REL RCSB RCSB RCSB 2013-04-12 2013-05-29 2013-05-29 2013-06-12 Cryo-electron tomography reconstruction of native HIV-1 core Zhao G Perilla JR Yufenyuy E Meng X Chen B Ning J Ahn J Gronenborn AM Schulten K Aiken C Zhang P cryo-electron tomography, HIV-1 core Zhao G Perilla JR Yufenyuy EL Meng X Chen B Ning J Ahn J Gronenborn AM Schulten K Aiken C Zhang P Mature HIV-1 capsid structure by cryo-electron microscopy and all-atom molecular dynamics. NATURE 497 643 646 2013 23719463 doi:10.1038/nature12162 3j3y FULLOVERLAP HIV-1 core with A14C/E45C cross-linked capsid protein HIV-1 core with A14C/E45C cross-linked capsid protein
The sample was purified from HIV-1 virions
1 Human immunodeficiency virus 1
HIV-1 core was isolated from virions carrying A14C/E45C mutation in capsid protein.
Human immunodeficiency virus 1 R9 Homo sapiens VERTEBRATES VIRION STRAIN true false HIV-1 tomography particle 0.011 8.0
10 mM Tris-HCl, 100 mM NaCl, 1 mM EDTA
Quantifoil R2/2 200 mesh holey carbon copper grids
 ETHANE 70 90 HOMEMADE PLUNGER Purified 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. FEI POLARA 300 FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 2 8.0 8.0 39000.0 SIDE ENTRY, EUCENTRIC 80 85 82 Objective lens astigmatism was corrected at 115,000 times magnification 2010-09-11 GATAN ULTRASCAN 4000 (4k x 4k) 53 120 16. -70 66 2 OTHER tomo3d
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.
53 emd_5639.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 163 175 161 0 0 0 175 163 161 1018.75 1093.75 1006.25 90.0 90.0 90.0 X Y Z 0.0 0.62596595 0.06133261 0.12504502 6.25 6.25 6.25 0.355 AUTHOR The figure shows the simulated density of all-atom HIV-1 capsid model (3J3Y) overlaid with a slice of HIV-1 core tomogram.
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 3J34 FLEXIBLE FIT MD
The model was built using hexamer of hexamers (PDB entry 3J34) and pentamer of hexamers (computer-based MD model available upon request).
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