Antibodies |
|
Rabbit monoclonal anti-eEF1A1 antibody |
Abcam |
Cat. #ab140632 |
Rabbit polyclonal anti-uL6 antibody |
Santa Cruz |
Cat. #102085; RRID: AB_2182219
|
Rabbit polyclonal anti-uS9 antibody |
Santa Cruz |
Cat. #sc-102087; RRID: AB_2269633
|
|
Chemicals, Peptides, and Recombinant Proteins |
|
3XFlag-TEV WT Hbs1l (human) |
Shao et al., 2013 |
N/A |
3XFlag-TEV H348A Hbs1l-DN (human) |
Shao et al., 2013 |
N/A |
3XFlag-TEV eRF3a (human) |
This study |
N/A |
WT eRF1 (human) |
This study |
N/A |
eRF1(AAQ) (human) |
Brown et al., 2015b |
N/A |
His-Pelota (human) |
Shao et al., 2013 |
N/A |
E. coli Poly(A) polymerase |
New England Biolabs |
Cat. #M0276L |
3X Flag peptide |
Sigma-Aldrich |
Cat. #F4799 |
Anti-Flag M2 affinity resin |
Sigma-Aldrich |
Cat. #A2220 |
Ni-NTA agarose |
QIAGEN |
Cat. #30210 |
Didemnin B |
This study (Jack Taunton) |
CAS #77327-05-0 |
Cycloheximide |
Sigma-Aldrich |
Cat. #C4859; CAS #66-81-9 |
Emetine |
Calbiochem |
Cat. #324693; CAS #316-42-7 |
Anisomycin |
Sigma-Aldrich |
Cat. #A9789; CAS #22862-76-6 |
EasyTag L-[35S]-Methionine |
Perkin Elmer |
Cat. #NEG709A005MC |
CAP (diguanosine triphosphate cap) |
New England Biolabs |
Cat. #S1404L |
RNasin |
Promega |
Cat. #N251 |
SP6 polymerase |
New England Biolabs |
Cat. #M0207L |
Creatine kinase |
Roche |
Cat. #127566 |
Creatine phosphate |
Roche |
Cat. #621714 |
Amino acid kit |
Sigma |
Cat. #09416 |
|
Deposited Data |
|
80S⋅empty A site density map |
This study |
EMDB: 4129 |
80S⋅aa-tRNA⋅eEF1A density map |
This study |
EMDB: 4130 |
80S⋅eRF1⋅eRF3 density map |
This study |
EMDB: 4131 |
80S⋅eRF1 density map |
This study |
EMDB: 4132 |
80S⋅eRF1⋅ABCE1 (combined) density map |
This study |
EMDB: 4133 |
80S⋅Pelota⋅Hbs1l (truncated mRNA) density map |
This study |
EMDB: 4134 |
80S⋅Pelota⋅Hbs1l (stop mRNA) density map |
This study |
EMDB: 4135 |
80S⋅Pelota⋅Hbs1l (polyA mRNA) density map |
This study |
EMDB: 4136 |
80S⋅Pelota⋅Hbs1l (combined) density map |
This study |
EMDB: 4137 |
80S⋅aa-tRNA⋅eEF1A atomic model |
This study |
PDB: 5LZS
|
80S⋅eRF1⋅eRF3 atomic model |
This study |
PDB: 5LZT
|
80S⋅eRF1 atomic model |
This study |
PDB: 5LZU
|
80S⋅eRF1⋅ABCE1 (combined) atomic model |
This study |
PDB: 5LZV
|
80S⋅Pelota⋅Hbs1l (truncated mRNA) atomic model |
This study |
PDB: 5LZW
|
80S⋅Pelota⋅Hbs1l (stop mRNA) atomic model |
This study |
PDB: 5LZX
|
80S⋅Pelota⋅Hbs1l (polyA mRNA) atomic model |
This study |
PDB: 5LZY
|
80S⋅Pelota⋅Hbs1l (combined) atomic model |
This study |
PDB: 5LZZ
|
|
Experimental Models: Cell Lines |
|
HEK293T |
ATCC |
CRL-3216 |
|
Experimental Models: Organisms/Strains |
|
E. coli BL21 (DE3) |
Thermo Fisher |
C600003 |
E. coli BL21 (DE3) pLysS |
Thermo Fisher |
C606003 |
|
Recombinant DNA |
|
pcDNA 3XFlag-TEV WT Hbs1l |
Shao et al., 2013 |
N/A |
pcDNA 3XFlag-TEV H348A Hbs1l |
Shao et al., 2013 |
N/A |
pcDNA 3XFlag-TEV eRF3a |
This study |
N/A |
pRSETA 6XHis-TEV eRF1 |
This study |
N/A |
pRSETA 6XHis-TEV eRF1(AAQ) |
Brown et al., 2015b |
N/A |
pSP64 3XFlag VHP Sec61-UGA(68) |
Brown et al., 2015b |
N/A |
pSP64 3XFlag VHP Sec61-68 |
Shao et al., 2013 |
N/A |
pSP64 3XFlag KRas |
This study |
N/A |
Primer: SP64 5′ Fwd: TCATACACATACGATTTAGG |
Sharma et al., 2010 |
N/A |
Primer: SP64 Rev: CAATACGCAAACCGCCTC |
Sharma et al., 2010 |
N/A |
Primer: Val68 Rev: AACTTTGAGCCCAGGTGAATC |
Shao et al., 2013 |
N/A |
|
Software and Algorithms |
|
EPU software |
FEI |
https://www.fei.com/software/epu/ |
Motioncorr |
Li et al., 2013 |
http://cryoem.ucsf.edu/software/driftcorr.html |
Gctf v0.5 |
Zhang, 2016 |
http://www.mrc-lmb.cam.ac.uk/kzhang/Gctf/ |
RELION v1.4 |
Scheres, 2015 |
http://www2.mrc-lmb.cam.ac.uk/relion |
ResMap v1.1.4 |
Kucukelbir et al., 2014 |
http://resmap.sourceforge.net/ |
Coot v0.8 |
Emsley et al., 2010 |
http://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/ |
REFMAC v5.8 |
Murshudov et al., 2011 |
https://www2.mrc-lmb.cam.ac.uk/groups/murshudov/content/refmac/refmac.html |
MolProbity v4.3 |
Chen et al., 2010 |
http://molprobity.biochem.duke.edu/ |
Phenix.elbow dev-2499 |
Adams et al., 2010 |
http://www.phenix-online.org/documentation/reference/elbow.html |
UCSF Chimera v1.10.2 |
Pettersen et al., 2004 |
https://www.cgl.ucsf.edu/chimera/ |
PyMOL v1.7 |
Schrödinger, LLC |
http://www.pymol.org |
|
Other |
|
RRL in vitro translation mix |
Sharma et al., 2010 |
N/A |
TransIT 293 |
Mirus |
MIR 2705 |