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- EMDB-18216: Structure of CUL9-RBX1 ubiquitin E3 ligase complex in unneddylate... -

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Entry
Database: EMDB / ID: EMD-18216
TitleStructure of CUL9-RBX1 ubiquitin E3 ligase complex in unneddylated and neddylated conformation - focused cullin dimer
Map dataDeepEMhancer map
Sample
  • Complex: Structure of CUL9-RBX1 ubiquitin E3 ligase complex in unneddylated and neddylated conformation - focused cullin dimer
    • Protein or peptide: Cullin-9
    • Protein or peptide: E3 ubiquitin-protein ligase RBX1
    • Protein or peptide: NEDD8
    • Protein or peptide: Unknown
  • Ligand: ZINC ION
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 / RNA polymerase II transcription initiation surveillance / protein neddylation ...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 / regulation of mitotic nuclear division / Cul4B-RING E3 ubiquitin ligase complex / negative regulation of mitophagy / Prolactin receptor signaling / TGF-beta receptor signaling activates SMADs / cullin family protein binding / regulation of proteolysis / regulation of postsynapse assembly / anatomical structure morphogenesis / protein monoubiquitination / protein K48-linked ubiquitination / Nuclear events stimulated by ALK signaling in cancer / Regulation of BACH1 activity / transcription-coupled nucleotide-excision repair / regulation of cellular response to insulin stimulus / positive regulation of TORC1 signaling / post-translational protein modification / negative regulation of insulin receptor signaling pathway / T cell activation / Degradation of DVL / Iron uptake and transport / 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 / modification-dependent protein catabolic process / 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 / negative regulation of canonical Wnt signaling pathway / Formation of Incision Complex in GG-NER / protein tag activity / Regulation of expression of SLITs and ROBOs / 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 / protein modification process / Regulation of RAS by GAPs / microtubule cytoskeleton organization / Regulation of RUNX2 expression and activity / KEAP1-NFE2L2 pathway / UCH proteinases / protein polyubiquitination / positive regulation of protein catabolic process / Cargo recognition for clathrin-mediated endocytosis / Antigen processing: Ubiquitination & Proteasome degradation / cellular response to UV / ubiquitin protein ligase activity / intracellular protein localization / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / Neddylation / MAPK cascade / cellular response to oxidative stress / ubiquitin-dependent protein catabolic process / spermatogenesis / molecular adaptor activity / proteasome-mediated ubiquitin-dependent protein catabolic process / Potential therapeutics for SARS / RNA polymerase II-specific DNA-binding transcription factor binding / positive regulation of canonical NF-kappaB signal transduction / postsynapse / protein ubiquitination / ubiquitin protein ligase binding
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 / Nedd8-like ubiquitin / 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 / : / Ubiquitin domain / Ubiquitin domain signature. / Ubiquitin conserved site / Zinc finger RING-type profile. / Zinc finger, RING-type / Armadillo-like helical / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Armadillo-type fold / Ubiquitin-like domain superfamily / Zinc finger, RING/FYVE/PHD-type / Ribosomal protein L2, domain 2 / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
E3 ubiquitin-protein ligase RBX1 / Ubiquitin-like protein NEDD8 / Cullin-9
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.1 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: Horn-Ghetko D / Hopf LVM / Tripathi-Giesgen I / Du J / Kostrhon S / Vu DT / Beier V / Steigenberger B / Prabu JR / Stier L / Bruss EM / Mann M / Xiong Y / Schulman BA
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

Downloads & links

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Map

FileDownload / File: emd_18216.map.gz / Format: CCP4 / Size: 488.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationDeepEMhancer map
Voxel sizeX=Y=Z: 0.8512 Å
Density
Contour LevelBy AUTHOR: 0.063
Minimum - Maximum-0.0017793869 - 2.094444
Average (Standard dev.)0.0010601684 (±0.022821931)
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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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 cullin dimer
Components
  • Complex: Structure of CUL9-RBX1 ubiquitin E3 ligase complex in unneddylated and neddylated conformation - focused cullin dimer
    • Protein or peptide: Cullin-9
    • Protein or peptide: E3 ubiquitin-protein ligase RBX1
    • Protein or peptide: NEDD8
    • Protein or peptide: Unknown
  • Ligand: ZINC ION

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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 cullin dimer
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4 / Details: Structure of dimeric subunit
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Cullin-9

MacromoleculeName: Cullin-9 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 281.686062 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: GPMVGERHAG DLMVPLGPRL QAYPEELIRQ RPGHDGHPEY LIRWSVLKCG EVGKVGVEEG KAEHILMWLS APEVYANCPG LLGERALSK GLQHEPAGVS GSFPRDPGGL DEVAMGEMEA DVQALVRRAA RQLAESGTPS LTAAVLHTIH VLSAYASIGP L TGVFRETG ...String:
GPMVGERHAG DLMVPLGPRL QAYPEELIRQ RPGHDGHPEY LIRWSVLKCG EVGKVGVEEG KAEHILMWLS APEVYANCPG LLGERALSK GLQHEPAGVS GSFPRDPGGL DEVAMGEMEA DVQALVRRAA RQLAESGTPS LTAAVLHTIH VLSAYASIGP L TGVFRETG ALDLLMHMLC NPEPQIRRSA GKMLQALAAH DAGSRAHVLL SLSQQDGIEQ HMDFDSRYTL LELFAETTSS EE HCMAFEG IHLPQIPGKL LFSLVKRYLC VTSLLDQLNS SPELGAGDQS SPCATREKSR GQRELEFSMA VGNLISELVR SMG WARNLS EQGMSPPRPT RSIFQPYISG PSLLLPTIVT TPRRQGWVFR QRSEFSSRSG YGEYVQQTLQ PGMRVRMLDD YEEI SAGDE GEFRQSNNGI PPVQVFWQST GRTYWVHWHM LEILGPEEAT EDKASAAVEK GAGATVLGTA FPSWDWNPMD GLYPL PYLQ PEPQKNERVG YLTQAEWWEL LFFIKKLDLC EQQPIFQNLW KNLDETLGEK ALGEISVSVE MAESLLQVLS SRFEGS TLN DLLNSQIYTK YGLLSNEPSS SSTSRNHSCT PDPEEESKSE ASFSEEETES LKAKAEAPKT EAEPTKTRTE TPMAQSD SQ LFNQLLVTEG MTLPTEMKEA ASEMARALRG PGPRSSLDQH VAAVVATVQI SSLDTNLQLS GLSALSQAVE EVTERDHP L VRPDRSLREK LVKMLVELLT NQVGEKMVVV QALRLLYLLM TKHEWRPLFA REGGIYAVLV CMQEYKTSVL VQQAGLAAL KMLAVASSSE IPTFVTGRDS IHSLFDAQMT REIFASIDSA TRPGSESLLL TVPAAVILML NTEGCSSAAR NGLLLLNLLL CNHHTLGDQ IITQELRDTL FRHSGIAPRT EPMPTTRTIL MMLLNRYSEP PGSPERAALE TPIIQGQDGS PELLIRSLVG G PSAELLLD LERVLCREGS PGGAVRPLLK RLQQETQPFL LLLRTLDAPG PNKTLLLSVL RVITRLLDFP EAMVLPWHEV LE PCLNCLS GPSSDSEIVQ ELTCFLHRLA SMHKDYAVVL CCLGAKEILS KVLDKHSAQL LLGCELRDLV TECEKYAQLY SNL TSSILA GCIQMVLGQI EDHRRTHQPI NIPFFDVFLR HLCQGSSVEV KEDKCWEKVE VSSNPHRASK LTDHNPKTYW ESNG STGSH YITLHMHRGV LVRQLTLLVA SEDSSYMPAR VVVFGGDSTS CIGTELNTVN VMPSASRVIL LENLNRFWPI IQIRI KRCQ QGGIDTRVRG VEVLGPKPTF WPLFREQLCR RTCLFYTIRA QAWSRDIAED HRRLLQLCPR LNRVLRHEQN FADRFL PDD EAAQALGKTC WEALVSPLVQ NITSPDAEGV SALGWLLDQY LEQRETSRNP LSRAASFASR VRRLCHLLVH VEPPPGP SP EPSTRPFSKN SKGRDRSPAP SPVLPSSSLR NITQCWLSVV QEQVSRFLAA AWRAPDFVPR YCKLYEHLQR AGSELFGP R AAFMLALRSG FSGALLQQSF LTAAHMSEQF ARYIDQQIQG GLIGGAPGVE MLGQLQRHLE PIMVLSGLEL ATTFEHFYQ HYMADRLLSF GSSWLEGAVL EQIGLCFPNR LPQLMLQSLS TSEELQRQFH LFQLQRLDKL FLEQEDEEEK RLEEEEEEEE EEEAEKELF IEDPSPAISI LVLSPRCWPV SPLCYLYHPR KCLPTEFCDA LDRFSSFYSQ SQNHPVLDMG PHRRLQWTWL G RAELQFGK QILHVSTVQM WLLLKFNQTE EVSVETLLKD SDLSPELLLQ ALVPLTSGNG PLTLHEGQDF PHGGVLRLHE PG PQRSGEA LWLIPPQAYL NVEKDEGRTL EQKRNLLSCL LVRILKAHGE KGLHIDQLVC LVLEAWQKGP NPPGTLGHTV AGG VACTST DVLSCILHLL GQGYVKRRDD RPQILMYAAP EPMGPCRGQA DVPFCGSQSE TSKPSPEAVA TLASLQLPAG RTMS PQEVE GLMKQTVRQV QETLNLEPDV AQHLLAHSHW GAEQLLQSYS EDPEPLLLAA GLCVHQAQAV PVRPDHCPVC VSPLG CDDD LPSLCCMHYC CKSCWNEYLT TRIEQNLVLN CTCPIADCPA QPTGAFIRAI VSSPEVISKY EKALLRGYVE SCSNLT WCT NPQGCDRILC RQGLGCGTTC SKCGWASCFN CSFPEAHYPA SCGHMSQWVD DGGYYDGMSV EAQSKHLAKL ISKRCPS CQ APIEKNEGCL HMTCAKCNHG FCWRCLKSWK PNHKDYYNCS AMVSKAARQE KRFQDYNERC TFHHQAREFA VNLRNRVS A IHEVPPPRSF TFLNDACQGL EQARKVLAYA CVYSFYSQDA EYMDVVEQQT ENLELHTNAL QILLEETLLR CRDLASSLR LLRADCLSTG MELLRRIQER LLAILQHSAQ DFRVGLQSPS VEAWEAKGPN MPGSQPQASS GPEAEEEEED DEDDVPEWQQ DEFDEELDN DSFSYDESEN LDQETFFFGD EEEDEDEAYD

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 / Number of copies: 2 / Enantiomer: LEVO / EC number: RING-type E3 ubiquitin transferase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 12.289977 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
MAAAMDVDTP SGTNSGAGKK RFEVKKWNAV ALWAWDIVVD NCAICRNHIM DLCIECQANQ ASATSEECTV AWGVCNHAFH FHCISRWLK TRQVCPLDNR EWEFQKYGH

UniProtKB: E3 ubiquitin-protein ligase RBX1

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Macromolecule #3: NEDD8

MacromoleculeName: NEDD8 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 9.086562 KDa
SequenceString:
MLIKVKTLTG KEIEIDIEPT DKVERIKERV EEKEGIPPQQ QRLIYSGKQM NDEKTAADYK ILGGSVLHLV LALRGGGGLR Q

UniProtKB: Ubiquitin-like protein NEDD8

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Macromolecule #4: Unknown

MacromoleculeName: Unknown / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 12.868854 KDa
SequenceString: (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) ...String:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)

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Macromolecule #5: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 5 / Number of copies: 10 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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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: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 71928
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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