|
Antibodies
|
| 1D4 primary antibody |
(Hodges et al., 1988) |
N/A |
|
Chemicals, peptides, and recombinant proteins
|
| CaCl2
|
Fisher Chemical |
Cat# C70-500 |
| Tris-Base |
Fisher BioReagents |
Cat# BP152-1 |
| Sucrose |
Fisher Chemical |
Cat# S3-212 |
| EDTA |
Fisher BioReagents |
Cat# BP120-1 |
| Protease inhibitor cocktail |
Sigma |
Cat# P8215 |
| PMSF |
Acros Organics |
Cat# 215740500 |
| HEPES |
Sigma |
Cat# H3375-500G |
| NaCl |
Fisher BioReagents |
Cat# BP358-10 |
| Glycerol |
Fisher BioReagents |
Cat# BP229-4 |
| Digitonin |
Millipore |
Cat# 300410-5GM |
| TCEP |
Pierce |
Cat# PG82090 |
| CnBr-activated sepharose beads |
Cytiva |
Cat# 17043001 |
|
Deposited data
|
| PDB |
This paper, https://www.rcsb.org/
|
6WHG |
| EMDB |
This paper, https://www.ebi.ac.uk/pdbe/emdb/
|
EMD-21672 |
|
Experimental models: Organisms/strains
|
|
Saccharomyces cerevisiae BJ5457 |
ATCC |
208282 |
|
Recombinant DNA
|
| YepM plasmid vector |
(Moiseenkova-Bell et al., 2008) |
N/A |
|
Software and algorithms
|
| RELION |
(Scheres, 2012, 2016; Zivanov et al., 2018) |
https://www3.mrc-lmb.cam.ac.uk/relion/index.php?title=Main_Page
|
| Coot |
(Emsley and Cowtan, 2004) |
https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/
|
| Phenix |
(Adams et al., 2002) |
https://phenix-online.org/documentation/index.html
|
| MotionCor2 |
(Zheng et al., 2017a; Zivanov et al., 2018) |
https://emcore.ucsf.edu/ucsf-software
|
| CTFFIND-4.1 |
(Rohou and Grigorieff, 2015) |
https://grigoriefflab.umassmed.edu/ctffind4
|
| ITASSER |
(Roy, Kucukural and Zhang, 2010; Yang and Zhang, 2015) |
https://zhanglab.dcmb.med.umich.edu/I-TASSER/
|
| eLBOW |
(Moriarty, Grosse-Kunstleve and Adams, 2009a) |
https://phenix-online.org/documentation/reference/elbow_gui.html
|
| Molprobity |
(Chen et al., 2010a) |
http://molprobity.biochem.duke.edu/
|
| EMRinger |
(Barad et al., 2015) |
https://github.com/fraser-lab/EMRinger
|
| EMAN2.1 |
(Bell et al., 2016) |
https://blake.bcm.edu/emanwiki/EMAN2
|
| HOLE |
(Smart et al., 1996) |
http://www.holeprogram.org/
|
| PyMOL |
(Schrodinger, 2015) |
https://pymol.org/2/
|
| APBS-PDB2PQR |
(Dolinsky et al., 2004) |
https://server.poissonboltzmann.org/
|
| Chimera |
(Pettersen, 2004) |
https://www.cgl.ucsf.edu/chimera/
|
| MODELLER |
(Fiser, Do and Sali, 2000) |
https://salilab.org/modeller/
|
| NAMD 2.12 |
(Phillips et al., 2005) |
http://www.ks.uiuc.edu/Research/namd/
|
| CHARMM36/ TIP3P |
(Jorgensen et al., 1983; Vanommeslaeghe and Mackerell, 2015) |
http://mackerell.umaryland.edu/charmm_ff.shtml, https://www.charmm.org/
|
| VMD and plugins |
(Humphrey, Dalke and Schulten, 1996) |
http://mackerell.umaryland.edu/charmm_ff.shtml, https://www.ks.uiuc.edu/Research/vmd/
|
| Carma in VMD |
(Glykos, 2006) |
http://utopia.duth.gr/~glykos/carma.html
|
| Anton2 simulation |
(Shaw et al., 2008) |
https://www.deshawresearch.com/
|
