REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
Rabbit polyclonal ANKRD26	GeneTex	Cat#GTX128255; RRID: AB_2885741
Rabbit polyclonal ARL13B	Proteintech	Cat#17711-1-AP; RRID: AB_2060867
Rabbit polyclonal CP110	Proteintech	Cat#12780-1-AP; RRID: AB_10638480
Rabbit polyclonal CEP164	Proteintech	Cat#22227-1-AP; RRID: AB_2651175
Mouse monoclonal CEP164	SantaCruz	Cat#sc-515403
Rabbit polyclonal CEP170	Abcam	Cat#ab72505; RRID: AB_1268101
Mouse monoclonal CNTROB	Abnova	Cat#H00116840-B01P; RRID: AB_1555868
Rabbit polyclonal FBF1	Atlas	Cat#HPA023677; RRID: AB_1848440
Rabbit polyclonal OFD1	Proteintech	Cat#22851-1-AP; RRID: AB_2879177
Mouse monoclonal γ-tubulin	Sigma	Cat#T9026; RRID: AB_477593
Rabbit polyclonal CP110	Proteintech	Cat#12780-1-AP; RRID: AB_10638480
Rabbit polyclonal CDK5RAP2	Produced in Gergely lab	N/A
Rabbit polyclonal CEP41	Bethyl	Cat#A301-798; RRID: AB_2780131
Rabbit polyclonal CEP83	Proteintech	Cat#26013-1-AP; RRID: AB_2880334
Rabbit polyclonal CEP128	Atlas	Cat#HPA001116; RRID: AB_1078323
Rabbit polyclonal CEP152	Bethyl	Cat#A302-479A; RRID: AB_1966085
Mouse monoclonal CETN3	Abnova	Cat#H00001070-M01; RRID: AB_464016
Rabbit polyclonal CRBN	Proteintech	Cat#11435-1-AP; RRID: AB_2085739
Rabbit polyclonal DDB1	Proteintech	Cat#11380-1-AP; RRID: AB_2088808
Rabbit polyclonal EDC4	Proteintech	Cat#17737-1-AP; RRID: AB_10665813
Mouse monoclonal NIN	Proteintech	Cat#67132-1-Ig; RRID: AB_2882431
Mouse monoclonal NIN	Santa Cruz	Cat#sc-376420; RRID: AB_11151570
Rabbit polyclonal NOP53	Proteintech	Cat#27353-1-AP; RRID: AB_2880852
Rabbit polyclonal PLK1	Novus	Cat#NB100-547; RRID: AB_10002724
Rabbit polyclonal PCNT	Abcam	Cat#ab4448; RRID: AB_304461
Rabbit polyclonal TRIM27	Proteintech	Cat#12205-1-AP; RRID: AB_2256660
Mouse monoclonal g-tubulin	Sigma	Cat#T6557; RRID: AB_477584
Mouse monoclonal SAS6	Santa Cruz	Cat#sc-81431; RRID: AB_1128357
Donkey polyclonal anti-Goat IgG (H+L) Cross- Adsorbed Secondary Antibody, Alexa Fluor 488	Life Technologies	Cat#A-11055; RRID: AB_2534102
Donkey polyclonal anti-Mouse IgG (H+L) Highly Cross-Adsorbed Secondary Antibody, Alexa Fluor 594	Life Technologies	Cat#A-21203; RRID: AB_141633
Polyclonal Donkey anti-Mouse IgG (H+L) Highly Cross-Adsorbed Secondary Antibody, Alexa Fluor 488	Life Technologies	Cat#A-21202; RRID: AB_141607
Donkey polyclonal anti-Rabbit IgG (H+L) Highly Cross-Adsorbed Secondary Antibody, Alexa Fluor 594	Life Technologies	Cat#A-21207; RRID: AB_141637
Donkey polyclonal anti-Mouse IgG (H+L) Highly Cross-Adsorbed Secondary Antibody, Alexa Fluor 647	Life Technologies	Cat#A-31571; RRID: AB_162542
Donkey polyclonal anti-Rabbit IgG (H+L) Highly Cross-Adsorbed Secondary Antibody, Alexa Fluor 647	Life Technologies	Cat#A-31573; RRID: AB_2536183
Amersham ECL Mouse IgG, HRP-linked whole Ab	Cytiva	Cat#NXA931-1ML; RRID: AB_772209
Donkey Anti-Rabbit IgG, Whole Ab ECL Antibody, HRP Conjugated	Cytiva	Cytiva Cat# NA934, RRID:AB_772206
Bacterial and virus strains
Escherichia coli DH5a	Thermo	EC0112
C41(DE3)	Cambridge Bioscience	60442
Chemicals, peptides, and recombinant proteins
Biotinylated CCDC61 peptide (Biotin- SPSPTGGRALRFDPTAFVKAKERKQREIQMKQQ)	Biomatik	N/A
Dynabeads™ M-280 Streptavidin	ThermoFisher Scientific	Cat# 11205D
cOmplete™, Mini, EDTA-free Protease Inhibitor Cocktail	Roche	Cat# 11836170001
10 nm gold	BBI Solutions	Cat# EM.GC10/4
5 ml HiTrap Q HP column	Cytiva	Cat# 17115401
Recombinant DNA
pLipo-3xFLAG-CCDC61 334-366	This paper	N/A
Deposited data
Proteomic dataset 1 (Tables S1, S2, S3, S4, and S5)	This paper	PRIDE: PXD040308
Proteomic dataset 2 (Table S6)	This paper	PRIDE: PXD040309
Proteomic dataset 3 (Table S5)	This paper	PRIDE: PXD043906
Proteomic dataset 4 (Table S7)	This paper	PRIDE: PXD043692
Experimental models: Cell lines
HEK293 CEP128KO	Produced in Gergely lab	N/A
HAP1 NIN-KO and CEP83-KO	Produced in van Breugel lab	N/A
Jurkat E6.1	ATCC	RRID: CVCL_0367
U2OS	ATCC	RRID: CVCL_0042
HEK293	ATCC	RRID: CVCL_0045
Raji	ATCC	RRID: CVCL_0511
HAP1	Horizon Discovery	RRID: CVCL_Y019
FS13b	Cambridge BRC hIPSCs core facility	N/A
U-251MG	ATCC	RRID: CVCL_0021
hTERT-RPE1	ATCC	RRID:CVCL_4388
Oligonucleotides
EDC4 CAGGUACAGCGCAUCGUUAtt	Ambion, Silencer Select	#1; s24265
EDC4 CCUGUUCUGUGACAACCAUtt	Ambion, Silencer Select	#2; s24266
TRIM27 CAAAAAUGUCUAUUCUUGAtt	Ambion, Silencer Select	#1; s11960
TRIM27 GCUGAACUCUUGAGCCUAAtt	Ambion, Silencer Select	#2; s11959
NOP53 GAACCAAAGUCCAGAAGAAtt	Ambion, Silencer Select	#1; s26871
NOP53 CUUCGAGACCGGUUCAAGAtt	Ambion, Silencer Select	#2; s26873
CCDC171 GGAGAAGCAUUGCGACAAAtt	Ambion, Silencer Select	#1; s47495
CCDC171 GGUCUGCAAAUGCAAUUAAtt	Ambion, Silencer Select	#2; s47493
CEP128gRNA_1 GTCGTGACCGATTGAGTCCA	Sigma-Aldrich	gRNA
CEP83 gRNA_1 GGCTGAAGTAGCGGAATTAA	Sigma-Aldrich	gRNA
CEP83 gRNA 2 TAATTTACGGGCAGAACGTT	Sigma-Aldrich	gRNA
Ninein gRNA 1 CTGGAAGACGCAACGCAGTG	Sigma-Aldrich	gRNA
CEP83_clone1_forward CCTTGTATGCTTTCTTTAAA ATTATTATTAGATTGCAAGACTGGAGGAAGATAAAG	Sigma-Aldrich	primer
CEP83_clone1_reverse GCTTGGGGGGCATACA TTTATGCTCTAAAAATCAAAGGCTTGTC	Sigma-Aldrich	primer
CEP83_clone2_forward GAAAAATGATGAATTTTAAA CTATTTTGTTTGTATGAAAGGCTGAAAAACAATC	Sigma-Aldrich	primer
CEP83_clone2_reverse CTAAAGAATGAAACAGAAAC ATAAAACAACTTACTTTACTGGACAATGTATTTATTTCTCG	Sigma-Aldrich	primer
Ninein_forward GCACACTAATCTTCTCTTGCCTTCT CTAGCACTG	Sigma-Aldrich	primer
Ninein_reverse CTTCCAGGCACGTCCTGACACACTC	Sigma-Aldrich	primer
CEP128_forward 1 CTGTGTGGCCTTTACCTGTG	Sigma-Aldrich	primer
CEP128_reverse 1 TTGAGACCCAGTGAGACCAG	Sigma-Aldrich	primer
CEP128_forward 2 AGCAGAGACAATGGAGGAGG	Sigma-Aldrich	primer
CEP128_reverse 2 GGCAGCCTCTAGAAACCAGA	Sigma-Aldrich	primer
Softwares and algorithms
Prism v9.5.1	Graphpad Software LLC	N/A
Chromagnon091Mac	https://doi.org/10.1038/nprot.2017.020 67	N/A
ImageJ 2.9.0/1.53t	https://imagej.net/downloads	N/A
SerialEM	https://doi.org/10.1016/j.jsb.2005.07.007 70	N/A
IMOD	https://doi.org/10.1006/jsbi.1996.0013 71	N/A
NovaCTF	https://doi.org/10.1016/j.jsb.2017.07.007 72	N/A
Others
Carbon Film 400 Mesh, Cu	Electron Microscopy Sciences	Cat# CF400-Cu-50
Quantifoil™ R 2/1 on 200 copper mesh	Quantifoil	Cat# X-102-Cu200