A 3.7 Angstrom structure of the EIAV CA-SP hexamer (C2) from Gag-deltaMA tubes assembled at pH8

2024-10-16 REL PDBe PDBe PDBe 2019-10-17 2020-01-08 2020-01-15 2024-10-16 Austrian Science Fund P31445 Austria National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) R01-AI147890 United States National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) R01-GM107013 United States National Science Foundation (United States) 1659534 United States National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) P30-GM110758 United States National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) P50AI150481 United States National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) AI142263 United States European Research Council ERC-2014-CoG 648432 - MEMBRANEFUSION United Kingdom Medical Research Council (United Kingdom) MC_UP_1201/16 United Kingdom German Research Foundation BR 3635/2-1 Germany A 3.7 Angstrom structure of the EIAV CA-SP hexamer (C2) from Gag-deltaMA tubes assembled at pH8 Dick RA Xu C Retrovirus, lentivirus, Equine infectious anemia virus, EIAV, Gag, capsid, IP6, phytic acid, inositolhexakiphosphate, VIRAL PROTEIN 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 Structures of immature EIAV Gag lattices reveal a conserved role for IP6 in lentivirus assembly. Plos Pathog. US 16 e1008277 e1008277 2020 31986188 doi:10.1371/journal.ppat.1008277 1553-7374 EMD-10383 other EM volume

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

EMD-10382 other EM volume

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

EMD-10384 other EM volume

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

EMD-10385 other EM volume

A representative tomogram containing tubes and spheres assembled at pH8

6t61 FULLOVERLAP 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 Capsid 700.0 VIRUS-LIKE PARTICLE OTHER false true Gag polyprotein Equine infectious anemia virus 0.054881535 18 Escherichia coli BL21(DE3) LEVO MGDPLTWSKALKKLEKVTVQGSQKLTTGNCNWALSLVDLFHDTNFVKEKDWQLRDVIPLLEDVTQTLSGQEREAFERTWW AISAVKMGLQINNVVDGKASFQLLRAKYEKKTANKKQSEPSEEYPIMIDGAGNRNFRPLTPRGYTTWVNTIQTNGLLNEA SQNLFGILSVDCTSEEMNAFLDVVPGQAGQKQILLDAIDKIADDWDNRHPLPNAPLVAPPQGPIPMTARFIRGLGVPRER QMEPAFDQFRQTYRQWIIEAMSEGIKVMIGKPKAQNIRQGAKEPYPEFVDRLLSQIKSEGHPQEISKFLTDTLTIQNANE ECRNAMRHLRPEDTLEEKMYACRDIGTTKQKMMLLAKALQTGLAGPFKGGALKGGPLKAAQTCYNCGKPGHLSSQCRAPK VCFKCKQPGHFSKQCRSVPKNGKQGAQGRPQKQTFPIQQKSQHNKSVVQETPQTQNLYPDLSEIKKEYNVKEKDQVEDLN LDSLWE P69730 subtomogramAveraging particle 8.0 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 30 AIR

20 mA

ETHANE 90 288 FEI VITROBOT MARK II

1-2 seconds blot time, offset -3mm.

Virus-like-particles (tubular) of EIAV Gag deltaMA-deltap9 (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

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.

C2 3.7 FSC 0.143 CUT-OFF AV3 TOM Toolbox 89860 20 308367 Subvolumes were defined according to their position on the VLPs 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 spline of the VLPs. Initially, positions were oversampled and subsequently cleaned during alignments using cross-correlation and distance thresholds.

PROJECTION MATCHING 1 CC AV3 TOM Toolbox

Subtomogram alignment was performed as described in the published manuscript.

emd_10381.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 192 192 192 0 0 0 192 192 192 259.2 259.2 259.2 90.0 90.0 90.0 X Y Z -2.2381835 2.9227679 0.00027298863 0.29104987 1.35 1.35 1.35 0.649 AUTHOR ::::EMDATABANK.org::::EMD-10381:::: A 3.7 Angstrom structure of the EIAV CA-SP hexamer (C2) from Gag-dMA tubes assembled at pH8 2EIA PDB experimental model OTHER

Rigid body fitting was done in Chimera. Missing residues were built de novo in Coot. Refinement was performed iteratively in Phenix and Coot.

Cross-correlation coefficient REAL