+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-12964 | |||||||||
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Title | Cryo-EM Structure of the DDB1-DCAF1-CUL4A-RBX1 Complex | |||||||||
Map data | ||||||||||
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Keywords | ubiquitin / E3 / protein degradation / LIGASE | |||||||||
Function / homology | Function and homology information histone H2AT120 kinase activity / cell competition in a multicellular organism / negative regulation of granulocyte differentiation / cullin-RING-type E3 NEDD8 transferase / cellular response to chemical stress / NEDD8 transferase activity / cullin-RING ubiquitin ligase complex / regulation of DNA damage checkpoint / V(D)J recombination / positive regulation by virus of viral protein levels in host cell ...histone H2AT120 kinase activity / cell competition in a multicellular organism / negative regulation of granulocyte differentiation / cullin-RING-type E3 NEDD8 transferase / cellular response to chemical stress / NEDD8 transferase activity / cullin-RING ubiquitin ligase complex / regulation of DNA damage checkpoint / V(D)J recombination / positive regulation by virus of viral protein levels in host cell / Cul7-RING ubiquitin ligase complex / ubiquitin-dependent protein catabolic process via the C-end degron rule pathway / regulation of nucleotide-excision repair / epigenetic programming in the zygotic pronuclei / Loss of Function of FBXW7 in Cancer and NOTCH1 Signaling / spindle assembly involved in female meiosis / positive regulation of protein autoubiquitination / Cul4-RING E3 ubiquitin ligase complex / UV-damage excision repair / protein neddylation / NEDD8 ligase activity / Cul5-RING ubiquitin ligase complex / biological process involved in interaction with symbiont / negative regulation of response to oxidative stress / regulation of mitotic cell cycle phase transition / ubiquitin-ubiquitin ligase activity / Cul4A-RING E3 ubiquitin ligase complex / SCF ubiquitin ligase complex / Cul2-RING ubiquitin ligase complex / WD40-repeat domain binding / 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 / positive regulation of G1/S transition of mitotic cell cycle / Prolactin receptor signaling / negative regulation of reproductive process / negative regulation of developmental process / protein monoubiquitination / cullin family protein binding / somatic stem cell population maintenance / hemopoiesis / viral release from host cell / ubiquitin-like ligase-substrate adaptor activity / ectopic germ cell programmed cell death / proteasomal protein catabolic process / protein K48-linked ubiquitination / positive regulation of viral genome replication / post-translational protein modification / Nuclear events stimulated by ALK signaling in cancer / regulation of cellular response to insulin stimulus / positive regulation of gluconeogenesis / positive regulation of TORC1 signaling / T cell activation / Regulation of BACH1 activity / intrinsic apoptotic signaling pathway / B cell differentiation / cellular response to amino acid stimulus / Degradation of DVL / regulation of circadian rhythm / nuclear estrogen receptor binding / nucleotide-excision repair / Recognition of DNA damage by PCNA-containing replication complex / Degradation of GLI1 by the proteasome / Negative regulation of NOTCH4 signaling / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / Vif-mediated degradation of APOBEC3G / Hedgehog 'on' state / Degradation of GLI2 by the proteasome / GLI3 is processed to GLI3R by the proteasome / Orc1 removal from chromatin / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / DNA Damage Recognition in GG-NER / RING-type E3 ubiquitin transferase / negative regulation of canonical Wnt signaling pathway / Degradation of beta-catenin by the destruction complex / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / G1/S transition of mitotic cell cycle / Formation of TC-NER Pre-Incision Complex / Dual Incision in GG-NER / Evasion by RSV of host interferon responses / NOTCH1 Intracellular Domain Regulates Transcription / Wnt signaling pathway / fibrillar center / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / Regulation of expression of SLITs and ROBOs / Formation of Incision Complex in GG-NER / Dual incision in TC-NER / Interleukin-1 signaling / Gap-filling DNA repair synthesis and ligation in TC-NER / Regulation of RAS by GAPs / protein polyubiquitination / positive regulation of protein catabolic process / rhythmic process / Regulation of RUNX2 expression and activity / cellular response to UV / MAPK cascade Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 8.4 Å | |||||||||
Authors | Mohamed WI / Schenk AD | |||||||||
Citation | Journal: EMBO J / Year: 2021 Title: The CRL4 cullin-RING ubiquitin ligase is activated following a switch in oligomerization state. Authors: Weaam I Mohamed / Andreas D Schenk / Georg Kempf / Simone Cavadini / Anja Basters / Alessandro Potenza / Wassim Abdul Rahman / Julius Rabl / Kurt Reichermeier / Nicolas H Thomä / Abstract: The cullin-4-based RING-type (CRL4) family of E3 ubiquitin ligases functions together with dedicated substrate receptors. Out of the ˜29 CRL4 substrate receptors reported, the DDB1- and CUL4- ...The cullin-4-based RING-type (CRL4) family of E3 ubiquitin ligases functions together with dedicated substrate receptors. Out of the ˜29 CRL4 substrate receptors reported, the DDB1- and CUL4-associated factor 1 (DCAF1) is essential for cellular survival and growth, and its deregulation has been implicated in tumorigenesis. We carried out biochemical and structural studies to examine the structure and mechanism of the CRL4 ligase. In the 8.4 Å cryo-EM map of CRL4 , four CUL4-RBX1-DDB1-DCAF1 protomers are organized into two dimeric sub-assemblies. In this arrangement, the WD40 domain of DCAF1 mediates binding with the cullin C-terminal domain (CTD) and the RBX1 subunit of a neighboring CRL4 protomer. This renders RBX1, the catalytic subunit of the ligase, inaccessible to the E2 ubiquitin-conjugating enzymes. Upon CRL4 activation by neddylation, the interaction between the cullin CTD and the neighboring DCAF1 protomer is broken, and the complex assumes an active dimeric conformation. Accordingly, a tetramerization-deficient CRL4 mutant has higher ubiquitin ligase activity compared to the wild-type. This study identifies a novel mechanism by which unneddylated and substrate-free CUL4 ligases can be maintained in an inactive state. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_12964.map.gz | 50.5 MB | EMDB map data format | |
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Header (meta data) | emd-12964-v30.xml emd-12964.xml | 16.4 KB 16.4 KB | Display Display | EMDB header |
Images | emd_12964.png | 73.2 KB | ||
Filedesc metadata | emd-12964.cif.gz | 7.6 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-12964 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-12964 | HTTPS FTP |
-Validation report
Summary document | emd_12964_validation.pdf.gz | 499.6 KB | Display | EMDB validaton report |
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Full document | emd_12964_full_validation.pdf.gz | 499.2 KB | Display | |
Data in XML | emd_12964_validation.xml.gz | 6.2 KB | Display | |
Data in CIF | emd_12964_validation.cif.gz | 7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-12964 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-12964 | HTTPS FTP |
-Related structure data
Related structure data | 7okqMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_12964.map.gz / Format: CCP4 / Size: 67 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 1.76 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : CRL4(DCAF1)
Entire | Name: CRL4(DCAF1) |
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Components |
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-Supramolecule #1: CRL4(DCAF1)
Supramolecule | Name: CRL4(DCAF1) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: DNA damage-binding protein 1
Macromolecule | Name: DNA damage-binding protein 1 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 129.394898 KDa |
Recombinant expression | Organism: Trichoplusia ni (cabbage looper) |
Sequence | String: MHHHHHHVDE NLYFQGGGRM SYNYVVTAQK PTAVNGCVTG HFTSAEDLNL LIAKNTRLEI YVVTAEGLRP VKEVGMYGKI AVMELFRPK GESKDLLFIL TAKYNACILE YKQSGESIDI ITRAHGNVQD RIGRPSETGI IGIIDPECRM IGLRLYDGLF K VIPLDRDN ...String: MHHHHHHVDE NLYFQGGGRM SYNYVVTAQK PTAVNGCVTG HFTSAEDLNL LIAKNTRLEI YVVTAEGLRP VKEVGMYGKI AVMELFRPK GESKDLLFIL TAKYNACILE YKQSGESIDI ITRAHGNVQD RIGRPSETGI IGIIDPECRM IGLRLYDGLF K VIPLDRDN KELKAFNIRL EELHVIDVKF LYGCQAPTIC FVYQDPQGRH VKTYEVSLRE KEFNKGPWKQ ENVEAEASMV IA VPEPFGG AIIIGQESIT YHNGDKYLAI APPIIKQSTI VCHNRVDPNG SRYLLGDMEG RLFMLLLEKE EQMDGTVTLK DLR VELLGE TSIAECLTYL DNGVVFVGSR LGDSQLVKLN VDSNEQGSYV VAMETFTNLG PIVDMCVVDL ERQGQGQLVT CSGA FKEGS LRIIRNGIGI HEHASIDLPG IKGLWPLRSD PNRETDDTLV LSFVGQTRVL MLNGEEVEET ELMGFVDDQQ TFFCG NVAH QQLIQITSAS VRLVSQEPKA LVSEWKEPQA KNISVASCNS SQVVVAVGRA LYYLQIHPQE LRQISHTEME HEVACL DIT PLGDSNGLSP LCAIGLWTDI SARILKLPSF ELLHKEMLGG EIIPRSILMT TFESSHYLLC ALGDGALFYF GLNIETG LL SDRKKVTLGT QPTVLRTFRS LSTTNVFACS DRPTVIYSSN HKLVFSNVNL KEVNYMCPLN SDGYPDSLAL ANNSTLTI G TIDEIQKLHI RTVPLYESPR KICYQEVSQC FGVLSSRIEV QDTSGGTTAL RPSASTQALS SSVSSSKLFS SSTAPHETS FGEEVEVHNL LIIDQHTFEV LHAHQFLQNE YALSLVSCKL GKDPNTYFIV GTAMVYPEEA EPKQGRIVVF QYSDGKLQTV AEKEVKGAV YSMVEFNGKL LASINSTVRL YEWTTEKELR TECNHYNNIM ALYLKTKGDF ILVGDLMRSV LLLAYKPMEG N FEEIARDF NPNWMSAVEI LDDDNFLGAE NAFNLFVCQK DSAATTDEER QHLQEVGLFH LGEFVNVFCH GSLVMQNLGE TS TPTQGSV LFGTVNGMIG LVTSLSESWY NLLLDMQNRL NKVIKSVGKI EHSFWRSFHT ERKTEPATGF IDGDLIESFL DIS RPKMQE VVANLQYDDG SGMKREATAD DLIKVVEELT RIH UniProtKB: DNA damage-binding protein 1 |
-Macromolecule #2: DDB1- and CUL4-associated factor 1
Macromolecule | Name: DDB1- and CUL4-associated factor 1 / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO / EC number: non-specific serine/threonine protein kinase |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 171.279094 KDa |
Recombinant expression | Organism: Trichoplusia ni (cabbage looper) |
Sequence | String: MASWSHPQFE KLEVLFQGPT TVVVHVDSKA ELTTLLEQWE KEHGSGQDMV PILTRMSQLI EKETEEYRKG DPDPFDDRHP GRADPECML GHLLRILFKN DDFMNALVNA YVMTSREPPL NTAACRLLLD IMPGLETAVV FQEKEGIVEN LFKWAREADQ P LRTYSTGL ...String: MASWSHPQFE KLEVLFQGPT TVVVHVDSKA ELTTLLEQWE KEHGSGQDMV PILTRMSQLI EKETEEYRKG DPDPFDDRHP GRADPECML GHLLRILFKN DDFMNALVNA YVMTSREPPL NTAACRLLLD IMPGLETAVV FQEKEGIVEN LFKWAREADQ P LRTYSTGL LGGAMENQDI AANYRDENSQ LVAIVLRRLR ELQLQEVALR QENKRPSPRK LSSEPLLPLD EEAVDMDYGD MA VDVVDGD QEEASGDMEI SFHLDSGHKT SSRVNSTTKP EDGGLKKNKS AKQGDRENFR KAKQKLGFSS SDPDRMFVEL SNS SWSEMS PWVIGTNYTL YPMTPAIEQR LILQYLTPLG EYQELLPIFM QLGSRELMMF YIDLKQTNDV LLTFEALKHL ASLL LHNKF ATEFVAHGGV QKLLEIPRPS MAATGVSMCL YYLSYNQDAM ERVCMHPHNV LSDVVNYTLW LMECSHASGC CHATM FFSI CFSFRAVLEL FDRYDGLRRL VNLISTLEIL NLEDQGALLS DDEIFASRQT GKHTCMALRK YFEAHLAIKL EQVKQS LQR TEGGILVHPQ PPYKACSYTH EQIVEMMEFL IEYGPAQLYW EPAEVFLKLS CVQLLLQLIS IACNWKTYYA RNDTVRF AL DVLAILTVVP KIQLQLAESV DVLDEAGSTV STVGISIILG VAEGEFFIHD AEIQKSALQI IINCVCGPDN RISSIGKF I SGTPRRKLPQ NPKSSEHTLA KMWNVVQSNN GIKVLLSLLS IKMPITDADQ IRALACKALV GLSRSSTVRQ IISKLPLFS SCQIQQLMKE PVLQDKRSDH VKFCKYAAEL IERVSGKPLL IGTDVSLARL QKADVVAQSR ISFPEKELLL LIRNHLISKG LGETATVLT KEADLPMTAA SHSSAFTPVT AAASPVSLPR TPRIANGIAT RLGSHAAVGA SAPSAPTAHP QPRPPQGPLA L PGPSYAGN SPLIGRISFI RERPSPCNGR KIRVLRQKSD HGAYSQSPAI KKQLDRHLPS PPTLDSIITE YLREQHARCK NP VATCPPF SLFTPHQCPE PKQRRQAPIN FTSRLNRRAS FPKYGGVDGG CFDRHLIFSR FRPISVFREA NEDESGFTCC AFS ARERFL MLGTCTGQLK LYNVFSGQEE ASYNCHNSAI THLEPSRDGS LLLTSATWSQ PLSALWGMKS VFDMKHSFTE DHYV EFSKH SQDRVIGTKG DIAHIYDIQT GNKLLTLFNP DLANNYKRNC ATFNPTDDLV LNDGVLWDVR SAQAIHKFDK FNMNI SGVF HPNGLEVIIN TEIWDLRTFH LLHTVPALDQ CRVVFNHTGT VMYGAMLQAD DEDDLMEERM KSPFGSSFRT FNATDY KPI ATIDVKRNIF DLCTDTKDCY LAVIENQGSM DALNMDTVCR LYEVGRQRLA EDEDEEEDQE EEEQEEEDDD EDDDDTD DL DELDTDQLLE AELEEDDNNE NAGEDGDNDF SPSDEELANL LEEGEDGEDE DSDADEEVEL ILGDTDSSDN SDLEDDII L SLNE UniProtKB: DDB1- and CUL4-associated factor 1 |
-Macromolecule #3: Cullin-4A
Macromolecule | Name: Cullin-4A / type: protein_or_peptide / ID: 3 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 86.702836 KDa |
Recombinant expression | Organism: Trichoplusia ni (cabbage looper) |
Sequence | String: MHHHHHHVDE ENLYFQGGGR GGSKKLVIKN FRDRPRLPDN YTQDTWRKLH EAVRAVQSST SIRYNLEELY QAVENLCSHK VSPMLYKQL RQACEDHVQA QILPFREDSL DSVLFLKKIN TCWQDHCRQM IMIRSIFLFL DRTYVLQNST LPSIWDMGLE L FRTHIISD ...String: MHHHHHHVDE ENLYFQGGGR GGSKKLVIKN FRDRPRLPDN YTQDTWRKLH EAVRAVQSST SIRYNLEELY QAVENLCSHK VSPMLYKQL RQACEDHVQA QILPFREDSL DSVLFLKKIN TCWQDHCRQM IMIRSIFLFL DRTYVLQNST LPSIWDMGLE L FRTHIISD KMVQSKTIDG ILLLIERERS GEAVDRSLLR SLLGMLSDLQ VYKDSFELKF LEETNCLYAA EGQRLMQERE VP EYLNHVS KRLEEEGDRV ITYLDHSTQK PLIACVEKQL LGEHLTAILQ KGLDHLLDEN RVPDLAQMYQ LFSRVRGGQQ ALL QHWSEY IKTFGTAIVI NPEKDKDMVQ DLLDFKDKVD HVIEVCFQKN ERFVNLMKES FETFINKRPN KPAELIAKHV DSKL RAGNK EATDEELERT LDKIMILFRF IHGKDVFEAF YKKDLAKRLL VGKSASVDAE KSMLSKLKHE CGAAFTSKLE GMFKD MELS KDIMVHFKQH MQNQSDSGPI DLTVNILTMG YWPTYTPMEV HLTPEMIKLQ EVFKAFYLGK HSGRKLQWQT TLGHAV LKA EFKEGKKEFQ VSLFQTLVLL MFNEGDGFSF EEIKMATGIE DSELRRTLQS LACGKARVLI KSPKGKEVED GDKFIFN GE FKHKLFRIKI NQIQMKETVE EQVSTTERVF QDRQYQIDAA IVRIMKMRKT LGHNLLVSEL YNQLKFPVKP GDLKKRIE S LIDRDYMERD KDNPNQYHYV A UniProtKB: Cullin-4A |
-Macromolecule #4: E3 ubiquitin-protein ligase RBX1
Macromolecule | Name: E3 ubiquitin-protein ligase RBX1 / type: protein_or_peptide / ID: 4 / Number of copies: 4 / Enantiomer: LEVO / EC number: RING-type E3 ubiquitin transferase |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 13.49724 KDa |
Recombinant expression | Organism: Trichoplusia ni (cabbage looper) |
Sequence | String: MHHHHHHVDE NLYFQGGGRG TNSGAGKKRF EVKKWNAVAL WAWDIVVDNC AICRNHIMDL CIECQANQAS ATSEECTVAW GVCNHAFHF HCISRWLKTR QVCPLDNREW EFQKYGH UniProtKB: E3 ubiquitin-protein ligase RBX1 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
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Vitrification | Cryogen name: ETHANE |
-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: 45.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: INSILICO MODEL |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 8.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 14000 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |
-Atomic model buiding 1
Initial model |
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Refinement | Space: REAL / Protocol: FLEXIBLE FIT / Overall B value: 596 / Target criteria: Real-space cross-correlation | ||||||
Output model | PDB-7okq: |