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Open data
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Basic information
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Title | CAND1-CUL1-RBX1-SKP1-SKP2-CKS1-CDK2 | |||||||||||||||
![]() | CUL1-RBX1-CAND1-SKP1-SKP2-CKS1-CDK2 | |||||||||||||||
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![]() | CAND1 / substrate receptor exchange factor / cullin-RING ligase / CRL / SCF / ligase / neddylation / DCNL1 co-E3 / ubiquitin signaling | |||||||||||||||
Function / homology | ![]() SCF complex assembly / positive regulation of protein polyubiquitination / Parkin-FBXW7-Cul1 ubiquitin ligase complex / F-box domain binding / PcG protein complex / Aberrant regulation of mitotic exit in cancer due to RB1 defects / negative regulation of catalytic activity / cullin-RING-type E3 NEDD8 transferase / cellular response to chemical stress / NEDD8 transferase activity ...SCF complex assembly / positive regulation of protein polyubiquitination / Parkin-FBXW7-Cul1 ubiquitin ligase complex / F-box domain binding / PcG protein complex / Aberrant regulation of mitotic exit in cancer due to RB1 defects / negative regulation of catalytic activity / cullin-RING-type E3 NEDD8 transferase / cellular response to chemical stress / NEDD8 transferase activity / mitotic cell cycle phase transition / cullin-RING ubiquitin ligase complex / Cul7-RING ubiquitin ligase complex / ubiquitin-dependent protein catabolic process via the C-end degron rule pathway / positive regulation of ubiquitin protein ligase activity / Loss of Function of FBXW7 in Cancer and NOTCH1 Signaling / maintenance of protein location in nucleus / positive regulation of protein autoubiquitination / protein neddylation / cyclin-dependent protein serine/threonine kinase activator activity / NEDD8 ligase activity / Cul5-RING ubiquitin ligase complex / negative regulation of response to oxidative stress / positive regulation of intracellular estrogen receptor signaling pathway / ubiquitin-ubiquitin ligase activity / Cul4A-RING E3 ubiquitin ligase complex / SCF ubiquitin ligase complex / Cul2-RING ubiquitin ligase complex / ubiquitin ligase complex scaffold activity / Cul4B-RING E3 ubiquitin ligase complex / negative regulation of type I interferon production / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / Cul3-RING ubiquitin ligase complex / cyclin A1-CDK2 complex / cyclin E2-CDK2 complex / cyclin E1-CDK2 complex / cyclin A2-CDK2 complex / positive regulation of DNA-templated DNA replication initiation / G2 Phase / cyclin-dependent protein kinase activity / Y chromosome / Phosphorylation of proteins involved in G1/S transition by active Cyclin E:Cdk2 complexes / positive regulation of heterochromatin formation / p53-Dependent G1 DNA Damage Response / Prolactin receptor signaling / X chromosome / PTK6 Regulates Cell Cycle / protein monoubiquitination / regulation of anaphase-promoting complex-dependent catabolic process / Defective binding of RB1 mutants to E2F1,(E2F2, E2F3) / cullin family protein binding / centriole replication / Regulation of APC/C activators between G1/S and early anaphase / telomere maintenance in response to DNA damage / centrosome duplication / protein K63-linked ubiquitination / G0 and Early G1 / Telomere Extension By Telomerase / positive regulation of double-strand break repair via homologous recombination / ubiquitin-like ligase-substrate adaptor activity / Activation of the pre-replicative complex / cellular response to nitric oxide / positive regulation of RNA polymerase II transcription preinitiation complex assembly / Regulation of MITF-M-dependent genes involved in cell cycle and proliferation / cyclin-dependent kinase / protein K48-linked ubiquitination / cyclin-dependent protein serine/threonine kinase activity / TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest / Nuclear events stimulated by ALK signaling in cancer / Activation of ATR in response to replication stress / Cyclin E associated events during G1/S transition / Cyclin A/B1/B2 associated events during G2/M transition / Cajal body / cyclin-dependent protein kinase holoenzyme complex / Cyclin A:Cdk2-associated events at S phase entry / ubiquitin ligase complex / condensed chromosome / mitotic G1 DNA damage checkpoint signaling / regulation of mitotic cell cycle / regulation of G2/M transition of mitotic cell cycle / positive regulation of TORC1 signaling / T cell activation / TBP-class protein binding / : / regulation of cellular response to insulin stimulus / Regulation of BACH1 activity / intrinsic apoptotic signaling pathway / cyclin binding / MAP3K8 (TPL2)-dependent MAPK1/3 activation / post-translational protein modification / positive regulation of DNA replication / meiotic cell cycle / ubiquitin binding / male germ cell nucleus / molecular function activator activity / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / Vpu mediated degradation of CD4 / Degradation of DVL / Dectin-1 mediated noncanonical NF-kB signaling Similarity search - Function | |||||||||||||||
Biological species | ![]() | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.1 Å | |||||||||||||||
![]() | Shaaban M / Clapperton JA / Ding S / Maeots ME / Enchev RI / Maslen S / Skehel JM | |||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural and mechanistic insights into the CAND1-mediated SCF substrate receptor exchange. Authors: Mohammed Shaaban / Julie A Clapperton / Shan Ding / Simone Kunzelmann / Märt-Erik Mäeots / Sarah L Maslen / J Mark Skehel / Radoslav I Enchev / ![]() Abstract: Modular SCF (SKP1-CUL1-Fbox) ubiquitin E3 ligases orchestrate multiple cellular pathways in eukaryotes. Their variable SKP1-Fbox substrate receptor (SR) modules enable regulated substrate recruitment ...Modular SCF (SKP1-CUL1-Fbox) ubiquitin E3 ligases orchestrate multiple cellular pathways in eukaryotes. Their variable SKP1-Fbox substrate receptor (SR) modules enable regulated substrate recruitment and subsequent proteasomal degradation. CAND proteins are essential for the efficient and timely exchange of SRs. To gain structural understanding of the underlying molecular mechanism, we reconstituted a human CAND1-driven exchange reaction of substrate-bound SCF alongside its co-E3 ligase DCNL1 and visualized it by cryo-EM. We describe high-resolution structural intermediates, including a ternary CAND1-SCF complex, as well as conformational and compositional intermediates representing SR- or CAND1-dissociation. We describe in molecular detail how CAND1-induced conformational changes in CUL1/RBX1 provide an optimized DCNL1-binding site and reveal an unexpected dual role for DCNL1 in CAND1-SCF dynamics. Moreover, a partially dissociated CAND1-SCF conformation accommodates cullin neddylation, leading to CAND1 displacement. Our structural findings, together with functional biochemical assays, help formulate a detailed model for CAND-SCF regulation. | |||||||||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 111.2 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 25.3 KB 25.3 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 11.3 KB | Display | ![]() |
Images | ![]() | 153.4 KB | ||
Filedesc metadata | ![]() | 8.3 KB | ||
Others | ![]() ![]() | 98.6 MB 98.6 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8or0MC ![]() 8or2C ![]() 8or3C ![]() 8or4C M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
File | ![]() | ||||||||||||||||||||
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Annotation | CUL1-RBX1-CAND1-SKP1-SKP2-CKS1-CDK2 | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.08 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_17114_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_17114_half_map_2.map | ||||||||||||
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Density Histograms |
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Sample components
-Entire : CAND1-CUL1-RBX1-SKP1-SKP2-CKS1-CDK2
Entire | Name: CAND1-CUL1-RBX1-SKP1-SKP2-CKS1-CDK2 |
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Components |
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-Supramolecule #1: CAND1-CUL1-RBX1-SKP1-SKP2-CKS1-CDK2
Supramolecule | Name: CAND1-CUL1-RBX1-SKP1-SKP2-CKS1-CDK2 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#7 / Details: Ternary complex CAND1-SCF |
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Source (natural) | Organism: ![]() |
-Macromolecule #1: Cullin-1
Macromolecule | Name: Cullin-1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 93.730672 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MWSHPQFEKG SAGSAAGSGA GWSHPQFEKL EVLFQGPMSS TRSQNPHGLK QIGLDQIWDD LRAGIQQVYT RQSMAKSRYM ELYTHVYNY CTSVHQSNQA RGAGVPPSKS KKGQTPGGAQ FVGLELYKRL KEFLKNYLTN LLKDGEDLMD ESVLKFYTQQ W EDYRFSSK ...String: MWSHPQFEKG SAGSAAGSGA GWSHPQFEKL EVLFQGPMSS TRSQNPHGLK QIGLDQIWDD LRAGIQQVYT RQSMAKSRYM ELYTHVYNY CTSVHQSNQA RGAGVPPSKS KKGQTPGGAQ FVGLELYKRL KEFLKNYLTN LLKDGEDLMD ESVLKFYTQQ W EDYRFSSK VLNGICAYLN RHWVRRECDE GRKGIYEIYS LALVTWRDCL FRPLNKQVTN AVLKLIEKER NGETINTRLI SG VVQSYVE LGLNEDDAFA KGPTLTVYKE SFESQFLADT ERFYTRESTE FLQQNPVTEY MKKAEARLLE EQRRVQVYLH EST QDELAR KCEQVLIEKH LEIFHTEFQN LLDADKNEDL GRMYNLVSRI QDGLGELKKL LETHIHNQGL AAIEKCGEAA LNDP KMYVQ TVLDVHKKYN ALVMSAFNND AGFVAALDKA CGRFINNNAV TKMAQSSSKS PELLARYCDS LLKKSSKNPE EAELE DTLN QVMVVFKYIE DKDVFQKFYA KMLAKRLVHQ NSASDDAEAS MISKLKQACG FEYTSKLQRM FQDIGVSKDL NEQFKK HLT NSEPLDLDFS IQVLSSGSWP FQQSCTFALP SELERSYQRF TAFYASRHSG RKLTWLYQLS KGELVTNCFK NRYTLQA ST FQMAILLQYN TEDAYTVQQL TDSTQIKMDI LAQVLQILLK SKLLVLEDEN ANVDEVELKP DTLIKLYLGY KNKKLRVN I NVPMKTEQKQ EQETTHKNIE EDRKLLIQAA IVRIMKMRKV LKHQQLLGEV LTQLSSRFKP RVPVIKKCID ILIEKEYLE RVDGEKDTYS YLA UniProtKB: Cullin-1 |
-Macromolecule #2: E3 ubiquitin-protein ligase RBX1
Macromolecule | Name: E3 ubiquitin-protein ligase RBX1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: RING-type E3 ubiquitin transferase |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 12.289977 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MAAAMDVDTP SGTNSGAGKK RFEVKKWNAV ALWAWDIVVD NCAICRNHIM DLCIECQANQ ASATSEECTV AWGVCNHAFH FHCISRWLK TRQVCPLDNR EWEFQKYGH UniProtKB: E3 ubiquitin-protein ligase RBX1 |
-Macromolecule #3: Cullin-associated NEDD8-dissociated protein 1
Macromolecule | Name: Cullin-associated NEDD8-dissociated protein 1 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 137.358219 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: GSPEFPGRMA SASYHISNLL EKMTSSDKDF RFMATNDLMT ELQKDSIKLD DDSERKVVKM ILKLLEDKNG EVQNLAVKCL GPLVSKVKE YQVETIVDTL CTNMLSDKEQ LRDISSIGLK TVIGELPPAS SGSALAANVC KKITGRLTSA IAKQEDVSVQ L EALDIMAD ...String: GSPEFPGRMA SASYHISNLL EKMTSSDKDF RFMATNDLMT ELQKDSIKLD DDSERKVVKM ILKLLEDKNG EVQNLAVKCL GPLVSKVKE YQVETIVDTL CTNMLSDKEQ LRDISSIGLK TVIGELPPAS SGSALAANVC KKITGRLTSA IAKQEDVSVQ L EALDIMAD MLSRQGGLLV NFHPSILTCL LPQLTSPRLA VRKRTIIALG HLVMSCGNIV FVDLIEHLLS ELSKNDSMST TR TYIQCIA AISRQAGHRI GEYLEKIIPL VVKFCNVDDD ELREYCIQAF ESFVRRCPKE VYPHVSTIIN ICLKYLTYDP NYN YDDEDE DENAMDADGG DDDDQGSDDE YSDDDDMSWK VRRAAAKCLD AVVSTRHEML PEFYKTVSPA LISRFKEREE NVKA DVFHA YLSLLKQTRP VQSWLCDPDA MEQGETPLTM LQSQVPNIVK ALHKQMKEKS VKTRQCCFNM LTELVNVLPG ALTQH IPVL VPGIIFSLND KSSSSNLKID ALSCLYVILC NHSPQVFHPH VQALVPPVVA CVGDPFYKIT SEALLVTQQL VKVIRP LDQ PSSFDATPYI KDLFTCTIKR LKAADIDQEV KERAISCMGQ IICNLGDNLG SDLPNTLQIF LERLKNEITR LTTVKAL TL IAGSPLKIDL RPVLGEGVPI LASFLRKNQR ALKLGTLSAL DILIKNYSDS LTAAMIDAVL DELPPLISES DMHVSQMA I SFLTTLAKVY PSSLSKISGS ILNELIGLVR SPLLQGGALS AMLDFFQALV VTGTNNLGYM DLLRMLTGPV YSQSTALTH KQSYYSIAKC VAALTRACPK EGPAVVGQFI QDVKNSRSTD SIRLLALLSL GEVGHHIDLS GQLELKSVIL EAFSSPSEEV KSAASYALG SISVGNLPEY LPFVLQEITS QPKRQYLLLH SLKEIISSAS VVGLKPYVEN IWALLLKHCE CAEEGTRNVV A ECLGKLTL IDPETLLPRL KGYLISGSSY ARSSVVTAVK FTISDHPQPI DPLLKNCIGD FLKTLEDPDL NVRRVALVTF NS AAHNKPS LIRDLLDTVL PHLYNETKVR KELIREVEMG PFKHTVDDGL DIRKAAFECM YTLLDSCLDR LDIFEFLNHV EDG LKDHYD IKMLTFLMLV RLSTLCPSAV LQRLDRLVEP LRATCTTKVK ANSVKQEFEK QDELKRSAMR AVAALLTIPE AEKS PLMSE FQSQISSNPE LAAIFESIQK DSSSTNLESM DTS UniProtKB: Cullin-associated NEDD8-dissociated protein 1 |
-Macromolecule #4: S-phase kinase-associated protein 1
Macromolecule | Name: S-phase kinase-associated protein 1 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 18.679965 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MPSIKLQSSD GEIFEVDVEI AKQSVTIKTM LEDLGMDDEG DDDPVPLPNV NAAILKKVIQ WCTHHKDDPP PPEDDENKEK RTDDIPVWD QEFLKVDQGT LFELILAANY LDIKGLLDVT CKTVANMIKG KTPEEIRKTF NIKNDFTEEE EAQVRKENQW C EEK UniProtKB: S-phase kinase-associated protein 1 |
-Macromolecule #5: S-phase kinase-associated protein 2
Macromolecule | Name: S-phase kinase-associated protein 2 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 48.335312 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: GSPEFMHRKH LQEIPDLSSN VATSFTWGWD SSKTSELLSG MGVSALEKEE PDSENIPQEL LSNLGHPESP PRKRLKSKGS DKDFVIVRR PKLNRENFPG VSWDSLPDEL LLGIFSCLCL PELLKVSGVC KRWYRLASDE SLWQTLDLTG KNLHPDVTGR L LSQGVIAF ...String: GSPEFMHRKH LQEIPDLSSN VATSFTWGWD SSKTSELLSG MGVSALEKEE PDSENIPQEL LSNLGHPESP PRKRLKSKGS DKDFVIVRR PKLNRENFPG VSWDSLPDEL LLGIFSCLCL PELLKVSGVC KRWYRLASDE SLWQTLDLTG KNLHPDVTGR L LSQGVIAF RCPRSFMDQP LAEHFSPFRV QHMDLSNSVI EVSTLHGILS QCSKLQNLSL EGLRLSDPIV NTLAKNSNLV RL NLSGCSG FSEFALQTLL SSCSRLDELN LSWCFDFTEK HVQVAVAHVS ETITQLNLSG YRKNLQKSDL STLVRRCPNL VHL DLSDSV MLKNDCFQEF FQLNYLQHLS LSRCYDIIPE TLLELGEIPT LKTLQVFGIV PDGTLQLLKE ALPHLQINCS HFTT IARPT IGNKKNQEIW GIKCRLTLQK PSCL UniProtKB: S-phase kinase-associated protein 2 |
-Macromolecule #6: Cyclin-dependent kinases regulatory subunit 1
Macromolecule | Name: Cyclin-dependent kinases regulatory subunit 1 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 8.894114 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: GPLGSQIYYS DKYDDEEFEY RHVMLPKDIA KLVPKTHLMS ESEWRNLGVQ QSQGWVHYMI HEPEPHILLF RRPL UniProtKB: Cyclin-dependent kinases regulatory subunit 1 |
-Macromolecule #7: Cyclin-dependent kinase 2
Macromolecule | Name: Cyclin-dependent kinase 2 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO / EC number: cyclin-dependent kinase |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 33.976488 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MENFQKVEKI GEGTYGVVYK ARNKLTGEVV ALKKIRLDTE TEGVPSTAIR EISLLKELNH PNIVKLLDVI HTENKLYLVF EFLHQDLKK FMDASALTGI PLPLIKSYLF QLLQGLAFCH SHRVLHRDLK PQNLLINTEG AIKLADFGLA RAFGVPVRTY T HEVVTLWY ...String: MENFQKVEKI GEGTYGVVYK ARNKLTGEVV ALKKIRLDTE TEGVPSTAIR EISLLKELNH PNIVKLLDVI HTENKLYLVF EFLHQDLKK FMDASALTGI PLPLIKSYLF QLLQGLAFCH SHRVLHRDLK PQNLLINTEG AIKLADFGLA RAFGVPVRTY T HEVVTLWY RAPEILLGCK YYSTAVDIWS LGCIFAEMVT RRALFPGDSE IDQLFRIFRT LGTPDEVVWP GVTSMPDYKP SF PKWARQD FSKVVPPLDE DGRSLLSQML HYDPNKRISA KAALAHPFFQ DVTKPVPHLR L UniProtKB: Cyclin-dependent kinase 2 |
-Macromolecule #8: ZINC ION
Macromolecule | Name: ZINC ION / type: ligand / ID: 8 / Number of copies: 3 / Formula: ZN |
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Molecular weight | Theoretical: 65.409 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.5 Component:
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Grid | Model: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 400 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. | ||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 49.1 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.7000000000000001 µm / Nominal magnification: 130000 |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |