REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
Human monoclonal HDAC6 antibody	Cell Signaling	Cat#7558; RRID: AB_10891804
Monoclonal ANTI-FLAG® M2 antibody produced in mouse	Sigma-Aldrich	Cat#F3165; RRID: AB_259529
Pan-Ubiquitin antibody(P4D1)	Santa Cruz	Cat#sc-8017; RRID: AB_2762364
Pan-actin antibody	Sigma-Aldrich	Cat#SAB4502632; RRID: AB_10746710
Anti-His tag antibody	Santa Cruz	Cat#sc-53073; RRID: AB_783791
GFP-antibody	Cell Signaling	Cat#2037
Monoclonal Anti-α-Tubulin antibody produced in mouse	Sigma-Aldrich	Cat#T9026; RRID: AB_477593
Monoclonal Anti-Acetylated Tubulin antibody produced in mouse	Sigma-Aldrich	Cat#T7451; RRID: AB_609894
Goat anti-Mouse IgG (H+L), Superclonal™ Recombinant Secondary Antibody, Alexa Fluor 488	Invitrogen	Cat#A28175; RRID: AB_2536161
Goat anti-Mouse IgG (H+L) Highly Cross-Adsorbed Secondary Antibody, Alexa Fluor 568	Invitrogen	Cat#A-11031; RRID: AB_144696
Anti-HA tag antibody	Abcam	Cat#ab18181; RRID: AB_444303
G3BP antibody - N-terminal region	Aviva Systems Biology	Cat#ARP37713_T100; RRID: AB_2107232
Influenza A virus M1 antibody	ATCC	Cat#HB-64
Ubiquitin antibody (clone: P4D1)	Cytoskeleton	Cat#AUB01; RRID: AB_2884970
ZIKA virus E-protein antibody	ATCC	Cat#HB-112
Bacterial and virus strains
E. coli strain BL21(DE3)	NEB	Cat#C2527H
E. coli strain DH5α	NEB	Cat#C2987H
Influenza A virus strain H3N2 X31A	Virapur	Cat#Lot B1707C
ZIKV, Asian lineage strain, Puerto Rico	Public Health England (PHE)	ZIKV PRVABC59 (GenBank KX377337)
ZIKV, African lineage strain	Public Health England (PHE)	MP1751 (Genbank DQ859059)
Chemicals, peptides, and recombinant proteins
MG132, Ready-Made solution	Sigma-Aldrich	Cat#M7449
Sodium Arsenite Solution	Sigma-Aldrich	Cat#1.06277
dTAG-13	Novartis	N/A
Bafilomycin A1	Sigma-Aldrich	Cat#SML1661
Carfilzomib	Biovision	Cat#2385-5
Bortezomib	Merck-Millipore	Cat#CAS 179324-69-7
DARPin F10	This work	N/A
Mono ubiquitin	BostonBioChem	Cat#U-100H
His-Avi-hsHDAC6(1108-1215)	This paper	N/A
His-hsHDAC6 (1108-1215)	This paper	N/A
hsHDAC6 (1108-1215)	This paper	N/A
3C protease	This paper	FMI facility
Original DARPin proteins (A10 to H12)	This paper	Table S1
Original Nanobody (including VHH733, ZnF_97, ZnF_166, ZnF_213, ZnF_214)	This paper	N/A
Critical commercial assays
Invitrogen™ NuPAGE™ 4 to 12%, Bis-Tris, 1.5 mm, Mini Protein Gel	Invitrogen	Cat#NP0335BOX
LDS sample buffer	Invitrogen	Cat#NP0007
Ni-NTA agarose	Promega	Cat#30210
Broadford Dye	Biorad	Cat#5000006
FuGENE HD	Promega	Cat#E2311
Q5® Site-Directed Mutagenesis Kit	New England BioLabs	Cat# E0554S
FastStart Universal SYBR Green Master (Rox)	Roche	Cat# 4913850001
Reverse Transcription System	Promega	Cat#A3500
Proteinase K	Merck	Cat# 3115887001
DAPI	Invitrogen	Cat#D1306
Opti-MEM	Gibco	Cat#31985062
ProLong™ Gold Antifade Mountant	Invitrogen	Cat#P10144
Trans-Blot Turbo Transfer System	Biorad	N/A
ECL™ Detection Reagents	GE healthcare	Cat#GERPN2209
GFP_Trap M	Chromotek	Cat#Gtm-20
Dynabeads Protein G	Invitrogen	Cat#10007D
Gibbson Assembly Master Mix	NEB	Cat#E2611
RNeasy Mini Kit	QIAGEN	Cat#74104
Lenti-X™ Concentrator	Takara	Cat#631231
Nunc® Lab-Tek® Chamber Slide™ system	Millipore	Cat#C7182
HiLoad 16/600 Superdex 200pg	Sigma-Aldrich	Cat#GE28-9893-35
Superdex 200 increase 10/300 GL	Sigma-Aldrich	Cat#GE28-9909-44
Deposited data
DARPin cell line RNA sequencing	This paper	ArrayExpress E-MTAB-11101
RNA-seq of GFP-DARPin F10/CTR transfected & WT A549 cells	This paper	ArrayExpress E-MTAB-11496
DARPin F10 interactome with AP-MS	This paper	ProteomeXchange PXD031799
HDAC6 ZnF-DARPin F10 structure	This paper	PDB:7ATT
Original data	This paper	Mendeley https://doi.org/10.17632/s3xw35xczs.1
HDAC6 ZnF-Ubiquitin C-terminal peptide RLRGG structure	Ouyang et al., 2012	PDB: 3GV4
Lama VHH domain unliganded structure	Spinelli et al., 2001	PDB:1I3V
Crystal structure of a designed full consensus ankyrin	Merz et al., 2008	PDB:2QYJ
Experimental models: Cell lines
HEK 293T	ATCC	Cat#ATCC® CRL-3216
Vero	ATCC	Cat#CCL-81
A549	ATCC	Cat#ATCC® CCL-185
MDCKII	ATCC	Cat#CCL-34
Oligonucleotides
Oligonucleotide primers are listed in Table S4	This paper	N/A
Recombinant DNA
Plasmid: pOPINF-His-HDAC6(1108-1215)	This paper	N/A
Plasmid: pOPINF-His-Avi-HDAC6(1108-1215)	This paper	N/A
Plasmid: pLenti-Puro-Flag-HA-F10-FKBP12(F36V)	This paper	N/A
Plasmid: pLenti-Puro-Flag-HA-FKBP12(F36V)	This paper	N/A
Plasmid: pcDNA3.1-eGFP-DARPin E3_5/F10	This paper	N/A
Plasmid: pcDNA3.1-GFP (1-9)	This paper	N/A
Plasmid: pcDNA3.1-GFP (10)-Ub	This paper	N/A
Plasmid: pcDNA3.1-GFP (11)-ZnF	This paper	N/A
Plasmid: pcDNA3.1-HA-F10/A10	This paper	N/A
Plasmid: pcDNA3.1-GFP (11)-ZnF(W1182A)	This paper	N/A
Plasmid: pQiq_K_MRGS_His10-HA-3C-1766_F10	This paper	N/A
Plasmid: pLVX-puro-(Nb1∼4)	This paper	N/A
Plasmid: Pol-Gag	This paper	N/A
Plasmid: VSV-G	This paper	N/A
Plasmid: pet21a-BirA	This paper	N/A
Plasmid: plenti-puro-PGK-POI (GFP cleaved)	Addgene	Cat#19070
Software and algorithms
proteomicsDB	Schmidt et al., 2017	https://doi.org/10.1093/nar/gkx1029
Perseus	Max Planck Institute of Biochemistry	Version 1.5.2.6/ https://maxquant.net/perseus/
ImageJ	Schneider et al., 2012	Version 1.8.0_112/ https://imagej.nih.gov/ij/
ImageJ/Stress Granule Counter	ImageJ Plugin	https://imagej.nih.gov/ij/plugins/stress_granule_counter/index.html
Graphpad-Prism	Graphpad Software	Version 8/ https://www.graphpad.com/scientific-software/prism/
Phenix	Liebschner et al., 2019	Version 1.18/ https://www.phenix-online.org/
CCP4	Winn et al., 2011	Version 7.1/ https://www.ccp4.ac.uk/
Pymol	Schrödinger, LLC	Version 1.2r3pre/ https://pymol.org/2/
MicroCal ITC Origin Analysis software	Malvern Panalytical	Version 1.0/ https://www.malvernpanalytical.com/
Rstudio	Rstudio	Version 1.3/ https://rstudio.com/
Other
MicroCal VP-ITC	Malvern Panalytical	N/A
Spinning disk confocal scanning unit Yokogawa CSU W1 with Dual camera T2	Yokogawa	N/A
Z1 ZEISS-Wide Field Microscope	ZEISS	N/A