FEZ1 Is Recruited to a Conserved Cofactor Site on Capsid to Promote HIV-1 Trafficking

. Author manuscript; available in PMC: 2019 Sep 10.

Published in final edited form as: Cell Rep. 2019 Aug 14;28(9):2373–2385.e7. doi: 10.1016/j.celrep.2019.07.079

KEY RESOURCES TABLE

REAGENT or RESOURCE	SOURCE	IDENTIFIER
Bacterial and Virus Strains
E. coli BL21(DE3)	Lucigen	Cat#60401
E. coli XL10-Gold Ultracompetent Cells	Agilent	Cat#200315
Chemicals, Peptides, and Recombinant Proteins
Terrific Broth	Research Products International	Cat#T5100–5000.0
Luria Broth	Research Products International	Cat#L24400
Isopropyl β-D-1-thiogalactopyranoside (IPTG)	American Bioanalytical	Cat#AB00841–00010
complete EDTA-free protease inhibitor cocktail	Sigma	Cat#11873580001
Tris (2-Carboxylethyl) phosphine Hydrochloride (TCEP)	Gold Bio	Cat#TCEP
phenylmethane sulfonyl fluoride (PMSF)	dot scientific	Cat#DSP20270–25
2-Mercaptoethanol (BME)	Alfa Aesar	Cat#J66742–0B
NuPAGE LDS Sample Buffer (4X)	Thermo Fisher	Cat#NP0008
Dithiothreitol (DTT)	American Bioanalytical	Cat#AB00490–00100
SimplyBlue SafeStain	Thermo Fisher	Cat#LC6060
KOD Hot Start DNA polymerase	Novagen	Cat#710863
Recombinant 6xHis-FEZ1_1–392	This paper	N/A
Recombinant 6xHis-FEZ1_1–92	This paper	N/A
Recombinant 6xHis-FEZ1_92–198	This paper	N/A
Recombinant 6xHis-FEZ1_198–392	This paper	N/A
Recombinant 6xHis-FEZ1_92–158	This paper	N/A
Recombinant 6xHis-FEZ1_92–227	This paper	N/A
Recombinant 6xHis-FEZ1_{92–198 182EA}	This paper	N/A
Recombinant 6xHis-FEZ1_178–188	This paper	N/A
Recombinant 6xHis-FEZ1_158–198	This paper	N/A
Recombinant 6xHis-FEZ1_{158–198 182EA}	This paper	N/A
Recombinant 6xHis-FEZ1_158–182	This paper	N/A
Recombinant CA 14C/45C	(Pornillos et al., 2009)	N/A
Recombinant CA 14C/45C/R18D	This paper	N/A
Recombinant CA 14C/45C/R18D/184A/185A	This paper	N/A
Recombinant CA 14C/45C/R18A	This paper	N/A
Recombinant CA 14C/45C/G89V	(Smaga et al., 2019)	N/A
Recombinant CA 14C/45C/P207S	(Smaga et al., 2019)	N/A
Recombinant CA 14C/45C/G208R	(Smaga et al., 2019)	N/A
Recombinant CA 14C/45C/T210K	(Smaga et al., 2019)	N/A
Recombinant CA 14C/184A/185A	(Summers et al., 2019)	N/A
Recombinant CA 45C/184A/185A	(Summers et al., 2019)	N/A
Recombinant CA 14C/42E/184A/185A	(Summers et al., 2019)	N/A
Recombinant CA 45C/54E/184A/185A	(Summers et al., 2019)	N/A
Recombinant CA 14C/42E-Mpro-184A/185A	(Summers et al., 2019)	N/A
Recombinant CA 45C/54C/184A/185A	(Summers et al., 2019)	N/A
Recombinant CA 42C/184A/185A	(Summers et al., 2019)	N/A
Recombinant CA 42C/54E/184A/185A	(Summers et al., 2019)	N/A
Recombinant CA 45C	(Summers et al., 2019)	N/A
Recombinant CA 14C	(Summers et al., 2019)	N/A
Recombinant CA 45C/54E	(Summers et al., 2019)	N/A
Recombinant CA 14C/42E	(Summers et al., 2019)	N/A
Recombinant CA 45C/54E(1–226)-foldon	(Summers et al., 2019)	N/A
Recombinant CA 14C/42E/204D/(1–221)	(Summers et al., 2019)	N/A
Recombinant CA 14C/45C/184A/185A	(Pornillos et al., 2009)	N/A
Recombinant CA 14C/45C-5L-SpyCatcher-6xHis	(Summers et al., 2019)	N/A
Recombinant CA 14C/45C-5L-SpyTag-MBP-6xHis	(Summers et al., 2019)	N/A
Recombinant CA 14C/45C/184A/185A-5L-Spy Tag-MBP-6xHis	(Summers et al., 2019)	N/A
Recombinant CA 14C/45C/184A/185A-5L-SpyCat-6xHis	(Summers et al., 2019)	N/A
Recombinant CA 14C/45C/P90A	(Summers et al., 2019)	N/A
Recombinant CA 45C/54C/184A/185A/P90A	(Summers et al., 2019)	N/A
Recombinant CA 14C/42E/184A/185A/P90A	(Summers et al., 2019)	N/A
Recombinant CA 42C/54E/184A/185A/P90A	(Summers et al., 2019)	N/A
Recombinant CA 14C/45C/P90A-5L-SpyCatcher-6xHis	(Summers et al., 2019)	N/A
Recombinant CA 14C/45C/P90A-5L-SpyTag-MBP-6xHis	(Summers et al., 2019)	N/A
Recombinant CA 14C/45C/184A/185A/P90A	(Summers et al., 2019)	N/A
Recombinant Mpro protease	(Yang et al., 2003)	N/A
Deposited Data
Crystal structure of CA R18D	This paper	PDB: 6EC2
Oligonucleotides
All standard cloning primers for site-directed mutagenesis and Gibson assembly	Integrated DNA Technologies	N/A
Recombinant DNA
pET-11a	EMD Millipore	Cat#69436
pRSFDUET-1	EMD Millipore	Cat#71341
pET28-a	EMD Millipore	Cat#69864
pETDUET-1	EMD Millipore	Cat#71146
pMAL system	New England Biolabs	Cat#E8200S
Recombinant 6xHis-FEZ1_1–392	This paper	N/A
Recombinant 6xHis-FEZ1_1–92	This paper	N/A
Recombinant 6xHis-FEZ1_92–198	This paper	N/A
Recombinant 6xHis-FEZ1_198–392	This paper	N/A
Recombinant 6xHis-FEZ1_92–158	This paper	N/A
Recombinant 6xHis-FEZ1_92–227	This paper	N/A
Recombinant 6xHis-FEZ1_{92–198 182EA}	This paper	N/A
Recombinant 6xHis-FEZ1_178–188	This paper	N/A
Recombinant 6xHis-FEZ1_158–198	This paper	N/A
Recombinant 6xHis-FEZ1_{158–198 182EA}	This paper	N/A
Recombinant 6xHis-FEZ1_158–182	This paper	N/A
Plasmid: CA 14C/45C/R18D in pET-11a	This paper	N/A
Plasmid: CA 14C/45C/R18D/184A/185A in pET-11a	This paper	N/A
Plasmid: CA 14C/45C/R18A in pET-11a	This paper	N/A
Plasmid: CA 14C/45C/G89V in pET-11a	(Smaga et al., 2019)	N/A
Plasmid: CA 14C/45C/P207S in pET-11a	(Smaga et al., 2019)	N/A
Plasmid: CA 14C/45C/G208R in pET-11a	(Smaga et al., 2019)	N/A
Plasmid: CA 14C/45C/T210K in pET-11a	(Smaga et al., 2019)	N/A
Plasmid: CA 14C/184A/185A in pET-11 a	(Summers et al., 2019)	N/A
Plasmid: CA 45C/184A/185A in pET-11 a	(Summers et al., 2019)	N/A
Plasmid: CA 14C/42E/184A/185A in pET-11a	(Summers et al., 2019)	N/A
Plasmid: CA 45C/54E/184A/185A in pET-11 a	(Summers et al., 2019)	N/A
Plasmid: CA 14C/42E-Mpro-184A/185A in pET-11a	(Summers et al., 2019)	N/A
Plasmid: CA 45C/54C/184A/185A in pET-11 a	(Summers et al., 2019)	N/A
Plasmid: CA 42C/184A/185A in pET-11 a	(Summers et al., 2019)	N/A
Plasmid: CA 42C/54E/184A/185A in pET-11 a	(Summers et al., 2019)	N/A
Plasmid: CA 45C in pET-11a	(Summers et al., 2019)	N/A
Plasmid: CA 14C in pET-11a	(Summers et al., 2019)	N/A
Plasmid: CA 45C/54E in pET-11a	(Summers et al., 2019)	N/A
Plasmid: CA 14C/42E in pET-11a	(Summers et al., 2019)	N/A
Plasmid: CA 45C/54E(1–226)-foldon in pET-11a	(Summers et al., 2019)	N/A
Plasmid: CA 14C/42E/204D/(1–221) in pET-11a	(Summers et al., 2019)	N/A
Plasmid: CA 14C/45C/184A/185A in pET-11a	(Summers et al., 2019)	N/A
Plasmid: CA 14C/45C-5L-SpyCatcher-6xHis in pET-11a	(Summers et al., 2019)	N/A
Plasmid: CA 14C/45C-5L-SpyTag-MBP-6xHis in pET-11a	(Summers et al., 2019)	N/A
Plasmid: CA 14C/45C/184A/185A-5L-SpyTag-MBP-6xHis in pET-11a	(Summers et al., 2019)	N/A
Plasmid: CA 14C/45C/184A/185A-5L-SpyCat-6xHis in pET-11a	(Summers et al., 2019)	N/A
Plasmid: CA 14C/45C/P90A in pET-11a	(Summers et al., 2019)	N/A
Plasmid: CA 45C/54C/184A/185A/P90A in pET-11 a	(Summers et al., 2019)	N/A
Plasmid: CA 14C/42E/184A/185A/P90A in pET-11 a	(Summers et al., 2019)	N/A
Plasmid: CA 42C/54E/184A/185A/P90A in pET-11 a	(Summers et al., 2019)	N/A
Plasmid: CA 14C/45C/P90A-5L-SpyCatcher-6xHis in pET-11a	(Summers et al., 2019)	N/A
Plasmid: CA 14C/45C/P90A-5L-SpyTag-MBP-6xHis in pET-11a	(Summers et al., 2019)	N/A
Plasmid: CA 14C/45C/184A/185A/P90A in pET-11a	(Summers et al., 2019)	N/A
Plasmid: nanobody 37E7-6xHis in pET28-a	(Gray et al., 2017)	N/A
Software and Algorithms
NanoAnalyze v3.6.0	TA Instruments	https://www.tainstruments.com/support/software-downloads-support/downloads/
XDS	(Kabsch, 2010a, 2010b)	http://xds.mpimf-heidelberg.mpg.de/
Phaser	(McCoy et al., 2007; Winn et al., 2011)	http://www.ccp4.ac.uk/html/phaser.html
Refmac5	(Adams et al., 2010)	http://www.ccp4.ac.uk/dist/html/refmac5.html
Phenix	(Emsley and Cowtan, 2004)	https://www.phenix-online.org/
Coot	(Murshudov et al., 1997)	https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/
PyMOL(v1.6.0.0)	(Schrodinger, 2015)	https://pymol.org/2/
Chimera (v13.0)	(Pettersen et al., 2004)	https://www.cgl.ucsf.edu/chimera/
Other
Ni-NTA Agarose	QIAGEN	Cat#30230
HiTrap Q HP 5mL	GE Healthcare	Cat#17115401
HiTrap SP HP 5mL	GE Healthcare	Cat#17115201
HiLoad 16/600 Superdex 200 PG	GE Healthcare	Cat#28990945
Yarra SEC-3000	Phenomenex	Cat#00F–4513–E0
Superose6 10/300 GL	GE Healthcare	Cat#17517201
Superdex 200 Increase 5/150 GL	GE Healthcare	Cat#28990945
Pre-treated RC Tubing MWCO 10kD	Spectrum Labs	Cat#132120
Slide-A-Lyzer Dialysis Cassettes, 10K MWCO, 0.5mL	Thermo Fisher	Cat#PI66383
Amicon Ultra-15 Centrifugal Filter Units 10kDa	Millipore Sigma	Cat#UFC901024
Amicon Ultra-15 Centrifugal Filter Units 30kDa	Millipore Sigma	Cat#UFC903024
NuPAGE 4–12% Bis-Tris Midi gels	Invitrogen	Cat#WG1403B0X
Gen10 BT⁺ (Bis-Tris) Protein Mini Gel 4–12%	ConnSTEM	Cat#13A12