2020-07-29 REL PDBe PDBe PDBe 2019-10-17 2020-01-08 2020-01-15 2020-07-29 German Research Foundation BR 3635/2-1 Germany Austrian Science Fund P31445 Austria National Institutes of Health/National Institute of General Medical Sciences R01-GM107013 United States National Institutes of Health/National Institute Of Allergy and Infectious Diseases R01-AI147890 United States National Institutes of Health/National Institute of General Medical Sciences P30-GM110758 United States National Science Foundation (United States) 1659534 United States National Institutes of Health/National Institute Of Allergy and Infectious Diseases AI142263 United States National Institutes of Health/National Institute Of Allergy and Infectious Diseases P50AI150481 United States Medical Research Council (United Kingdom) MC_UP_1201/16 United Kingdom European Research Council ERC-2014-CoG 648432 - MEMBRANEFUSION United Kingdom Dick RA Xu C Morado DR Kravchuk V Ricana CL Lyddon TD Broad AM Feathers JR Johnson MC Vogt VM Perilla JR Briggs JAG Schur FKM Dick RA Xu C Morado DR Kravchuk V Ricana CL Lyddon TD Broad AM Feathers JR Johnson MC Vogt VM Perilla JR Briggs JAG Schur FKM Plos Pathog. US 16 e1008277 e1008277 2020 31986188 doi:10.1371/journal.ppat.1008277 1553-7374 EMD-10381 other EM volume

This entry contains the structure for EIAV Gag-deltaMA tubes assembled at pH8

EMD-10383 other EM volume

This entry contains the structure for EIAV Gag-deltaMA tubes assembled at pH6

EMD-10384 other EM volume

This entry contains the structure for EIAV Gag-deltaMA spheres assembled at pH6

EMD-10385 other EM volume

This entry contains a tomogram of EIAV Gag-deltaMA spheres and tubes assembled at pH8

EMD-10382 associated EM volume Equine infectious anemia virus Equine infectious anemia virus 0 1

Gag construct was expressed in E.coli and purified using the SUMO-tag system

Equine infectious anemia virus Equus caballus Escherichia coli BL21 Capsid 1000.0 VIRUS-LIKE PARTICLE OTHER false true subtomogramAveraging particle 8 50.0 Tris-HCl 100.0 NaCl Sodium Chloride 2.0 TCEP tris(2-carboxyethyl)phosphine C-flat-2/2 COPPER 300 CARBON HOLEY GLOW DISCHARGE AIR

20 mA

ETHANE 90 288 FEI VITROBOT MARK II

1-2 seconds blot time, offset -3mm 10 nm colloidal gold was added prior to vitrification.

Virus-like-particles (spherical) of EIAV Gag deltaMAdeltap9 (referred to as Gag deltaMA) assembled at pH8.

FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 50.0 2.7 -1.5 -5.0 105000.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN GIF Quantum LS 20

nanoprobe

GATAN K2 QUANTUM (4k x 4k) SUPER-RESOLUTION 3708 3838 1 1.8 3.4

Data was acquired using a dose-symmetric tilt acquisition scheme, as described in Hagen et al, 2017, J. Struct. Biol, 197(2):191-8

1

Tilt series were low-pass filtered according to their cumulative dose using exposure filters that were calculated using an exposure-dependent amplitude attenuation function and critical exposure constants (as published in Grant & Grigorieff, Elife, 2015). Tilt series were aligned and reconstructed in IMOD.

1 C6 3.9 FSC 0.143 CUT-OFF AV3 TOM Toolbox 65807 37 191612 MATLAB partially based on the TOM toolbox

Subtomogram extraction positions were defined in Amira using the electron microscopy toolbox by determing the radii and the center of the VLPs. Initially, positions were oversampled and subsequently cleaned during alignments using cross-correlation and distance thresholds.

CTFFIND 4 CTFPHASEFLIP NOVACTF

CTF-correction was initially performed using ctfphaseflip in IMOD and NovaCTF in the final steps

PROJECTION MATCHING 1 CC AV3 TOM Toolbox

Subtomogram alignment was performed as described in the published manuscript.

REAL