2018-07-04 REL PDBe PDBe PDBe 2018-03-28 2018-04-04 2018-07-04 2018-07-04 Structure of the herpes-simplex virus portal-vertex McElwee M Vijayakrishnan S Rixon FJ Bhella D McElwee M Vijayakrishnan S Rixon F Bhella D Structure of the herpes simplex virus portal-vertex. PLoS Biol. US 16 e2006191 e2006191 2018 29924793 doi:10.1371/journal.pbio.2006191 1545-7885 EMD-4347 associated EM volume Herpes simplex virus (type 1 / strain 17) Herpes simplex virus (type 1 / strain 17) 0
Virus was propagated in BHK cells
Herpes simplex virus (type 1 / strain 17) Homo sapiens Capsid 1250.0 16 VIRION STRAIN true false Portal 1
Dodecameric portal comprised of the pUL6 protein
Herpes simplex virus (type 1 / strain 17) Portal-vertex associated tegument protein 1
portal associated tail-like density comprised of ten copies of the pUL25 protein
Herpes simplex virus (type 1 / strain 17) singleParticle particle 1 7.2
Phosphate buffered saline
 Quantifoil R2/2 COPPER 400 CARBON HOLEY ARRAY GLOW DISCHARGE AIR ETHANE 100 277 FEI VITROBOT MARK IV
Purified enveloped virions
FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 2.7 81000. FEI FALCON III (4k x 4k) INTEGRATING 1 3702 12.0 78.0
Images were acquired as 40 fractions per micrograph at 1.78 angstroms/pixel sampling.
 1
Images were motion-corrected using motioncor2 Defocus estimation was performed using GCTF
12431
Autopicking in Relion
 Gctf
CTF correction was implemented through Relion
Starting model was calculated ab initio in Relion 2.1 assuming full icosahedral symmetry (I2).
 1 C5 BACK PROJECTION 7.7 FSC 0.143 CUT-OFF RELION 2.1
Following definition of the class that featured the unique portal vertex, the metadata file was parsed to change sampling from 5x binning to 1.5x binning, and divide the dataset into two halves. Half-maps were calculated and processed to evaluate the FSC and for b-factor estimation.
5337 PROJECTION MATCHING RELION 2.1 MAXIMUM LIKELIHOOD RELION 2.1 10 RELION 2.1
Origin and orientation values were determined by 3D auto refine in RELION, assuming full icosahedral symmetry (i.e. with full gold-standard methods). To compute the C5 symmetric map, we performed focussed classification on the refined dataset. Briefly, the symmetry of the dataset was expanded yielding a metadata file in which each particle image had 60 assigned views, corresponding to the 60-fold icosahedral redundancy. A cylindrical mask was prepared in SPIDER, that covered a single five-fold vertex. 3D classification in RELION was then performed, without orientation refinement (k=10). This led to the definition of a single class in which we could see the portal-vertex associated tegument (tail). The above analysis was performed on data with 5x binning. The final reconstruction was calculated using 1.5x binned data. The portal-vertex class comprised 26,891 views from 5,337 particle images. Particle images contributed a median 5 views each, thus C5 symmetry is assumed to be applied.
 emd_4347.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 600 600 600 0 0 0 600 600 600 1602.0 1602.0 1602.0 90.0 90.0 90.0 X Y Z -0.1443535 0.21554615 0.00019707222 0.02158095 2.67 2.67 2.67 0.05 AUTHOR Reconstruction of the herpes simplex virus type 1 virion, with relaxed (C5) symmetry. The map is sharpened. emd_4347_additional.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 600 600 600 0 0 0 600 600 600 1602.0 1602.0 1602.0 90.0 90.0 90.0 X Y Z -0.08962618 0.12478677 0.00019707222 0.015881985 2.67 2.67 2.67 0.015 AUTHOR Reconstruction of the herpes simplex virus type 1 virion, with relaxed (C5) symmetry. The map is NOT sharpened.