTING	UCSF Chimera
RECONSTRUCTION	IMOD

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
	No CTF correction applied

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.