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- PDB-9pvh: Human Cullin-4 in complex with CAND2 -

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Basic information

Entry
Database: PDB / ID: 9pvh
TitleHuman Cullin-4 in complex with CAND2
Components
  • Cullin-4A
  • Cullin-associated NEDD8-dissociated protein 2
KeywordsLIGASE / Complex
Function / homology
Function and homology information


SCF complex assembly / regulation of mitotic cytokinesis / regulation of miRNA-mediated gene silencing / regulation of cell cycle phase transition / regulation of stem cell population maintenance / regulation of natural killer cell activation / negative regulation of adipose tissue development / regulation of cellular response to stress / regulation of DNA-templated DNA replication initiation / ubiquitin-dependent protein catabolic process via the C-end degron rule pathway ...SCF complex assembly / regulation of mitotic cytokinesis / regulation of miRNA-mediated gene silencing / regulation of cell cycle phase transition / regulation of stem cell population maintenance / regulation of natural killer cell activation / negative regulation of adipose tissue development / regulation of cellular response to stress / regulation of DNA-templated DNA replication initiation / ubiquitin-dependent protein catabolic process via the C-end degron rule pathway / Cul4A-RING E3 ubiquitin ligase complex / Cul4-RING E3 ubiquitin ligase complex / ubiquitin ligase complex scaffold activity / replication fork processing / regulation of embryonic development / intrinsic apoptotic signaling pathway / epigenetic regulation of gene expression / TBP-class protein binding / regulation of autophagy / T cell activation / G1/S transition of mitotic cell cycle / nucleotide-excision repair / cell population proliferation / Recognition of DNA damage by PCNA-containing replication complex / DNA Damage Recognition in GG-NER / Dual Incision in GG-NER / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / in utero embryonic development / Formation of TC-NER Pre-Incision Complex / Formation of Incision Complex in GG-NER / positive regulation of protein catabolic process / cellular response to UV / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / ubiquitin protein ligase activity / regulation of cell population proliferation / rhythmic process / Neddylation / ribosome biogenesis / spermatogenesis / regulation of apoptotic process / proteasome-mediated ubiquitin-dependent protein catabolic process / protein ubiquitination / ubiquitin protein ligase binding / DNA damage response / positive regulation of DNA-templated transcription / DNA-templated transcription / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
TATA-binding protein interacting (TIP20) / Cullin-associated NEDD8-dissociated protein 1/2 / TATA-binding protein interacting (TIP20) / CAND1-like, TPR repeats / HEAT-like repeat / Cullin protein neddylation domain / Cullin, conserved site / Cullin family signature. / Cullin, N-terminal / Cullin repeat-like-containing domain superfamily ...TATA-binding protein interacting (TIP20) / Cullin-associated NEDD8-dissociated protein 1/2 / TATA-binding protein interacting (TIP20) / CAND1-like, TPR repeats / HEAT-like repeat / Cullin protein neddylation domain / Cullin, conserved site / Cullin family signature. / Cullin, N-terminal / Cullin repeat-like-containing domain superfamily / Cullin protein, neddylation domain / Cullin / Cullin protein neddylation domain / Cullin alpha solenoid domain / Cullin / : / Cullin alpha+beta domain / Cullin homology domain / Cullin homology domain superfamily / Cullin family profile. / Armadillo-like helical / Armadillo-type fold / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
Cullin-associated NEDD8-dissociated protein 2 / Cullin-4A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.38 Å
AuthorsKenny, S. / Liu, X. / Das, C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM138016 United States
CitationJournal: Structure / Year: 2026
Title: CAND1 and CAND2 drive CUL4 substrate receptor exchange with largely comparable biochemical efficiency, unlike their relative effects on CUL1.
Authors: Kankan Wang / Sebastian Kenny / Zhana Chagan / Lihong Li / Chittaranjan Das / Xing Liu /
Abstract: Cullin-RING ubiquitin ligases (CRLs) regulate diverse cellular processes by dynamically recruiting substrate receptors onto conserved cullin-RING scaffolds. CAND1 and CAND2 function as substrate ...Cullin-RING ubiquitin ligases (CRLs) regulate diverse cellular processes by dynamically recruiting substrate receptors onto conserved cullin-RING scaffolds. CAND1 and CAND2 function as substrate receptor exchange factors for CRL1, but CAND2 displays reduced efficiency in CRL1 disassembly, exhibits tissue-specific expression, and shows distinct disease associations, raising questions about its function in other CRL subfamilies. Here, we define the regulatory roles of CAND1 and CAND2 in CRL4 remodeling. Using genetic perturbation, real-time kinetic analyses, and quantitative interaction proteomics, we show that both CAND proteins promote CRL4-mediated protein degradation and enhance the dynamic exchange of DDB1·DCAF substrate receptor modules, likely through conserved yet distinct structural features. In contrast to their differential efficiencies in CRL1 disassembly, CAND1 and CAND2 exhibit similar kinetic parameters and comparable exchange efficiencies across most of the CRL4 complexes. These findings establish CAND1 and CAND2 as bona fide CRL4 exchange factors and reveal biochemical distinctions between CRL4 and CRL1 regulation.
History
DepositionAug 1, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 10, 2026Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Jun 17, 2026Group: Data collection / Database references / Category: citation / em_admin
Item: _citation.journal_volume / _citation.page_first / _em_admin.last_update
Revision 1.1Jun 17, 2026Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Database references / Experimental summary / Data content type: EM metadata / EM metadata / Category: citation / em_admin / Data content type: EM metadata / EM metadata / EM metadata
Item: _citation.journal_volume / _citation.page_first / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cullin-4A
C: Cullin-associated NEDD8-dissociated protein 2


Theoretical massNumber of molelcules
Total (without water)221,2622
Polymers221,2622
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Cullin-4A / CUL-4A


Mass: 84592.531 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CUL4A / Production host: Escherichia coli (E. coli) / References: UniProt: Q13619
#2: Protein Cullin-associated NEDD8-dissociated protein 2 / Cullin-associated and neddylation-dissociated protein 2 / Epididymis tissue protein Li 169 / TBP- ...Cullin-associated and neddylation-dissociated protein 2 / Epididymis tissue protein Li 169 / TBP-interacting protein of 120 kDa B / TBP-interacting protein 120B / p120 CAND2


Mass: 136669.500 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CAND2, KIAA0667, TIP120B / Production host: Escherichia coli (E. coli) / References: UniProt: O75155
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: CAND2-CUL4 / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK II / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm
Image recordingAverage exposure time: 3.19 sec. / Electron dose: 1.52 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 5666
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV

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Processing

EM software
IDNameVersionCategory
1cryoSPARC3.2.0particle selection
4cryoSPARC3.2.0CTF correction
7Coot0.8.9.2model fitting
9PHENIX1.19.2_4158model refinement
10cryoSPARC3.2.0initial Euler assignment
11cryoSPARC3.2.0final Euler assignment
12cryoSPARC3.2.0classification
13cryoSPARC3.2.03D reconstruction
CTF correctionType: NONE
Particle selectionNum. of particles selected: 3883614
3D reconstructionResolution: 4.38 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 46496 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL / Target criteria: Cross-correlation coefficient
Atomic model buildingSource name: AlphaFold / Type: in silico model
RefinementHighest resolution: 4.38 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00314829
ELECTRON MICROSCOPYf_angle_d0.65820045
ELECTRON MICROSCOPYf_dihedral_angle_d4.4621999
ELECTRON MICROSCOPYf_chiral_restr0.0412333
ELECTRON MICROSCOPYf_plane_restr0.0052585

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