EMDB-18218: Structure of CUL9-RBX1 ubiquitin E3 ligase complex in unneddylate...

Basic information

Entry

Database: EMDB / ID: EMD-18218

• Title: Structure of CUL9-RBX1 ubiquitin E3 ligase complex in unneddylated and neddylated conformation - focused dimeric core
• Map data: deepEMhancer map

Sample

• Complex: Structure of CUL9-RBX1 ubiquitin E3 ligase complex in unneddylated and neddylated conformation - focused dimeric core
  • Protein or peptide: Cullin-9
  • Protein or peptide: E3 ubiquitin-protein ligase RBX1

• Keywords: Cullin-RING RBR E3 Ligase / LIGASE

Function / homology

Function:

negative regulation of beige fat cell differentiation / cullin-RING-type E3 NEDD8 transferase / NEDD8 transferase activity / cullin-RING ubiquitin ligase complex / negative regulation of mitophagy / regulation of xenophagy / cellular response to chemical stress / Loss of Function of FBXW7 in Cancer and NOTCH1 Signaling / Cul7-RING ubiquitin ligase complex / regulation of cell cycle process / neural crest cell differentiation / RNA polymerase II transcription initiation surveillance / positive regulation of protein autoubiquitination / protein neddylation / regulation of BMP signaling pathway / NEDD8 ligase activity / regulation of mitophagy / negative regulation of response to oxidative stress / regulation of centrosome duplication / regulation of mitotic nuclear division / protein K27-linked ubiquitination / positive regulation of cilium assembly / Cul5-RING ubiquitin ligase complex / ubiquitin-ubiquitin ligase activity / regulation of TOR signaling / ubiquitin-dependent protein catabolic process via the C-end degron rule pathway / Cul2-RING ubiquitin ligase complex / negative regulation of DNA-templated DNA replication / SCF ubiquitin ligase complex / regulation of DNA damage checkpoint / regulation of mitotic cytokinesis / negative regulation of type I interferon production / Cul3-RING ubiquitin ligase complex / regulation of miRNA-mediated gene silencing / regulation of natural killer cell activation / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / Prolactin receptor signaling / nucleotide-excision repair complex / regulation of cell cycle phase transition / Cul4-RING E3 ubiquitin ligase complex / regulation of stem cell population maintenance / Cul4A-RING E3 ubiquitin ligase complex / ubiquitin ligase complex scaffold activity / negative regulation of adipose tissue development / Cul4B-RING E3 ubiquitin ligase complex / regulation of cellular response to stress / limb development / protein monoubiquitination / cullin family protein binding / centrosome duplication / regulation of DNA-templated DNA replication initiation / cilium assembly / ribosome-associated ubiquitin-dependent protein catabolic process / signal transduction in response to DNA damage / negative regulation of insulin receptor signaling pathway / protein K63-linked ubiquitination / Nuclear events stimulated by ALK signaling in cancer / regulation of cellular response to insulin stimulus / protein K48-linked ubiquitination / transcription-coupled nucleotide-excision repair / post-translational protein modification / positive regulation of TORC1 signaling / regulation of embryonic development / replication fork processing / cellular response to amino acid stimulus / regulation of mitotic cell cycle / negative regulation of canonical NF-kappaB signal transduction / site of DNA damage / negative regulation of canonical Wnt signaling pathway / Regulation of BACH1 activity / T cell activation / negative regulation of smoothened signaling pathway / G1/S transition of mitotic cell cycle / protein processing / epigenetic regulation of gene expression / microtubule cytoskeleton organization / Degradation of DVL / Degradation of CRY and PER proteins / nucleotide-excision repair / regulation of autophagy / Degradation of GLI1 by the proteasome / Recognition of DNA damage by PCNA-containing replication complex / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / Negative regulation of NOTCH4 signaling / RING-type E3 ubiquitin transferase / Hedgehog 'on' state / Vif-mediated degradation of APOBEC3G / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / Degradation of GLI2 by the proteasome / GLI3 is processed to GLI3R by the proteasome / GSK3B-mediated proteasomal degradation of PD-L1(CD274) / Evasion by RSV of host interferon responses / NOTCH1 Intracellular Domain Regulates Transcription / regulation of circadian rhythm / Degradation of beta-catenin by the destruction complex / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / DNA Damage Recognition in GG-NER / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / cell population proliferation

Domain/homology:

: / : / : / : / : / : / CUL7/CUL9, N-terminal beta-barrel domain / CUL7/CUL9 ARM repeat domain / Cullin-9-like, TPR repeats / E3 ubiquitin-protein ligase ARIH2, N-terminal UBA domain / CPH domain / Mouse development and cellular proliferation protein Cullin-7 / CPH (CUL7, PARC, and HERC2) domain profile. / IBR domain, a half RING-finger domain / IBR domain / APC10/DOC domain / Anaphase-promoting complex, subunit 10 (APC10) / DOC domain profile. / Anaphase-promoting complex, subunit 10 (APC10) / IBR domain / In Between Ring fingers / TRIAD supradomain / TRIAD supradomain profile. / Zinc finger, RING-H2-type / RING-H2 zinc finger domain / : / Cullin, conserved site / Cullin family signature. / Cullin, N-terminal / Cullin protein, neddylation domain / Cullin / Cullin protein neddylation domain / Cullin alpha solenoid domain / : / Cullin alpha+beta domain / Cullin homology domain / Cullin homology domain superfamily / Cullin family profile. / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Galactose-binding-like domain superfamily / Zinc finger RING-type profile. / Zinc finger, RING-type / Armadillo-like helical / Zinc finger, RING/FYVE/PHD-type / Armadillo-type fold / Ribosomal protein L2, domain 2 / Winged helix-like DNA-binding domain superfamily

Component:

E3 ubiquitin-protein ligase RBX1 / Cullin-9

• Biological species: Homo sapiens (human)
• Method: single particle reconstruction / cryo EM / Resolution: 3.5 Å
• Authors: Hopf LVM / Horn-Ghetko D / Schulman BA

Funding support

European Union, Germany, 2 items

Organization	Grant number	Country
European Research Council (ERC)	789016	European Union
Max Planck Society		Germany

• Citation: Journal: Nat Struct Mol Biol / Year: 2024; Title: Noncanonical assembly, neddylation and chimeric cullin-RING/RBR ubiquitylation by the 1.8 MDa CUL9 E3 ligase complex.; Authors: Daniel Horn-Ghetko / Linus V M Hopf / Ishita Tripathi-Giesgen / Jiale Du / Sebastian Kostrhon / D Tung Vu / Viola Beier / Barbara Steigenberger / J Rajan Prabu / Luca Stier / Elias M Bruss / Matthias Mann / Yue Xiong / Brenda A Schulman / ; Abstract: Ubiquitin ligation is typically executed by hallmark E3 catalytic domains. Two such domains, 'cullin-RING' and 'RBR', are individually found in several hundred human E3 ligases, and collaborate with E2 enzymes to catalyze ubiquitylation. However, the vertebrate-specific CUL9 complex with RBX1 (also called ROC1), of interest due to its tumor suppressive interaction with TP53, uniquely encompasses both cullin-RING and RBR domains. Here, cryo-EM, biochemistry and cellular assays elucidate a 1.8-MDa hexameric human CUL9-RBX1 assembly. Within one dimeric subcomplex, an E2-bound RBR domain is activated by neddylation of its own cullin domain and positioning from the adjacent CUL9-RBX1 in trans. Our data show CUL9 as unique among RBX1-bound cullins in dependence on the metazoan-specific UBE2F neddylation enzyme, while the RBR domain protects it from deneddylation. Substrates are recruited to various upstream domains, while ubiquitylation relies on both CUL9's neddylated cullin and RBR domains achieving self-assembled and chimeric cullin-RING/RBR E3 ligase activity.

History

Deposition	Aug 16, 2023	-
Header (metadata) release	Apr 17, 2024	-
Map release	Apr 17, 2024	-
Update	Jul 31, 2024	-
Current status	Jul 31, 2024	Processing site: PDBe / Status: Released

Map

• File: Download / File: emd_18218.map.gz / Format: CCP4 / Size: 488.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
• Annotation: deepEMhancer map
• Voxel size: X=Y=Z: 0.8512 Å

Density

Contour Level	By AUTHOR: 0.0564
Minimum - Maximum	-0.0017764473 - 2.011857
Average (Standard dev.)	0.00054702564 (±0.01617327)

• Symmetry: Space group: 1

Details

EMDB XML:

Map geometry	Axis order X Y Z Origin 0 0 0 Dimensions 504 504 504 Spacing 504 504 504
Cell	A=B=C: 429.0048 Å α=β=γ: 90.0 °

Supplemental data

Mask #1

• File: emd_18218_msk_1.map

Additional map: Relion postprocess map

• File: emd_18218_additional_1.map
• Annotation: Relion postprocess map

Half map: #2

• File: emd_18218_half_map_1.map

Half map: #1

• File: emd_18218_half_map_2.map

Sample components

Entire : Structure of CUL9-RBX1 ubiquitin E3 ligase complex in unneddylate...

• Entire: Name: Structure of CUL9-RBX1 ubiquitin E3 ligase complex in unneddylated and neddylated conformation - focused dimeric core

Components

• Complex: Structure of CUL9-RBX1 ubiquitin E3 ligase complex in unneddylated and neddylated conformation - focused dimeric core
  • Protein or peptide: Cullin-9
  • Protein or peptide: E3 ubiquitin-protein ligase RBX1

Supramolecule #1: Structure of CUL9-RBX1 ubiquitin E3 ligase complex in unneddylate...

• Supramolecule: Name: Structure of CUL9-RBX1 ubiquitin E3 ligase complex in unneddylated and neddylated conformation - focused dimeric core; type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
• Source (natural): Organism: Homo sapiens (human)

Macromolecule #1: Cullin-9

• Macromolecule: Name: Cullin-9 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
• Source (natural): Organism: Homo sapiens (human)
• Recombinant expression: Organism: Homo sapiens (human)

Sequence

String:

MVGERHAGDL MVPLGPRLQA YPEELIRQRP GHDGHPEYLI RWSVLKCGEV GKVGVEEGKA EHILMWLSAP EVYANCPGLL GERALSKGL QHEPAGVSGS FPRDPGGLDE VAMGEMEADV QALVRRAARQ LAESGTPSLT AAVLHTIHVL SAYASIGPLT G VFRETGAL DLLMHMLCNP EPQIRRSAGK MLQALAAHDA GSRAHVLLSL SQQDGIEQHM DFDSRYTLLE LFAETTSSEE HC MAFEGIH LPQIPGKLLF SLVKRYLCVT SLLDQLNSSP ELGAGDQSSP CATREKSRGQ RELEFSMAVG NLISELVRSM GWA RNLSEQ GMSPPRPTRS IFQPYISGPS LLLPTIVTTP RRQGWVFRQR SEFSSRSGYG EYVQQTLQPG MRVRMLDDYE EISA GDEGE FRQSNNGIPP VQVFWQSTGR TYWVHWHMLE ILGPEEATED KASAAVEKGA GATVLGTAFP SWDWNPMDGL YPLPY LQPE PQKNERVGYL TQAEWWELLF FIKKLDLCEQ QPIFQNLWKN LDETLGEKAL GEISVSVEMA ESLLQVLSSR FEGSTL NDL LNSQIYTKYG LLSNEPSSSS TSRNHSCTPD PEEESKSEAS FSEEETESLK AKAEAPKTEA EPTKTRTETP MAQSDSQ LF NQLLVTEGMT LPTEMKEAAS EMARALRGPG PRSSLDQHVA AVVATVQISS LDTNLQLSGL SALSQAVEEV TERDHPLV R PDRSLREKLV KMLVELLTNQ VGEKMVVVQA LRLLYLLMTK HEWRPLFARE GGIYAVLVCM QEYKTSVLVQ QAGLAALKM LAVASSSEIP TFVTGRDSIH SLFDAQMTRE IFASIDSATR PGSESLLLTV PAAVILMLNT EGCSSAARNG LLLLNLLLCN HHTLGDQII TQELRDTLFR HSGIAPRTEP MPTTRTILMM LLNRYSEPPG SPERAALETP IIQGQDGSPE LLIRSLVGGP S AELLLDLE RVLCREGSPG GAVRPLLKRL QQETQPFLLL LRTLDAPGPN KTLLLSVLRV ITRLLDFPEA MVLPWHEVLE PC LNCLSGP SSDSEIVQEL TCFLHRLASM HKDYAVVLCC LGAKEILSKV LDKHSAQLLL GCELRDLVTE CEKYAQLYSN LTS SILAGC IQMVLGQIED HRRTHQPINI PFFDVFLRHL CQGSSVEVKE DKCWEKVEVS SNPHRASKLT DHNPKTYWES NGST GSHYI TLHMHRGVLV RQLTLLVASE DSSYMPARVV VFGGDSTSCI GTELNTVNVM PSASRVILLE NLNRFWPIIQ IRIKR CQQG GIDTRVRGVE VLGPKPTFWP LFREQLCRRT CLFYTIRAQA WSRDIAEDHR RLLQLCPRLN RVLRHEQNFA DRFLPD DEA AQALGKTCWE ALVSPLVQNI TSPDAEGVSA LGWLLDQYLE QRETSRNPLS RAASFASRVR RLCHLLVHVE PPPGPSP EP STRPFSKNSK GRDRSPAPSP VLPSSSLRNI TQCWLSVVQE QVSRFLAAAW RAPDFVPRYC KLYEHLQRAG SELFGPRA A FMLALRSGFS GALLQQSFLT AAHMSEQFAR YIDQQIQGGL IGGAPGVEML GQLQRHLEPI MVLSGLELAT TFEHFYQHY MADRLLSFGS SWLEGAVLEQ IGLCFPNRLP QLMLQSLSTS EELQRQFHLF QLQRLDKLFL EQEDEEEKRL EEEEEEEEEE EAEKELFIE DPSPAISILV LSPRCWPVSP LCYLYHPRKC LPTEFCDALD RFSSFYSQSQ NHPVLDMGPH RRLQWTWLGR A ELQFGKQI LHVSTVQMWL LLKFNQTEEV SVETLLKDSD LSPELLLQAL VPLTSGNGPL TLHEGQDFPH GGVLRLHEPG PQ RSGEALW LIPPQAYLNV EKDEGRTLEQ KRNLLSCLLV RILKAHGEKG LHIDQLVCLV LEAWQKGPNP PGTLGHTVAG GVA CTSTDV LSCILHLLGQ GYVKRRDDRP QILMYAAPEP MGPCRGQADV PFCGSQSETS KPSPEAVATL ASLQLPAGRT MSPQ EVEGL MKQTVRQVQE TLNLEPDVAQ HLLAHSHWGA EQLLQSYSED PEPLLLAAGL CVHQAQAVPV RPDHCPVCVS PLGCD DDLP SLCCMHYCCK SCWNEYLTTR IEQNLVLNCT CPIADCPAQP TGAFIRAIVS SPEVISKYEK ALLRGYVESC SNLTWC TNP QGCDRILCRQ GLGCGTTCSK CGWASCFNCS FPEAHYPASC GHMSQWVDDG GYYDGMSVEA QSKHLAKLIS KRCPSCQ AP IEKNEGCLHM TCAKCNHGFC WRCLKSWKPN HKDYYNCSAM VSKAARQEKR FQDYNERCTF HHQAREFAVN LRNRVSAI H EVPPPRSFTF LNDACQGLEQ ARKVLAYACV YSFYSQDAEY MDVVEQQTEN LELHTNALQI LLEETLLRCR DLASSLRLL RADCLSTGME LLRRIQERLL AILQHSAQDF RVGLQSPSVE AWEAKGPNMP GSQPQASSGP EAEEEEEDDE DDVPEWQQDE FDEELDNDS FSYDESENLD QETFFFGDEE EDEDEAYD

UniProtKB: Cullin-9

Macromolecule #2: E3 ubiquitin-protein ligase RBX1

• Macromolecule: Name: E3 ubiquitin-protein ligase RBX1 / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
• Source (natural): Organism: Homo sapiens (human)
• Recombinant expression: Organism: Homo sapiens (human)

Sequence

String:

MDVDTPSGTN SGAGKKRFEV KKWNAVALWA WDIVVDNCAI CRNHIMDLCI ECQANQASAT SEECTVAWGV CNHAFH FHC ISRWLKTRQV CPLDNREWEF QKYGH

UniProtKB: E3 ubiquitin-protein ligase RBX1

Experimental details

Structure determination

• Method: cryo EM
• Processing: single particle reconstruction
• Aggregation state: particle

Sample preparation

• Concentration: 3 mg/mL
• Buffer: pH: 7.5
• Vitrification: Cryogen name: ETHANE

Electron microscopy

• Microscope: FEI TITAN KRIOS
• Image recording: Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 60.0 e/Ų
• Electron beam: Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
• Electron optics: Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.8000000000000003 µm / Nominal defocus min: 0.7000000000000001 µm
• Experimental equipment: Model: Titan Krios / Image courtesy: FEI Company

Image processing

• Startup model: Type of model: NONE
• Final reconstruction: Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 71928
• Initial angle assignment: Type: MAXIMUM LIKELIHOOD
• Final angle assignment: Type: MAXIMUM LIKELIHOOD