+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-36961 | |||||||||||||||
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Title | Structure of CUL3-RBX1-KLHL22 complex | |||||||||||||||
Map data | ||||||||||||||||
Sample |
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Keywords | Cullin Ring E3 ubiquitin ligase / LIGASE | |||||||||||||||
Function / homology | Function and homology information liver morphogenesis / positive regulation of mitotic cell cycle phase transition / trophectodermal cellular morphogenesis / POZ domain binding / nuclear protein quality control by the ubiquitin-proteasome system / regulation protein catabolic process at postsynapse / polar microtubule / COPII vesicle coating / anaphase-promoting complex-dependent catabolic process / stem cell division ...liver morphogenesis / positive regulation of mitotic cell cycle phase transition / trophectodermal cellular morphogenesis / POZ domain binding / nuclear protein quality control by the ubiquitin-proteasome system / regulation protein catabolic process at postsynapse / polar microtubule / COPII vesicle coating / anaphase-promoting complex-dependent catabolic process / stem cell division / RHOBTB3 ATPase cycle / cellular response to L-leucine / embryonic cleavage / cell projection organization / positive regulation of mitotic metaphase/anaphase transition / fibroblast apoptotic process / Notch binding / RHOBTB1 GTPase cycle / negative regulation of Rho protein signal transduction / mitotic metaphase chromosome alignment / negative regulation of type I interferon production / ubiquitin ligase complex scaffold activity / Cul3-RING ubiquitin ligase complex / intercellular bridge / stress fiber assembly / positive regulation of cytokinesis / mitotic spindle assembly checkpoint signaling / protein monoubiquitination / mitotic sister chromatid segregation / ubiquitin-like ligase-substrate adaptor activity / sperm flagellum / endoplasmic reticulum to Golgi vesicle-mediated transport / RHOBTB2 GTPase cycle / protein autoubiquitination / protein K48-linked ubiquitination / gastrulation / 14-3-3 protein binding / positive regulation of TORC1 signaling / intrinsic apoptotic signaling pathway / regulation of cellular response to insulin stimulus / negative regulation of autophagy / cyclin binding / positive regulation of protein ubiquitination / integrin-mediated signaling pathway / Degradation of DVL / cellular response to amino acid stimulus / protein destabilization / Hedgehog 'on' state / mitotic spindle / Wnt signaling pathway / spindle pole / protein polyubiquitination / Regulation of RAS by GAPs / G1/S transition of mitotic cell cycle / microtubule cytoskeleton / ubiquitin protein ligase activity / KEAP1-NFE2L2 pathway / cell migration / Antigen processing: Ubiquitination & Proteasome degradation / Neddylation / gene expression / ubiquitin-dependent protein catabolic process / positive regulation of cell growth / proteasome-mediated ubiquitin-dependent protein catabolic process / postsynapse / Potential therapeutics for SARS / lysosome / protein ubiquitination / inflammatory response / cell division / intracellular membrane-bounded organelle / centrosome / glutamatergic synapse / ubiquitin protein ligase binding / positive regulation of cell population proliferation / Golgi apparatus / negative regulation of transcription by RNA polymerase II / extracellular exosome / nucleoplasm / identical protein binding / membrane / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | |||||||||||||||
Biological species | Homo sapiens (human) | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.8 Å | |||||||||||||||
Authors | Wang W / Ling L / Dai Z / Zuo P / Yin Y | |||||||||||||||
Funding support | China, 4 items
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Citation | Journal: Nat Commun / Year: 2024 Title: A conserved N-terminal motif of CUL3 contributes to assembly and E3 ligase activity of CRL3. Authors: Weize Wang / Ling Liang / Zonglin Dai / Peng Zuo / Shang Yu / Yishuo Lu / Dian Ding / Hongyi Chen / Hui Shan / Yan Jin / Youdong Mao / Yuxin Yin / Abstract: The CUL3-RING E3 ubiquitin ligases (CRL3s) play an essential role in response to extracellular nutrition and stress stimuli. The ubiquitin ligase function of CRL3s is activated through dimerization. ...The CUL3-RING E3 ubiquitin ligases (CRL3s) play an essential role in response to extracellular nutrition and stress stimuli. The ubiquitin ligase function of CRL3s is activated through dimerization. However, how and why such a dimeric assembly is required for its ligase activity remains elusive. Here, we report the cryo-EM structure of the dimeric CRL3 complex and reveal a conserved N-terminal motif in CUL3 that contributes to the dimerization assembly and the E3 ligase activity of CRL3. We show that deletion of the CUL3 N-terminal motif impairs dimeric assembly and the E3 ligase activity of both CRL3 and several other CRL3s. In addition, we found that the dynamics of dimeric assembly of CRL3 generates a variable ubiquitination zone, potentially facilitating substrate recognition and ubiquitination. These findings demonstrate that a CUL3 N-terminal motif participates in the assembly process and provide insights into the assembly and activation of CRL3s. | |||||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_36961.map.gz | 395.3 MB | EMDB map data format | |
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Header (meta data) | emd-36961-v30.xml emd-36961.xml | 18 KB 18 KB | Display Display | EMDB header |
Images | emd_36961.png | 57.6 KB | ||
Filedesc metadata | emd-36961.cif.gz | 6.7 KB | ||
Others | emd_36961_additional_1.map.gz | 251 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-36961 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-36961 | HTTPS FTP |
-Validation report
Summary document | emd_36961_validation.pdf.gz | 330.4 KB | Display | EMDB validaton report |
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Full document | emd_36961_full_validation.pdf.gz | 329.9 KB | Display | |
Data in XML | emd_36961_validation.xml.gz | 8.2 KB | Display | |
Data in CIF | emd_36961_validation.cif.gz | 9.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-36961 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-36961 | HTTPS FTP |
-Related structure data
Related structure data | 8k8tMC 8k9iC C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_36961.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.821 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: Raw map of CUL3-RBX1-KLHL22 dimer complex
File | emd_36961_additional_1.map | ||||||||||||
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Annotation | Raw map of CUL3-RBX1-KLHL22 dimer complex | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : CUL3-RBX1-KLHL22 complex without CUL3 NA motif
Entire | Name: CUL3-RBX1-KLHL22 complex without CUL3 NA motif |
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Components |
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-Supramolecule #1: CUL3-RBX1-KLHL22 complex without CUL3 NA motif
Supramolecule | Name: CUL3-RBX1-KLHL22 complex without CUL3 NA motif / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: Cullin-3
Macromolecule | Name: Cullin-3 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 90.134555 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | String: MSNLSKGTGS RKDTKMRIRA FPMTMDEKYV NSIWDLLKNA IQEIQRKNNS GLSFEELYRN AYTMVLHKHG EKLYTGLREV VTEHLINKV REDVLNSLNN NFLQTLNQAW NDHQTAMVMI RDILMYMDRV YVQQNNVENV YNLGLIIFRD QVVRYGCIRD H LRQTLLDM ...String: MSNLSKGTGS RKDTKMRIRA FPMTMDEKYV NSIWDLLKNA IQEIQRKNNS GLSFEELYRN AYTMVLHKHG EKLYTGLREV VTEHLINKV REDVLNSLNN NFLQTLNQAW NDHQTAMVMI RDILMYMDRV YVQQNNVENV YNLGLIIFRD QVVRYGCIRD H LRQTLLDM IARERKGEVV DRGAIRNACQ MLMILGLEGR SVYEEDFEAP FLEMSAEFFQ MESQKFLAEN SASVYIKKVE AR INEEIER VMHCLDKSTE EPIVKVVERE LISKHMKTIV EMENSGLVHM LKNGKTEDLG CMYKLFSRVP NGLKTMCECM SSY LREQGK ALVSEEGEGK NPVDYIQGLL DLKSRFDRFL LESFNNDRLF KQTIAGDFEY FLNLNSRSPE YLSLFIDDKL KKGV KGLTE QEVETILDKA MVLFRFMQEK DVFERYYKQH LARRLLTNKS VSDDSEKNMI SKLKTECGCQ FTSKLEGMFR DMSIS NTTM DEFRQHLQAT GVSLGGVDLT VRVLTTGYWP TQSATPKCNI PPAPRHAFEI FRRFYLAKHS GRQLTLQHHM GSADLN ATF YGPVKKEDGS EVGVGGAQVT GSNTRKHILQ VSTFQMTILM LFNNREKYTF EEIQQETDIP ERELVRALQS LACGKPT QR VLTKEPKSKE IENGHIFTVN DQFTSKLHRV KIQTVAAKQG ESDPERKETR QKVDDDRKHE IEAAIVRIMK SRKKMQHN V LVAEVTQQLK ARFLPSPVVI KKRIEGLIER EYLARTPEDR KVYTYVAKLH HHHHH UniProtKB: Cullin-3 |
-Macromolecule #2: Kelch-like protein 22
Macromolecule | Name: Kelch-like protein 22 / type: protein_or_peptide / ID: 2 / Details: his-tev cleave site-klhl22 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 74.978117 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | String: MSYYHHHHHH DYDIPTTENL YFQGAMMAEE QEFTQLCKLP AQPSHPHCVN NTYRSAQHSQ ALLRGLLALR DSGILFDVVL VVEGRHIEA HRILLAASCD YFRGMFAGGL KEMEQEEVLI HGVSYNAMCQ ILHFIYTSEL ELSLSNVQET LVAACQLQIP E IIHFCCDF ...String: MSYYHHHHHH DYDIPTTENL YFQGAMMAEE QEFTQLCKLP AQPSHPHCVN NTYRSAQHSQ ALLRGLLALR DSGILFDVVL VVEGRHIEA HRILLAASCD YFRGMFAGGL KEMEQEEVLI HGVSYNAMCQ ILHFIYTSEL ELSLSNVQET LVAACQLQIP E IIHFCCDF LMSWVDEENI LDVYRLAELF DLSRLTEQLD TYILKNFVAF SRTDKYRQLP LEKVYSLLSS NRLEVSCETE VY EGALLYH YSLEQVQADQ ISLHEPPKLL ETVRFPLMEA EVLQRLHDKL DPSPLRDTVA SALMYHRNES LQPSLQSPQT ELR SDFQCV VGFGGIHSTP STVLSDQAKY LNPLLGEWKH FTASLAPRMS NQGIAVLNNF VYLIGGDNNV QGFRAESRCW RYDP RHNRW FQIQSLQQEH ADLSVCVVGR YIYAVAGRDY HNDLNAVERY DPATNSWAYV APLKREVYAH AGATLEGKMY ITCGR RGED YLKETHCYDP GSNTWHTLAD GPVRRAWHGM ATLLNKLYVI GGSNNDAGYR RDVHQVACYS CTSGQWSSVC PLPAGH GEP GIAVLDNRIY VLGGRSHNRG SRTGYVHIYD VEKDCWEEGP QLDNSISGLA ACVLTLPRSL LLEPPRGTPD RSQADPD FA SEVMSVSDWE EFDNSSED UniProtKB: Kelch-like protein 22 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 2.00 mg/mL | ||||||||||||
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Buffer | pH: 7.5 Component:
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Grid | Model: Quantifoil R1.2/1.3 / Support film - Material: CARBON / Support film - topology: CONTINUOUS | ||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: DIFFRACTION / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.5 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |