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- EMDB-36961: Structure of CUL3-RBX1-KLHL22 complex -

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Basic information

Entry
Database: EMDB / ID: EMD-36961
TitleStructure of CUL3-RBX1-KLHL22 complex
Map data
Sample
  • Complex: CUL3-RBX1-KLHL22 complex without CUL3 NA motif
    • Protein or peptide: Cullin-3
    • Protein or peptide: Kelch-like protein 22
KeywordsCullin 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 / anaphase-promoting complex-dependent catabolic process / COPII vesicle coating / 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 / anaphase-promoting complex-dependent catabolic process / COPII vesicle coating / stem cell division / cellular response to L-leucine / RHOBTB3 ATPase cycle / embryonic cleavage / cell projection organization / positive regulation of mitotic metaphase/anaphase transition / Notch binding / RHOBTB1 GTPase cycle / fibroblast apoptotic process / negative regulation of Rho protein signal transduction / negative regulation of type I interferon production / ubiquitin ligase complex scaffold activity / mitotic metaphase chromosome alignment / Cul3-RING ubiquitin ligase complex / intercellular bridge / mitotic spindle assembly checkpoint signaling / stress fiber assembly / positive regulation of cytokinesis / protein monoubiquitination / mitotic sister chromatid segregation / ubiquitin-like ligase-substrate adaptor activity / sperm flagellum / protein autoubiquitination / protein K48-linked ubiquitination / RHOBTB2 GTPase cycle / endoplasmic reticulum to Golgi vesicle-mediated transport / gastrulation / 14-3-3 protein binding / positive regulation of TORC1 signaling / cyclin binding / intrinsic apoptotic signaling pathway / negative regulation of autophagy / positive regulation of protein ubiquitination / integrin-mediated signaling pathway / Degradation of DVL / cellular response to amino acid stimulus / Hedgehog 'on' state / protein destabilization / G1/S transition of mitotic cell cycle / mitotic spindle / Wnt signaling pathway / spindle pole / Regulation of RAS by GAPs / protein polyubiquitination / microtubule cytoskeleton / KEAP1-NFE2L2 pathway / ubiquitin protein ligase activity / cell migration / Antigen processing: Ubiquitination & Proteasome degradation / Neddylation / gene expression / ubiquitin-dependent protein catabolic process / positive regulation of cell growth / postsynapse / proteasome-mediated ubiquitin-dependent protein catabolic process / 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 / membrane / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Kelch-like protein 22 / Kelch motif / Galactose oxidase, central domain / BTB-kelch protein / BTB/Kelch-associated / BTB And C-terminal Kelch / BTB And C-terminal Kelch / Cullin protein neddylation domain / Cullin, conserved site / Cullin family signature. ...Kelch-like protein 22 / Kelch motif / Galactose oxidase, central domain / BTB-kelch protein / BTB/Kelch-associated / BTB And C-terminal Kelch / BTB And C-terminal Kelch / Cullin protein neddylation domain / Cullin, conserved site / Cullin family signature. / Cullin / Cullin repeat-like-containing domain superfamily / Cullin protein, neddylation domain / Cullin protein neddylation domain / Kelch / Kelch repeat type 1 / Kelch motif / Cullin / Cullin, N-terminal / Cullin homology domain / Cullin homology domain superfamily / Cullin family / Cullin family profile. / Kelch-type beta propeller / BTB/POZ domain / BTB domain profile. / Broad-Complex, Tramtrack and Bric a brac / BTB/POZ domain / SKP1/BTB/POZ domain superfamily / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
Cullin-3 / Kelch-like protein 22
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsWang W / Ling L / Dai Z / Zuo P / Yin Y
Funding support China, 4 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)2021YFA1300601 China
National Natural Science Foundation of China (NSFC)82030081 China
National Natural Science Foundation of China (NSFC)81874235 China
National Natural Science Foundation of China (NSFC)31800626 China
CitationJournal: 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
DepositionJul 31, 2023-
Header (metadata) releaseMay 22, 2024-
Map releaseMay 22, 2024-
UpdateMay 22, 2024-
Current statusMay 22, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_36961.png

Downloads & links

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Map

FileDownload / File: emd_36961.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.821 Å
Density
Contour LevelBy AUTHOR: 1.0
Minimum - Maximum-1.0081384 - 126.027690000000007
Average (Standard dev.)-0.0007052877 (±0.9712841)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 420.352 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Raw map of CUL3-RBX1-KLHL22 dimer complex

Fileemd_36961_additional_1.map
AnnotationRaw map of CUL3-RBX1-KLHL22 dimer complex
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : CUL3-RBX1-KLHL22 complex without CUL3 NA motif

EntireName: CUL3-RBX1-KLHL22 complex without CUL3 NA motif
Components
  • Complex: CUL3-RBX1-KLHL22 complex without CUL3 NA motif
    • Protein or peptide: Cullin-3
    • Protein or peptide: Kelch-like protein 22

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Supramolecule #1: CUL3-RBX1-KLHL22 complex without CUL3 NA motif

SupramoleculeName: CUL3-RBX1-KLHL22 complex without CUL3 NA motif / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Cullin-3

MacromoleculeName: Cullin-3 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 90.134555 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: 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

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Macromolecule #2: Kelch-like protein 22

MacromoleculeName: Kelch-like protein 22 / type: protein_or_peptide / ID: 2 / Details: his-tev cleave site-klhl22 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 74.978117 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: 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

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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

Concentration2.00 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
150.0 mMNaClSodium chloridesodium chloride
20.0 mMTristris(hydroxymethyl)aminomethane
1.0 mMTCEP2-Amino-2-(hydroxymethyl)propane-1,3-diol
GridModel: Quantifoil R1.2/1.3 / Support film - Material: CARBON / Support film - topology: CONTINUOUS
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: DIFFRACTION / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.5 µm
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC (ver. 4.2)
Final 3D classificationSoftware - Name: cryoSPARC (ver. 4.2)
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC (ver. 4.2)
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.2) / Number images used: 142416

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