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Title:Cryo-electron tomography reconstruction of native HIV-1 core
Authors:Zhao G, Perilla JR, Yufenyuy E, Meng X, Chen B, Ning J, Ahn J, Gronenborn AM, Schulten K, Aiken C, Zhang P
Sample:HIV-1 core with A14C/E45C cross-linked capsid protein
Red flagLatest update:2013-06-12
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Sample name: HIV-1 core with A14C/E45C cross-linked capsid protein
ID Type Name Exp. MW (MDa) Oligomeric details Recombinant expression Synthetic Organism UniProt identifier GO identifier InterPro identifier Virus identifier Details
1virusHuman immunodeficiency virus 1Human immunodeficiency virus 1HIV-1 core was isolated from virions carrying A14C/E45C mutation in capsid protein.
Specimen state: Particle
Specimen preparation:
pHSpecimen conc.DetailsStainingSpecimen support details
8.00.011 mg/mL10 mM Tris-HCl, 100 mM NaCl, 1 mM EDTAQuantifoil R2/2 200 mesh holey carbon copper grids
Cryogen nameHumidityTemp.Instr.MethodTime resolvedDetails
ETHANE70%90 KHOMEMADE PLUNGERPurified HIV-1 A14C/E45C cores (3 uL) were applied to the carbon side of glow-discharged, perforated R2/2 Quantifoil grids and quickly mixed with 3 uL of a 15 nM fiducial gold bead solution before plunge-freezing. ms
MicroscopeVoltageIllumination modeImaging modeCsDefocus min.Defocus max.Nominal mag.Calibrated mag.Electron sourceDetectorDetector distanceAstigmatism
FEI POLARA 300300 kVFLOOD BEAMBRIGHT FIELD2 mm8000 nm8000 nm39000FIELD EMISSION GUNGATAN ULTRASCAN 4000 (4k x 4k) mmObjective lens astigmatism was corrected at 115,000 times magnification

Specimen holderHolder modelTilt min.Tilt max.Energy filterEnergy windowTemp.Temp. min.Temp. max.Beam tiltElectron doseOther detailsDate
SIDE ENTRY, EUCENTRIC-70°66° eV82 K80 K85 K mrad120 e/Å211-SEP-2010
Number of tilts:53
Tilt angle increment:
Imposed symmetry:C1
Processing details:The raw tomogram was denoised using the nonlinear anisotropic diffusion edge-enhancing algorithm available in IMOD. The core density was segmented out using Volume Tracer in UCSF Chimera.
Scanned images:
Num. imagesSampling sizeOD rangeQuant. bit numberOther detailsScanner
53 μm/pixel16
PDBProtocolTarget crit.SoftwareB valueFitting spacePDB chainDetails
3J34 flexibleMDREALThe model was built using hexamer of hexamers (PDB entry 3J34) and pentamer of hexamers (computer-based MD model available upon request).