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- PDB-6v9i: cryo-EM structure of Cullin5 bound to RING-box protein 2 (Cul5-Rbx2) -

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Basic information

Entry
Database: PDB / ID: 6v9i
Titlecryo-EM structure of Cullin5 bound to RING-box protein 2 (Cul5-Rbx2)
Components
  • Immunoglobulin G-binding protein G,Cullin-5
  • RING-box protein 2
KeywordsLIGASE / E3 Ubiquitin Ligase / RING-box protein
Function / homology
Function and homology information


radial glia guided migration of Purkinje cell / Inactivation of CSF3 (G-CSF) signaling / cerebral cortex radially oriented cell migration / ERBB2 signaling pathway / Neddylation / reelin-mediated signaling pathway / cullin-RING-type E3 NEDD8 transferase / regulation of neuron migration / protein K11-linked ubiquitination / Antigen processing: Ubiquitination & Proteasome degradation ...radial glia guided migration of Purkinje cell / Inactivation of CSF3 (G-CSF) signaling / cerebral cortex radially oriented cell migration / ERBB2 signaling pathway / Neddylation / reelin-mediated signaling pathway / cullin-RING-type E3 NEDD8 transferase / regulation of neuron migration / protein K11-linked ubiquitination / Antigen processing: Ubiquitination & Proteasome degradation / protein neddylation / NEDD8 ligase activity / IgG binding / intrinsic apoptotic signaling pathway in response to oxidative stress / Cul5-RING ubiquitin ligase complex / SCF ubiquitin ligase complex / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / ubiquitin ligase complex scaffold activity / apoptotic mitochondrial changes / site of DNA damage / cullin family protein binding / intrinsic apoptotic signaling pathway / G1/S transition of mitotic cell cycle / Vif-mediated degradation of APOBEC3G / Inactivation of CSF3 (G-CSF) signaling / RING-type E3 ubiquitin transferase / Evasion by RSV of host interferon responses / calcium channel activity / Downregulation of ERBB2 signaling / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation / signaling receptor activity / Neddylation / protein-macromolecule adaptor activity / proteasome-mediated ubiquitin-dependent protein catabolic process / protein ubiquitination / ubiquitin protein ligase binding / negative regulation of apoptotic process / extracellular region / zinc ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
IgG-binding B / B domain / M protein-type anchor domain / GA-like domain / GA-like domain / Zinc finger, RING-H2-type / RING-H2 zinc finger domain / Cullin protein neddylation domain / : / Cullin, conserved site ...IgG-binding B / B domain / M protein-type anchor domain / GA-like domain / GA-like domain / 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 / Immunoglobulin/albumin-binding domain superfamily / Cullin / Cullin, N-terminal / Cullin homology domain / Cullin homology domain superfamily / Cullin alpha solenoid domain / Cullin family profile. / YSIRK Gram-positive signal peptide / LPXTG cell wall anchor motif / Gram-positive cocci surface proteins LPxTG motif profile. / LPXTG cell wall anchor domain / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, RING/FYVE/PHD-type / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
Immunoglobulin G-binding protein G / Cullin-5 / RING-box protein 2
Similarity search - Component
Biological speciesStreptococcus sp. group G (bacteria)
Homo sapiens (human)
Mus musculus (house mouse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 5.2 Å
AuthorsKomives, E.A. / Lumpkin, R.J. / Baker, R.W. / Leschziner, A.E.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)1817774 United States
CitationJournal: Nat Commun / Year: 2020
Title: Structure and dynamics of the ASB9 CUL-RING E3 Ligase.
Authors: Ryan J Lumpkin / Richard W Baker / Andres E Leschziner / Elizabeth A Komives /
Abstract: The Cullin 5 (CUL5) Ring E3 ligase uses adaptors Elongins B and C (ELOB/C) to bind different SOCS-box-containing substrate receptors, determining the substrate specificity of the ligase. The 18- ...The Cullin 5 (CUL5) Ring E3 ligase uses adaptors Elongins B and C (ELOB/C) to bind different SOCS-box-containing substrate receptors, determining the substrate specificity of the ligase. The 18-member ankyrin and SOCS box (ASB) family is the largest substrate receptor family. Here we report cryo-EM data for the substrate, creatine kinase (CKB) bound to ASB9-ELOB/C, and for full-length CUL5 bound to the RING protein, RBX2, which binds various E2s. To date, no full structures are available either for a substrate-bound ASB nor for CUL5. Hydrogen-deuterium exchange (HDX-MS) mapped onto a full structural model of the ligase revealed long-range allostery extending from the substrate through CUL5. We propose a revised allosteric mechanism for how CUL-E3 ligases function. ASB9 and CUL5 behave as rigid rods, connected through a hinge provided by ELOB/C transmitting long-range allosteric crosstalk from the substrate through CUL5 to the RBX2 flexible linker.
History
DepositionDec 13, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 29, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 11, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / em_admin / pdbx_entry_details / pdbx_initial_refinement_model / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _em_admin.last_update / _pdbx_entry_details.has_protein_modification

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Structure visualization

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Assembly

Deposited unit
C: Immunoglobulin G-binding protein G,Cullin-5
R: RING-box protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,3745
Polymers113,1782
Non-polymers1963
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Antibody Immunoglobulin G-binding protein G,Cullin-5 / IgG-binding protein G / CUL-5 / Vasopressin-activated calcium-mobilizing receptor 1 / VACM-1


Mass: 100456.500 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus sp. group G (bacteria), (gene. exp.) Homo sapiens (human)
Gene: spg, CUL5, VACM1 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P06654, UniProt: Q93034
#2: Protein RING-box protein 2 / Rbx2 / RING finger protein 7 / Sensitive to apoptosis gene protein


Mass: 12721.500 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Rnf7, Rbx2, Sag / Production host: Escherichia coli (E. coli) / References: UniProt: Q9WTZ1
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
Has ligand of interestN
Has protein modificationY

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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: cryo-EM structure of Cullin5 bound to RING-box protein 2 (Cul5-Rbx2)
Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Molecular weightValue: 0.1 MDa / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli (E. coli) / Strain: BL21
Buffer solutionpH: 7.5
SpecimenConc.: 0.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: UltrAuFoil
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K / Details: 4 second blot time, blot force 20

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 36000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 1200 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN
Image recordingAverage exposure time: 8 sec. / Electron dose: 59 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM software
IDNameVersionCategory
2Leginon3.3image acquisition
4CTFFIND4CTF correction
7UCSF Chimeramodel fitting
9Rosettamodel refinement
13cryoSPARC23D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 5.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 46877 / Details: Non-uniform refinement in cryoSPARC v2 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Atomic model building
IDPDB-ID 3D fitting-IDAccession codeInitial refinement model-IDSource nameType
14JGH

4jgh

14JGH1PDBexperimental model
23DPL

3dpl

13DPL2PDBexperimental model

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