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- EMDB-36987: Structure of CUL3-RBX1-KLHL22 complex without CUL3 NA motif -

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Basic information

Entry
Database: EMDB / ID: EMD-36987
TitleStructure of CUL3-RBX1-KLHL22 complex without CUL3 NA motif
Map data
Sample
  • Complex: CUL3-RBX1-KLHL22 complex without CUL3 NA motif
    • Protein or peptide: Cullin-3
    • Protein or peptide: Kelch-like protein 22
    • Protein or peptide: E3 ubiquitin-protein ligase RBX1, N-terminally processed
KeywordsCullin Ring E3 ubiquitin ligase / LIGASE
Function / homology
Function and homology information


positive regulation of mitotic cell cycle phase transition / trophectodermal cellular morphogenesis / liver morphogenesis / POZ domain binding / nuclear protein quality control by the ubiquitin-proteasome system / polar microtubule / regulation protein catabolic process at postsynapse / COPII vesicle coating / anaphase-promoting complex-dependent catabolic process / cullin-RING-type E3 NEDD8 transferase ...positive regulation of mitotic cell cycle phase transition / trophectodermal cellular morphogenesis / liver morphogenesis / POZ domain binding / nuclear protein quality control by the ubiquitin-proteasome system / polar microtubule / regulation protein catabolic process at postsynapse / COPII vesicle coating / anaphase-promoting complex-dependent catabolic process / cullin-RING-type E3 NEDD8 transferase / NEDD8 transferase activity / cellular response to L-leucine / RHOBTB3 ATPase cycle / cullin-RING ubiquitin ligase complex / positive regulation of T cell mediated immune response to tumor cell / embryonic cleavage / positive regulation of mitotic metaphase/anaphase transition / cell projection organization / 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 / Notch binding / NEDD8 ligase activity / fibroblast apoptotic process / VCB complex / RHOBTB1 GTPase cycle / 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 / stem cell division / ubiquitin-ubiquitin ligase activity / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / Cul4A-RING E3 ubiquitin ligase complex / Cul4-RING E3 ubiquitin ligase complex / mitotic metaphase chromosome alignment / Cul3-RING ubiquitin ligase complex / Cul4B-RING E3 ubiquitin ligase complex / stress fiber assembly / mitotic spindle assembly checkpoint signaling / ubiquitin ligase complex scaffold activity / negative regulation of mitophagy / negative regulation of Rho protein signal transduction / Prolactin receptor signaling / positive regulation of cytokinesis / cullin family protein binding / mitotic sister chromatid segregation / protein monoubiquitination / endoplasmic reticulum to Golgi vesicle-mediated transport / sperm flagellum / RHOBTB2 GTPase cycle / ubiquitin-like ligase-substrate adaptor activity / protein K48-linked ubiquitination / intercellular bridge / protein autoubiquitination / Nuclear events stimulated by ALK signaling in cancer / Regulation of BACH1 activity / gastrulation / positive regulation of protein ubiquitination / 14-3-3 protein binding / transcription-coupled nucleotide-excision repair / regulation of cellular response to insulin stimulus / positive regulation of TORC1 signaling / post-translational protein modification / intrinsic apoptotic signaling pathway / negative regulation of insulin receptor signaling pathway / negative regulation of autophagy / cyclin binding / T cell activation / Degradation of DVL / Recognition of DNA damage by PCNA-containing replication complex / Degradation of GLI1 by the proteasome / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / integrin-mediated 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 / cellular response to amino acid stimulus / Degradation of beta-catenin by the destruction complex / Evasion by RSV of host interferon responses / kidney development / NOTCH1 Intracellular Domain Regulates Transcription / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / 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 / G1/S transition of mitotic cell cycle / negative regulation of canonical Wnt signaling pathway / Formation of Incision Complex in GG-NER
Similarity search - Function
Kelch-like protein 22 / KLHDC2/KLHL20/DRC7 Kelch-repeats domain / Zinc finger, RING-H2-type / RING-H2 zinc finger domain / BTB-kelch protein / Cullin protein neddylation domain / BTB/Kelch-associated / BTB And C-terminal Kelch / BTB And C-terminal Kelch / : ...Kelch-like protein 22 / KLHDC2/KLHL20/DRC7 Kelch-repeats domain / Zinc finger, RING-H2-type / RING-H2 zinc finger domain / BTB-kelch protein / Cullin protein neddylation domain / BTB/Kelch-associated / BTB And C-terminal Kelch / BTB And C-terminal Kelch / : / Cullin, conserved site / Cullin family signature. / Cullin repeat-like-containing domain superfamily / Cullin protein, neddylation domain / Cullin / Kelch motif / Cullin protein neddylation domain / Kelch / Kelch repeat type 1 / 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 / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, RING/FYVE/PHD-type / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
E3 ubiquitin-protein ligase RBX1 / Cullin-3 / Kelch-like protein 22
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.2 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
DepositionAug 1, 2023-
Header (metadata) releaseMay 29, 2024-
Map releaseMay 29, 2024-
UpdateMay 29, 2024-
Current statusMay 29, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_36987.png

Downloads & links

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Map

FileDownload / File: emd_36987.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 512 pix.
= 420.352 Å		0.82 Å/pix.
x 512 pix.
= 420.352 Å		0.82 Å/pix.
x 512 pix.
= 420.352 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.821 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.03
Minimum - Maximum-0.0017606413 - 2.1750598
Average (Standard dev.)0.00019665023 (±0.010278317)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
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(NA motif deletion)-RBX1-KLHL22 complex

Fileemd_36987_additional_1.map
AnnotationRaw map of CUL3(NA motif deletion)-RBX1-KLHL22 complex
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Half map: half map B

Fileemd_36987_half_map_1.map
Annotationhalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map A

Fileemd_36987_half_map_2.map
Annotationhalf map A
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
    • Protein or peptide: E3 ubiquitin-protein ligase RBX1, N-terminally processed

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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: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 87.432312 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MDEKYVNSIW DLLKNAIQEI QRKNNSGLSF EELYRNAYTM VLHKHGEKLY TGLREVVTEH LINKVREDVL NSLNNNFLQT LNQAWNDHQ TAMVMIRDIL MYMDRVYVQQ NNVENVYNLG LIIFRDQVVR YGCIRDHLRQ TLLDMIARER KGEVVDRGAI R NACQMLMI ...String:
MDEKYVNSIW DLLKNAIQEI QRKNNSGLSF EELYRNAYTM VLHKHGEKLY TGLREVVTEH LINKVREDVL NSLNNNFLQT LNQAWNDHQ TAMVMIRDIL MYMDRVYVQQ NNVENVYNLG LIIFRDQVVR YGCIRDHLRQ TLLDMIARER KGEVVDRGAI R NACQMLMI LGLEGRSVYE EDFEAPFLEM SAEFFQMESQ KFLAENSASV YIKKVEARIN EEIERVMHCL DKSTEEPIVK VV ERELISK HMKTIVEMEN SGLVHMLKNG KTEDLGCMYK LFSRVPNGLK TMCECMSSYL REQGKALVSE EGEGKNPVDY IQG LLDLKS RFDRFLLESF NNDRLFKQTI AGDFEYFLNL NSRSPEYLSL FIDDKLKKGV KGLTEQEVET ILDKAMVLFR FMQE KDVFE RYYKQHLARR LLTNKSVSDD SEKNMISKLK TECGCQFTSK LEGMFRDMSI SNTTMDEFRQ HLQATGVSLG GVDLT VRVL TTGYWPTQSA TPKCNIPPAP RHAFEIFRRF YLAKHSGRQL TLQHHMGSAD LNATFYGPVK KEDGSEVGVG GAQVTG SNT RKHILQVSTF QMTILMLFNN REKYTFEEIQ QETDIPEREL VRALQSLACG KPTQRVLTKE PKSKEIENGH IFTVNDQ FT SKLHRVKIQT VAAKQGESDP ERKETRQKVD DDRKHEIEAA IVRIMKSRKK MQHNVLVAEV TQQLKARFLP SPVVIKKR I EGLIEREYLA RTPEDRKVYT YVAKLHHHHH H

UniProtKB: Cullin-3

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Macromolecule #2: Kelch-like protein 22

MacromoleculeName: Kelch-like protein 22 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 20.36534 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString:
MAEEQEFTQL CKLPAQPSHP HCVNNTYRSA QHSQALLRGL LALRDSGILF DVVLVVEGRH IEAHRILLAA SCDYFRGMFA GGLKEMEQE EVLIHGVSYN AMCQILHFIY TSELELSLSN VQETLVAACQ LQIPEIIHFC CDFLMSWVDE ENILDVYRLA E LFDLSRLT EQLDTYILKN

UniProtKB: Kelch-like protein 22

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Macromolecule #3: E3 ubiquitin-protein ligase RBX1, N-terminally processed

MacromoleculeName: E3 ubiquitin-protein ligase RBX1, N-terminally processed
type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 12.289977 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString:
MAAAMDVDTP SGTNSGAGKK RFEVKKWNAV ALWAWDIVVD NCAICRNHIM DLCIECQANQ ASATSEECTV AWGVCNHAFH FHCISRWLK TRQVCPLDNR EWEFQKYGH

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

Concentration2.00 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
150.0 mMNaClsodium 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
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 50.0 e/Å2
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
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 74279
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.2) / Number images used: 74279
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC (ver. 4.2)
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC (ver. 4.2)
Final 3D classificationSoftware - Name: cryoSPARC (ver. 4.2)
FSC plot (resolution estimation)

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