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- EMDB-18220: Structure of the hexameric CUL9-RBX1 complex with deletion of CUL... -

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Entry
Database: EMDB / ID: EMD-18220
TitleStructure of the hexameric CUL9-RBX1 complex with deletion of CUL9 CPH domain
Map datapostprocess map
Sample
  • Complex: Structure of the hexameric CUL9-RBX1 complex with deletion of CUL9 CPH domain
    • 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 / Cul5-RING ubiquitin ligase complex / negative regulation of response to oxidative stress / ubiquitin-ubiquitin ligase activity / SCF ubiquitin ligase complex / Cul2-RING ubiquitin ligase complex / Cul4A-RING E3 ubiquitin ligase complex / regulation of mitotic nuclear division / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / Cul4B-RING E3 ubiquitin ligase complex / negative regulation of type I interferon production / Cul3-RING ubiquitin ligase complex / Prolactin receptor signaling / protein monoubiquitination / cullin family protein binding / protein K48-linked ubiquitination / Nuclear events stimulated by ALK signaling in cancer / positive regulation of TORC1 signaling / post-translational protein modification / regulation of cellular response to insulin stimulus / Regulation of BACH1 activity / T cell activation / Degradation of DVL / cellular response to amino acid stimulus / Recognition of DNA damage by PCNA-containing replication complex / Degradation of GLI1 by the proteasome / Negative regulation of NOTCH4 signaling / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / 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 / negative regulation of canonical Wnt signaling pathway / Degradation of beta-catenin by the destruction complex / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / Formation of TC-NER Pre-Incision Complex / Dual Incision in GG-NER / Evasion by RSV of host interferon responses / NOTCH1 Intracellular Domain Regulates Transcription / 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 / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / Orc1 removal from chromatin / protein polyubiquitination / Regulation of RAS by GAPs / positive regulation of protein catabolic process / Regulation of RUNX2 expression and activity / cellular response to UV / MAPK cascade / ubiquitin protein ligase activity / KEAP1-NFE2L2 pathway / Antigen processing: Ubiquitination & Proteasome degradation / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / Neddylation / ubiquitin-dependent protein catabolic process / spermatogenesis / positive regulation of canonical NF-kappaB signal transduction / proteasome-mediated ubiquitin-dependent protein catabolic process / RNA polymerase II-specific DNA-binding transcription factor binding / Potential therapeutics for SARS / molecular adaptor activity / protein ubiquitination / DNA repair / DNA damage response / ubiquitin protein ligase binding / zinc ion binding / nucleoplasm / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
: / : / : / 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. ...: / : / : / 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: 9.5 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_18220.png

Downloads & links

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Map

FileDownload / File: emd_18220.map.gz / Format: CCP4 / Size: 381.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationpostprocess map
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.89 Å/pix.
x 464 pix.
= 874.64 Å		1.89 Å/pix.
x 464 pix.
= 874.64 Å		1.89 Å/pix.
x 464 pix.
= 874.64 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.885 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0195
Minimum - Maximum-0.010314939 - 0.052560594
Average (Standard dev.)0.000057565616 (±0.0017110633)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions464464464
Spacing464464464
CellA=B=C: 874.64 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: refinement map

Fileemd_18220_additional_1.map
Annotationrefinement map
Projections & Slices
AxesZYX

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Half map: #2

Fileemd_18220_half_map_1.map
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Histogram (log scale)

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Half map: #1

Fileemd_18220_half_map_2.map
Projections & Slices
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Sample components

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Entire : Structure of the hexameric CUL9-RBX1 complex with deletion of CUL...

EntireName: Structure of the hexameric CUL9-RBX1 complex with deletion of CUL9 CPH domain
Components
  • Complex: Structure of the hexameric CUL9-RBX1 complex with deletion of CUL9 CPH domain
    • Protein or peptide: Cullin-9
    • Protein or peptide: E3 ubiquitin-protein ligase RBX1

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Supramolecule #1: Structure of the hexameric CUL9-RBX1 complex with deletion of CUL...

SupramoleculeName: Structure of the hexameric CUL9-RBX1 complex with deletion of CUL9 CPH domain
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 GERALSKGLQ HEPAGVSGSF PRDPGGLDEV AMGEMEADVQ ALVRRAARQL AESGTPSLTA AVLHTIHVLS AYASIGPLTG VFRETGALDL ...String:
MVGERHAGDL MVPLGPRLQA YPEELIRQRP GHDGHPEYLI RWSVLKCGEV GKVGVEEGKA EHILMWLSAP EVYANCPGLL GERALSKGLQ HEPAGVSGSF PRDPGGLDEV AMGEMEADVQ ALVRRAARQL AESGTPSLTA AVLHTIHVLS AYASIGPLTG VFRETGALDL LMHMLCNPEP QIRRSAGKML QALAAHDAGS RAHVLLSLSQ QDGIEQHMDF DSRYTLLELF AETTSSEEHC MAFEGIHLPQ IPGKLLFSLV KRYLCVTSLL DQLNSSPELG AGDQSSPCAT REKSRGQREL EFSMAVGNLI SELVRSMGWA RNLSEQGMSP PRPTRSIFQP YISGPSLLLP TIVGSGSGSG SGTAFPSWDW NPMDGLYPLP YLQPEPQKNE RVGYLTQAEW WELLFFIKKL DLCEQQPIFQ NLWKNLDETL GEKALGEISV SVEMAESLLQ VLSSRFEGST LNDLLNSQIY TKYGLLSNEP SSSSTSRNHS CTPDPEEESK SEASFSEEET ESLKAKAEAP KTEAEPTKTR TETPMAQSDS QLFNQLLVTE GMTLPTEMKE AASEMARALR GPGPRSSLDQ HVAAVVATVQ ISSLDTNLQL SGLSALSQAV EEVTERDHPL VRPDRSLREK LVKMLVELLT NQVGEKMVVV QALRLLYLLM TKHEWRPLFA REGGIYAVLV CMQEYKTSVL VQQAGLAALK MLAVASSSEI PTFVTGRDSI HSLFDAQMTR EIFASIDSAT RPGSESLLLT VPAAVILMLN TEGCSSAARN GLLLLNLLLC NHHTLGDQII TQELRDTLFR HSGIAPRTEP MPTTRTILMM LLNRYSEPPG SPERAALETP IIQGQDGSPE LLIRSLVGGP SAELLLDLER VLCREGSPGG AVRPLLKRLQ QETQPFLLLL RTLDAPGPNK TLLLSVLRVI TRLLDFPEAM VLPWHEVLEP CLNCLSGPSS DSEIVQELTC FLHRLASMHK DYAVVLCCLG AKEILSKVLD KHSAQLLLGC ELRDLVTECE KYAQLYSNLT SSILAGSIQM VLGQIEDHRR THQPINIPFF DVFLRHLCQG SSVEVKEDKC WEKVEVSSNP HRASKLTDHN PKTYWESNGS TGSHYITLHM HRGVLVRQLT LLVASEDSSY MPARVVVFGG DSTSCIGTEL NTVNVMPSAS RVILLENLNR FWPIIQIRIK RCQQGGIDTR VRGVEVLGPK PTFWPLFREQ LCRRTCLFYT IRAQAWSRDI AEDHRRLLQL CPRLNRVLRH EQNFADRFLP DDEAAQALGK TCWEALVSPL VQNITSPDAE GVSALGWLLD QYLEQRETSR NPLSRAASFA SRVRRLCHLL VHVEPPPGPS PEPSTRPFSK NSKGRDRSPA PSPVLPSSSL RNITQCWLSV VQEQVSRFLA AAWRAPDFVP RYCKLYEHLQ RAGSELFGPR AAFMLALRSG FSGALLQQSF LTAAHMSEQF ARYIDQQIQG GLIGGAPGVE MLGQLQRHLE PIMVLSGLEL ATTFEHFYQH YMADRLLSFG SSWLEGAVLE QIGLCFPNRL PQLMLQSLST SEELQRQFHL FQLQRLDKLF LEQEDEEEKR LEEEEEEEEE EEAEKELFIE DPSPAISILV LSPRCWPVSP LCYLYHPRKC LPTEFCDALD RFSSFYSQSQ NHPVLDMGPH RRLQWTWLGR AELQFGKQIL HVSTVQMWLL LKFNQTEEVS VETLLKDSDL SPELLLQALV PLTSGNGPLT LHEGQDFPHG GVLRLHEPGP QRSGEALWLI PPQAYLNVEK DEGRTLEQKR NLLSCLLVRI LKAHGEKGLH IDQLVCLVLE AWQKGPNPPG TLGHTVAGGV ACTSTDVLSC ILHLLGQGYV KRRDDRPQIL MYAAPEPMGP CRGQADVPFC GSQSETSKPS PEAVATLASL QLPAGRTMSP QEVEGLMKQT VRQVQETLNL EPDVAQHLLA HSHWGAEQLL QSYSEDPEPL LLAAGLCVHQ AQAVPVRPDH CPVCVSPLGC DDDLPSLCCM HYCCKSCWNE YLTTRIEQNL VLNCTCPIAD CPAQPTGAFI RAIVSSPEVI SKYEKALLRG YVESCSNLTW CTNPQGCDRI LCRQGLGCGT TCSKCGWASC FNCSFPEAHY PASCGHMSQW VDDGGYYDGM SVEAQSKHLA KLISKRCPSC QAPIEKNEGC LHMTCAKCNH GFCWRCLKSW KPNHKDYYNC SAMVSKAARQ EKRFQDYNER CTFHHQAREF AVNLRNRVSA IHEVPPPRSF TFLNDACQGL EQARKVLAYA CVYSFYSQDA EYMDVVEQQT ENLELHTNAL QILLEETLLR CRDLASSLRL LRADCLSTGM ELLRRIQERL LAILQHSAQD FRVGLQSPSV EAWEAKGPNM PGSQPQASSG PEAEEEEEDD EDDVPEWQQD EFDEELDNDS 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 ECQANQ ASA TSEECTVAWG VCNHAFHFHC 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

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.3000000000000003 µm / Nominal defocus min: 1.2 µm

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 9.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 30949
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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