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- PDB-7z8r: CAND1-CUL1-RBX1 -

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Basic information

Entry
Database: PDB / ID: 7z8r
TitleCAND1-CUL1-RBX1
Components
  • Cullin-1
  • Cullin-associated NEDD8-dissociated protein 1
  • E3 ubiquitin-protein ligase RBX1, N-terminally processed
KeywordsLIGASE / cullin-RING E3 ubiquitin ligase / Assembly factor / CAND1
Function / homology
Function and homology information


SCF complex assembly / Parkin-FBXW7-Cul1 ubiquitin ligase complex / negative regulation of catalytic activity / cullin-RING-type E3 NEDD8 transferase / NEDD8 transferase activity / cullin-RING ubiquitin ligase complex / cellular response to chemical stress / Cul7-RING ubiquitin ligase complex / ubiquitin-dependent protein catabolic process via the C-end degron rule pathway / Loss of Function of FBXW7 in Cancer and NOTCH1 Signaling ...SCF complex assembly / Parkin-FBXW7-Cul1 ubiquitin ligase complex / negative regulation of catalytic activity / cullin-RING-type E3 NEDD8 transferase / NEDD8 transferase activity / cullin-RING ubiquitin ligase complex / cellular response to chemical stress / Cul7-RING ubiquitin ligase complex / ubiquitin-dependent protein catabolic process via the C-end degron rule pathway / Loss of Function of FBXW7 in Cancer and NOTCH1 Signaling / positive regulation of protein autoubiquitination / RNA polymerase II transcription initiation surveillance / protein neddylation / NEDD8 ligase activity / VCB complex / negative regulation of response to oxidative stress / Cul5-RING ubiquitin ligase complex / SCF ubiquitin ligase complex / Cul2-RING ubiquitin ligase complex / negative regulation of type I interferon production / ubiquitin-ubiquitin ligase activity / Cul4A-RING E3 ubiquitin ligase complex / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / Cul4-RING E3 ubiquitin ligase complex / Cul3-RING ubiquitin ligase complex / Cul4B-RING E3 ubiquitin ligase complex / ubiquitin ligase complex scaffold activity / negative regulation of mitophagy / Prolactin receptor signaling / cullin family protein binding / positive regulation of RNA polymerase II transcription preinitiation complex assembly / protein monoubiquitination / ubiquitin ligase complex / protein K48-linked ubiquitination / Nuclear events stimulated by ALK signaling in cancer / Regulation of BACH1 activity / MAP3K8 (TPL2)-dependent MAPK1/3 activation / transcription-coupled nucleotide-excision repair / regulation of cellular response to insulin stimulus / positive regulation of TORC1 signaling / post-translational protein modification / intrinsic apoptotic signaling pathway / negative regulation of insulin receptor signaling pathway / NIK-->noncanonical NF-kB signaling / SCF-beta-TrCP mediated degradation of Emi1 / TBP-class protein binding / T cell activation / Degradation of DVL / Dectin-1 mediated noncanonical NF-kB signaling / animal organ morphogenesis / Iron uptake and transport / Activation of NF-kappaB in B cells / Recognition of DNA damage by PCNA-containing replication complex / Degradation of GLI1 by the proteasome / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / Negative regulation of NOTCH4 signaling / Vif-mediated degradation of APOBEC3G / Hedgehog 'on' state / Degradation of GLI2 by the proteasome / GLI3 is processed to GLI3R by the proteasome / DNA Damage Recognition in GG-NER / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / cellular response to amino acid stimulus / Degradation of beta-catenin by the destruction complex / Evasion by RSV of host interferon responses / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / NOTCH1 Intracellular Domain Regulates Transcription / Dual Incision in GG-NER / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / Formation of TC-NER Pre-Incision Complex / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / G1/S transition of mitotic cell cycle / CLEC7A (Dectin-1) signaling / SCF(Skp2)-mediated degradation of p27/p21 / negative regulation of canonical Wnt signaling pathway / Formation of Incision Complex in GG-NER / Regulation of expression of SLITs and ROBOs / FCERI mediated NF-kB activation / RING-type E3 ubiquitin transferase / Interleukin-1 signaling / Orc1 removal from chromatin / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / Regulation of RAS by GAPs / Cyclin D associated events in G1 / Regulation of RUNX2 expression and activity / KEAP1-NFE2L2 pathway / : / protein polyubiquitination / Regulation of PLK1 Activity at G2/M Transition / positive regulation of protein catabolic process / Downstream TCR signaling / Antigen processing: Ubiquitination & Proteasome degradation / cellular response to UV / ubiquitin protein ligase activity / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / Neddylation / MAPK cascade / cellular response to oxidative stress
Similarity search - Function
Ring Box Chain A; domain 5 / Ring Box Chain A; domain 5 / TATA-binding protein interacting (TIP20) / Cullin-associated NEDD8-dissociated protein 1/2 / TATA-binding protein interacting (TIP20) / HEAT-like repeat / Zinc finger, RING-H2-type / RING-H2 zinc finger domain / Cullin protein neddylation domain / : ...Ring Box Chain A; domain 5 / Ring Box Chain A; domain 5 / TATA-binding protein interacting (TIP20) / Cullin-associated NEDD8-dissociated protein 1/2 / TATA-binding protein interacting (TIP20) / HEAT-like repeat / Zinc finger, RING-H2-type / RING-H2 zinc finger domain / Cullin protein neddylation domain / : / Cullin, conserved site / Cullin family signature. / Cullin repeat-like-containing domain superfamily / Cullin protein, neddylation domain / Cullin / Cullin protein neddylation domain / Cullin / Cullin, N-terminal / Cullin homology domain / Cullin homology domain superfamily / Cullin family / Cullin family profile. / Zinc finger RING-type profile. / Zinc finger, RING-type / Few Secondary Structures / Irregular / Armadillo-like helical / Armadillo-type fold / Zinc finger, RING/FYVE/PHD-type / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
E3 ubiquitin-protein ligase RBX1 / Cullin-1 / Cullin-associated NEDD8-dissociated protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsBaek, K. / Schulman, B.A.
Funding support Germany, European Union, 2items
OrganizationGrant numberCountry
Max Planck Society Germany
European Research Council (ERC)789016European Union
CitationJournal: Cell / Year: 2023
Title: Systemwide disassembly and assembly of SCF ubiquitin ligase complexes.
Authors: Kheewoong Baek / Daniel C Scott / Lukas T Henneberg / Moeko T King / Matthias Mann / Brenda A Schulman /
Abstract: Cells respond to environmental cues by remodeling their inventories of multiprotein complexes. Cellular repertoires of SCF (SKP1-CUL1-F box protein) ubiquitin ligase complexes, which mediate much ...Cells respond to environmental cues by remodeling their inventories of multiprotein complexes. Cellular repertoires of SCF (SKP1-CUL1-F box protein) ubiquitin ligase complexes, which mediate much protein degradation, require CAND1 to distribute the limiting CUL1 subunit across the family of ∼70 different F box proteins. Yet, how a single factor coordinately assembles numerous distinct multiprotein complexes remains unknown. We obtained cryo-EM structures of CAND1-bound SCF complexes in multiple states and correlated mutational effects on structures, biochemistry, and cellular assays. The data suggest that CAND1 clasps idling catalytic domains of an inactive SCF, rolls around, and allosterically rocks and destabilizes the SCF. New SCF production proceeds in reverse, through SKP1-F box allosterically destabilizing CAND1. The CAND1-SCF conformational ensemble recycles CUL1 from inactive complexes, fueling mixing and matching of SCF parts for E3 activation in response to substrate availability. Our data reveal biogenesis of a predominant family of E3 ligases, and the molecular basis for systemwide multiprotein complex assembly.
History
DepositionMar 18, 2022Deposition site: PDBE / Processing site: PDBE
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Revision 1.1May 10, 2023Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Cullin-1
D: Cullin-associated NEDD8-dissociated protein 1
R: E3 ubiquitin-protein ligase RBX1, N-terminally processed
hetero molecules


Theoretical massNumber of molelcules
Total (without water)239,4736
Polymers239,2763
Non-polymers1963
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area11060 Å2
ΔGint-43 kcal/mol
Surface area87650 Å2
MethodPISA

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Components

#1: Protein Cullin-1 / CUL-1


Mass: 89800.367 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CUL1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q13616
#2: Protein Cullin-associated NEDD8-dissociated protein 1 / Cullin-associated and neddylation-dissociated protein 1 / TBP-interacting protein of 120 kDa A / ...Cullin-associated and neddylation-dissociated protein 1 / TBP-interacting protein of 120 kDa A / TBP-interacting protein 120A / p120 CAND1


Mass: 137386.281 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CAND1, KIAA0829, TIP120, TIP120A / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q86VP6
#3: Protein E3 ubiquitin-protein ligase RBX1, N-terminally processed / E3 ubiquitin-protein transferase RBX1 / N-terminally processed


Mass: 12089.677 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RBX1, RNF75, ROC1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P62877
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
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: CAND1-CUL1-RBX1 / Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
SpecimenConc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.19.2_4158: / Classification: refinement
EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 351565 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00215377
ELECTRON MICROSCOPYf_angle_d0.50920849
ELECTRON MICROSCOPYf_dihedral_angle_d3.4772085
ELECTRON MICROSCOPYf_chiral_restr0.0382493
ELECTRON MICROSCOPYf_plane_restr0.0042631

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