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

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Entry
Database: EMDB / ID: EMD-18218
TitleStructure of CUL9-RBX1 ubiquitin E3 ligase complex in unneddylated and neddylated conformation - focused dimeric core
Map datadeepEMhancer 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
KeywordsCullin-RING RBR E3 Ligase / LIGASE
Function / homology
Function and homology information


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 / protein neddylation / NEDD8 ligase 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 / protein neddylation / NEDD8 ligase activity / negative regulation of response to oxidative stress / Cul5-RING ubiquitin ligase complex / SCF ubiquitin ligase complex / Cul2-RING ubiquitin ligase complex / Cul4A-RING E3 ubiquitin ligase complex / ubiquitin-ubiquitin ligase activity / regulation of mitotic nuclear division / negative regulation of type I interferon production / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / Cul3-RING ubiquitin ligase complex / Cul4B-RING E3 ubiquitin ligase complex / negative regulation of mitophagy / Prolactin receptor signaling / cullin family protein binding / protein monoubiquitination / protein K48-linked ubiquitination / Nuclear events stimulated by ALK signaling in cancer / regulation of cellular response to insulin stimulus / positive regulation of TORC1 signaling / negative regulation of insulin receptor signaling pathway / post-translational protein modification / T cell activation / Regulation of BACH1 activity / cellular response to amino acid stimulus / Degradation of DVL / 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 canonical Wnt signaling pathway / 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 / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / DNA Damage Recognition in GG-NER / RING-type E3 ubiquitin transferase / Degradation of beta-catenin by the destruction complex / Evasion by RSV of host interferon responses / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / Dual Incision in GG-NER / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / NOTCH1 Intracellular Domain Regulates Transcription / Formation of TC-NER Pre-Incision Complex / microtubule cytoskeleton organization / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / Regulation of expression of SLITs and ROBOs / Formation of Incision Complex in GG-NER / Interleukin-1 signaling / Orc1 removal from chromatin / Dual incision in TC-NER / Regulation of RAS by GAPs / protein polyubiquitination / positive regulation of protein catabolic process / Gap-filling DNA repair synthesis and ligation in TC-NER / Regulation of RUNX2 expression and activity / cellular response to UV / KEAP1-NFE2L2 pathway / ubiquitin protein ligase activity / MAPK cascade / Antigen processing: Ubiquitination & Proteasome degradation / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / Neddylation / cellular response to oxidative stress / ubiquitin-dependent protein catabolic process / spermatogenesis / molecular adaptor activity / RNA polymerase II-specific DNA-binding transcription factor binding / proteasome-mediated ubiquitin-dependent protein catabolic process / Potential therapeutics for SARS / positive regulation of canonical NF-kappaB signal transduction / protein ubiquitination / DNA repair / ubiquitin protein ligase binding / DNA damage response / zinc ion binding / nucleoplasm / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
: / : / : / : / : / CUL7/CUL9, N-terminal beta-barrel domain / CUL7/CUL9 ARM repeat domain / CPH domain / Mouse development and cellular proliferation protein Cullin-7 / IBR domain, a half RING-finger domain ...: / : / : / : / : / CUL7/CUL9, N-terminal beta-barrel domain / CUL7/CUL9 ARM repeat domain / CPH domain / Mouse development and cellular proliferation protein Cullin-7 / 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 protein, neddylation domain / Cullin / Cullin protein neddylation domain / Cullin, N-terminal / Cullin homology domain / Cullin homology domain superfamily / Cullin family / 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 / Armadillo-type fold / Ribosomal protein L2, domain 2 / Zinc finger, RING/FYVE/PHD-type / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
E3 ubiquitin-protein ligase RBX1 / Cullin-9
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsHopf LVM / Horn-Ghetko D / Schulman BA
Funding supportEuropean Union, Germany, 2 items
OrganizationGrant numberCountry
European Research Council (ERC)789016European Union
Max Planck Society Germany
CitationJournal: 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 / ...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 ...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
DepositionAug 16, 2023-
Header (metadata) releaseApr 17, 2024-
Map releaseApr 17, 2024-
UpdateJul 31, 2024-
Current statusJul 31, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_18218.png

Downloads & links

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Map

FileDownload / File: emd_18218.map.gz / Format: CCP4 / Size: 488.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationdeepEMhancer map
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 504 pix.
= 429.005 Å		0.85 Å/pix.
x 504 pix.
= 429.005 Å		0.85 Å/pix.
x 504 pix.
= 429.005 Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8512 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0564
Minimum - Maximum-0.0017764473 - 2.011857
Average (Standard dev.)0.00054702564 (±0.01617327)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions504504504
Spacing504504504
CellA=B=C: 429.0048 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_18218_msk_1.map
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Additional map: Relion postprocess map

Fileemd_18218_additional_1.map
AnnotationRelion postprocess map
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Half map: #2

Fileemd_18218_half_map_1.map
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Half map: #1

Fileemd_18218_half_map_2.map
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Sample components

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

EntireName: 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

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

SupramoleculeName: 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)

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Macromolecule #1: Cullin-9

MacromoleculeName: Cullin-9 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MVGERHAGDL MVPLGPRLQA YPEELIRQRP GHDGHPEYLI RWSVLKCGEV GKVGVEEGKA EHILMWLSAP EVYANCPGLL GERALSKGL QHEPAGVSGS FPRDPGGLDE VAMGEMEADV QALVRRAARQ LAESGTPSLT AAVLHTIHVL SAYASIGPLT G VFRETGAL ...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

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Macromolecule #2: E3 ubiquitin-protein ligase RBX1

MacromoleculeName: E3 ubiquitin-protein ligase RBX1 / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
MDVDTPSGTN SGAGKKRFEV KKWNAVALWA WDIVVDNCAI CRNHIMDLCI ECQANQASAT SEECTVAWGV CNHAFH FHC ISRWLKTRQV CPLDNREWEF QKYGH

UniProtKB: E3 ubiquitin-protein ligase RBX1

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration3 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination 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

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 71928
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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