REL PDBe PDBe PDBe 2013-08-08 2013-09-04 2013-09-18 2013-11-20 Hui W Tang Q Liu H Atanasov I Zhu H Zhou ZH cytomegalovirus; herpes simplex virus type 1; electron cryo microscopy; three-dimensional; major capsid protein. Hui WH Tang Q Liu H Atanasov I Liu F Zhu H Zhou ZH PROTEIN CELL 4 833 845 2013 24006185 doi:10.1007/s13238-013-3060-7 Murine cytomegalovirus capsid Murine cytomegalovirus capsid

The sample is monodisperse in PBS buffer

icosahedral virus capsid 4 186.4 Murid herpesvirus 1

The virus is enveloped but the structure presented here is for the capsid only.

Murid herpesvirus 1 strain Smith Murine strain Smith INVERTEBRATES 186.4 Capsid 1310 16 OTHER STRAIN true true Murine cytomegalovirus singleParticle particle 1 7.0

PBS

NEGATIVE

vitreous ice, no staining

across holes in Quantifoil grids

ETHANE 100 90 FEI VITROBOT MARK I

Vitrification instrument: FEI Vitrobot

Blot for 7-9 seconds before plunging FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 2.7 1.5 3.0 47000.0 FEI TITAN KRIOS AUTOGRID HOLDER 80 100 90 objective lens astigmatism was corrected at 250,000 times magnification 0 FEI 2009-10-15 KODAK SO-163 FILM NIKON SUPER COOLSCAN 9000 6.35 1299 20 16. Autoloader of Titan Krios at liquid nitrogen temperature

Individual particle images were automatically boxed out from micrographs by the autoBox program in the IMIRS package, followed by manual screening to select good capsid particle images that appear perfectly intact and without contamination and signs of specimen charging. Defocus value and astigmatism parameters of each micrographs were determined with CTFFIND. Subsequent data processing includes the determination of particle orientation/center parameters, 3D reconstruction and iterative, projection-based refinement by a distributed computing approach using modular programs in the IMIRS package with recent enhancements. The distributed computing was performed entirely through on six Microsoft Windows personal computers and four Windows servers within a custom-designed MPI network. Astigmatism was taken into consideration during the correction of contrast transfer function (CTF) both in the orientation/center refinement step and the 3D reconstruction step. Using this procedure, we first obtained a 3D map from 6402 particle images from the Polara micrographs. This map has a resolution of about 11 angstrom and was used as the starting model to assist processing the higher resolution particle images of the Titan micrographs. To process the Titan micrographs, we discarded micrographs with specimen charging by evaluating the Fourier transform of the micrographs and selected 669 micrographs for in-depth data processing. From the 669 good Titan micrographs selected out through this process, we boxed 5383 particle images and determined their orientation/center parameters by using the 11 angstrom map as the starting model. These orientation/center parameters were iteratively refined against the latest 3D map by gradually including Fourier data at regions of higher spatial frequency. The iterative process was terminated when the reconstruction converges to a stable solution and no further improvement in the resolution of the map was observed. Our reconstruction converges when the high spatial frequency cut-off of the included image data reached 1/6.9 angstrom-1. The final map was obtained from 3467 particles images, all from the Titan micrographs.

CTFFIND

I OTHER 9.1 FSC 0.5 CUT-OFF IMIRS 3467 1NO7 A RIGID BODY FIT Chimera

Manual fitting in Chimera

Chimera fit-to-map REAL

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