4CC8 | pdb_00004cc8

Pre-fusion structure of trimeric HIV-1 envelope glycoprotein determined by cryo-electron microscopy


ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3SE8 
experimental modelPDB 3HMG 
Sample
COMPLEX OF KNH1144 SOSIP GP140 TRIMER WITH VRC03 FAB.
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification InstrumentFEI VITROBOT MARK IV
Cryogen NameETHANE
Sample Vitrification DetailsBLOT FOR 6 SECONDS, BLOT OFFSET OF -2, PLUNGE INTO AN ETHANE SLURRY COOLED BY LIQUID NITROGEN
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles88125
Reported Resolution (Å)6
Resolution Method
Other Details3SE8, CHAIN G AND CHAINS H, L FITTED AS TWO SEPARATE RIGID BODIES INTO MAP. ONLY HELIX RESIDUES 92-122 OF CHAIN B FITTED BY HAND INTO MAP. SUBMISSION ...3SE8, CHAIN G AND CHAINS H, L FITTED AS TWO SEPARATE RIGID BODIES INTO MAP. ONLY HELIX RESIDUES 92-122 OF CHAIN B FITTED BY HAND INTO MAP. SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-2484. (DEPOSITION ID: 12023).
Refinement Type
Symmetry TypePOINT
Point SymmetryC3
Map-Model Fitting and Refinement
Id1 (3SE8, 3HMG)
Refinement SpaceRECIPROCAL
Refinement ProtocolRIGID BODY FIT
Refinement Target
Overall B Value
Fitting Procedure
DetailsREFINEMENT PROTOCOL--RIGID BODY
Data Acquisition
Detector TypeGATAN ULTRASCAN 4000 (4k x 4k)
Electron Dose (electrons/Å**2)10
Imaging Experiment1
Date of Experiment2011-08-09
Temperature (Kelvin)80
Microscope ModelFEI TITAN KRIOS
Minimum Defocus (nm)1500
Maximum Defocus (nm)2500
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS2.7
Imaging ModeBRIGHT FIELD
Specimen Holder Model
Nominal Magnification75000
Calibrated Magnification
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)80
Imaging Details
EM Software
TaskSoftware PackageVersion
MODEL FITTINGUCSF Chimera
RECONSTRUCTIONEMAN
RECONSTRUCTIONFREALIGN
RECONSTRUCTIONIMAGIC