CRL4WDR1 ubiquitin ligase complex

cellstructuremech:crl4wdr1_ubiquitin_ligase_complex · Other · Multiprotein complex · Proposed

A WDR1-containing Cullin4-DDB1 protein complex characterized in procyclic Trypanosoma brucei. The named CRL4WDR1 association participates in regulation of TbPLK protein turnover; its complete catalytic composition and direct ubiquitination of TbPLK have not been established. [DOI:10.1371/journal.ppat.1006146]

WDR1 subunit localization and interaction assays, not a resolved image of the entire CRL4WDR1 complex. Panels E-F show procyclic T. brucei: endogenous WDR1-3HA is green; TbPLK (E) or the anti-LdCen1 marker (F) is red; DAPI is blue. WDR1 is enriched at the basal-body/bilobe region in G1/S and remains detectable at lower levels later. Scale bars, 5 micrometers. Panels A-D show constructs, yeast two-hybrid, GST/lysate pull-down and co-immunoprecipitation assays; their hosts are not additional canonical organisms. Original Figure 2, unchanged. FLUORESCENCE · *Trypanosoma brucei* (`NCBITaxon:5691`) · Huiqing Hu, Qing Zhou, Xianxian Han, Ziyin Li; CC BY, via PubMed Central · CC_BY_4_0 · source: PMC PMC5241021.1 ppat.1006146.g002 · `DOI:10.1371/journal.ppat.1006146`

Synonyms: CRL4WDR1

UniProt location names: UniProt Consortium, CC BY 4.0. Reference label and route sources.

Components

Component	Type	Part of / acts on	Grounding	Genes	Essential	Role
Cullin4 scaffold subunit	Protein	part of	Reviewed label only (reviewed name; no accession asserted)	CUL4	UNKNOWN	Defining cullin scaffold co-isolated with WDR1 and DDB1; direct contacts and copy number are unresolved. `DOI:10.1371/journal.ppat.1006146` Figure 3B-D and the complex-identification Results identify TbCUL4 as Tb927.3.1290. WDR1 immunoprecipitation from a cell line with endogenously tagged WDR1, TbCUL4 and TbDDB1 recovers both partners. Other tested cullins, including TbCUL1/Tb927.11.11430, did not co-precipitate WDR1 in that assay.
DDB1 adaptor subunit	Protein	part of	Reviewed label only (reviewed name; no accession asserted)	DDB1	UNKNOWN	Adaptor co-isolated with WDR1; a WDR1 N-terminal fragment retrieves DDB1 from cell lysate. `DOI:10.1371/journal.ppat.1006146` Figure 3C-E identifies TbDDB1 as Tb927.6.5110. The WDR1 1-300 amino-acid GST fusion pulls down tagged DDB1 from trypanosome lysate; this is not a binding experiment with two purified partners.
WDR1 substrate-recognition subunit	Protein	part of	Reviewed label only (reviewed name; no accession asserted)	WDR1	UNKNOWN	Receptor-class constituent that associates with DDB1 through its N-terminal region and recognizes TbPLK through C-terminal fragments. Its depletion slows TbPLK turnover. `DOI:10.1371/journal.ppat.1006146` Results and Figures 2-3 identify WDR1 as Tb927.10.15080. Directional yeast two-hybrid and GST/lysate pull-down support TbPLK recognition by C-terminal fragments; the PDZ domain alone is insufficient and is not required. Deleting the TbPLK PEST motif disrupts fragment-mediated association. Full-length WDR1 was not tested in yeast because cloning failed. Growth defects after RNAi do not establish essentiality for complex assembly.

Canonical examples

NCBITaxon:5691 Trypanosoma brucei — The paper studies procyclic cells: strain 29-13 for inducible RNAi and Lister 427 for endogenous tagging, with tagging also performed in RNAi lines. Two nonoverlapping WDR1 RNAi fragments and two clones per fragment were tested; the paper presents one representative clone after reporting similar phenotypes. The 927 locus identifiers are reference annotations, not the cultured strain. Yeast two-hybrid hosts and recombinant E. coli expression hosts are not canonical organisms for this complex. [DOI:10.1371/journal.ppat.1006146]

Functions

regulation of TbPLK protein turnover — WDR1 depletion slows the loss of TbPLK during a cycloheximide chase and increases its abundance in procyclic T. brucei. This supports a turnover-regulatory role for the named association, but does not establish direct covalent ubiquitination of TbPLK by a purified complex.
- DOI:10.1371/journal.ppat.1006146 Figure 6A-C measures abundance at 24/48 hours of RNAi and a 0-6-hour chase after 24 hours of induction. Figure 6D detects less polyubiquitinated material in TbPLK immunoprecipitates, but the Results explicitly leave its identity unresolved: TbPLK itself and/or associated proteins.
support of bilobe duplication and flagellum attachment — WDR1 RNAi impairs bilobe duplication, basal-body segregation and new flagellum-attachment-zone assembly, with detached flagella at 48 hours. These are perturbation-supported cellular outputs, not proof that every phenotype is mediated exclusively by direct TbPLK ubiquitination.
- DOI:10.1371/journal.ppat.1006146 Figures 4-5 show basal-body, bilobe, FAZ and attachment phenotypes after 48 hours of WDR1 RNAi. Figure 7 shows persistent phospho-Ser54 TbCentrin2 staining in late-cycle cells at 24 hours. TbPLK overexpression in S4 Figure phenocopies several effects, but is not a rescue or an epistasis test.

Mechanism graphs

Measured outputs of WDR1 depletion (FUNCTION)

Source-bounded protein and cellular readouts of a receptor-subunit intervention.

Subject	Predicate	Object	Evidence
WDR1 RNAi induction	decreases abundance of	WDR1 substrate-recognition subunit	`DOI:10.1371/journal.ppat.1006146` Figures 4A and 6A monitor tagged WDR1 protein. Figure 6A includes 24- and 48-hour induction samples; this is protein depletion, not proof of complex disassembly.
WDR1 RNAi induction	reduces	TbPLK degradation rate in chase	`DOI:10.1371/journal.ppat.1006146` Figure 6B-C: 0-6-hour chase, normalized to TbPSA6; three independent experiments. The edge is a measured turnover effect, not a direct catalytic reaction.
WDR1 RNAi induction	increases	whole-cell TbPLK abundance	`DOI:10.1371/journal.ppat.1006146` Figure 6A: anti-TbPLK immunoblot with TbPSA6 loading control; three repeats reported as similar.
WDR1 RNAi induction	decreases	polyubiquitinated material in TbPLK immunoprecipitate	`DOI:10.1371/journal.ppat.1006146` Figure 6D and accompanying Results explicitly warn that the detected polyubiquitinated proteins could include TbPLK or co-precipitated partners. No substrate identity is assigned.
WDR1 RNAi induction	yields cells retaining	late-cycle TbCentrin2 phospho-Ser54 staining	`DOI:10.1371/journal.ppat.1006146` Figure 7: PS54 detects phospho-Ser54 TbCentrin2, with 20H5 marking the bilobe. This does not directly measure kinase flux or prove the complete proposed mediation chain.
WDR1 RNAi induction	increases	flagellum detachment	`DOI:10.1371/journal.ppat.1006146` Figure 4D-E quantifies the attachment phenotype. This later readout is not treated as a direct consequence of any single 24-hour biochemical readout.

Discussions

CURATION_TODO (RESOLVED): Separate CRL4WDR1 from generic Cul4 and other DDB1 complexes. Shared cullin or receptor names do not establish equivalence.
CURATION_TODO (RESOLVED): Keep the WDR1-specific assembly distinct from Cullin-E and broader Cullin-D isolates. A scaffold identity is not the identity of all its receptor-specific complexes.
CURATION_TODO (OPEN): Resolve exact component-family mappings and studied-strain protein examples. Broad families and reference-genome annotations do not supply exact experimental examples.
CURATION_TODO (RESOLVED): Do not convert captured client proteins or experimental markers into obligatory constituents. Co-isolation and downstream readouts have different biological roles.
CURATION_TODO (OPEN): Establish the complete catalytic assembly and direct covalent substrate reaction. Co-immunoprecipitation and chase data do not identify all catalytic subunits or ubiquitinated proteins.
CURATION_TODO (OPEN): Resolve localization and architecture of the assembled CRL4WDR1 particle. Subunit immunofluorescence does not demonstrate colocalization of all constituents.

Evidence

DOI:10.1371/journal.ppat.1006146 Hu, Zhou, Han and Li; PMID:28052114. Current PMC5241021.1 JATS identity, license and checksum verified. Complex-identification, depletion, turnover and overexpression Results, Discussion and relevant Methods inspected. Native Figures 2, 3 and 6 were visually inspected with media checksums verified. Supports the named association and measured intervention outputs; the Figure 8 causal model exceeds the direct biochemical resolution.
DOI:10.1038/s41598-025-32077-9 PMID:41413177; Table 1 maps the same Tb927.3.1290 scaffold to TbCul-D, not TbCul-E. The newer scaffold-isolation study identifies additional DCAF proteins and Rbx1, without resolving their membership in the WDR1-specific assembly. Used for nomenclature and boundary comparison only.

Curation history

2026-10-04T19:38:22Z codex · CREATED_RECORD — Scaffolded by scripts/new_record.py
2026-10-04T19:40:32Z codex · CURATED_RECORD — Added three source-bounded constituent classes, verified broad Cul4 parent, procyclic Trypanosoma example, turnover and inheritance functions, nonmechanistic depletion graph, bounded native Figure 2 with verified CC BY 4.0 provenance, and explicit identity, catalytic, family and imaging limits.

Source: data/structures/other/crl4wdr1_ubiquitin_ligase_complex.yaml