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- EMDB-12964: Cryo-EM Structure of the DDB1-DCAF1-CUL4A-RBX1 Complex -

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Basic information

Entry
Database: EMDB / ID: EMD-12964
TitleCryo-EM Structure of the DDB1-DCAF1-CUL4A-RBX1 Complex
Map data
Sample
  • Complex: CRL4(DCAF1)
    • Protein or peptide: DNA damage-binding protein 1
    • Protein or peptide: DDB1- and CUL4-associated factor 1
    • Protein or peptide: Cullin-4A
    • Protein or peptide: E3 ubiquitin-protein ligase RBX1
Keywordsubiquitin / E3 / protein degradation / LIGASE
Function / homology
Function and homology information


cell competition in a multicellular organism / histone H2AT120 kinase activity / negative regulation of granulocyte differentiation / cullin-RING-type E3 NEDD8 transferase / NEDD8 transferase activity / cullin-RING ubiquitin ligase complex / V(D)J recombination / Cul7-RING ubiquitin ligase complex / ubiquitin-dependent protein catabolic process via the C-end degron rule pathway / regulation of DNA damage checkpoint ...cell competition in a multicellular organism / histone H2AT120 kinase activity / negative regulation of granulocyte differentiation / cullin-RING-type E3 NEDD8 transferase / NEDD8 transferase activity / cullin-RING ubiquitin ligase complex / V(D)J recombination / Cul7-RING ubiquitin ligase complex / ubiquitin-dependent protein catabolic process via the C-end degron rule pathway / regulation of DNA damage checkpoint / positive regulation by virus of viral protein levels in host cell / cellular response to chemical stress / Loss of Function of FBXW7 in Cancer and NOTCH1 Signaling / positive regulation of protein autoubiquitination / spindle assembly involved in female meiosis / RNA polymerase II transcription initiation surveillance / protein neddylation / regulation of nucleotide-excision repair / epigenetic programming in the zygotic pronuclei / UV-damage excision repair / NEDD8 ligase activity / VCB complex / negative regulation of response to oxidative stress / Cul5-RING ubiquitin ligase complex / biological process involved in interaction with symbiont / SCF ubiquitin ligase complex / regulation of mitotic cell cycle phase transition / negative regulation of type I interferon production / WD40-repeat domain binding / ubiquitin-ubiquitin ligase activity / Cul2-RING ubiquitin ligase complex / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / Cul4A-RING E3 ubiquitin ligase complex / Cul4-RING E3 ubiquitin ligase complex / Cul3-RING ubiquitin ligase complex / Cul4B-RING E3 ubiquitin ligase complex / ubiquitin ligase complex scaffold activity / negative regulation of mitophagy / Prolactin receptor signaling / negative regulation of reproductive process / negative regulation of developmental process / cullin family protein binding / viral release from host cell / hemopoiesis / somatic stem cell population maintenance / protein monoubiquitination / positive regulation of G1/S transition of mitotic cell cycle / ectopic germ cell programmed cell death / positive regulation of viral genome replication / ubiquitin-like ligase-substrate adaptor activity / protein K48-linked ubiquitination / proteasomal protein catabolic process / Nuclear events stimulated by ALK signaling in cancer / transcription-coupled nucleotide-excision repair / positive regulation of gluconeogenesis / positive regulation of TORC1 signaling / regulation of cellular response to insulin stimulus / intrinsic apoptotic signaling pathway / negative regulation of insulin receptor signaling pathway / post-translational protein modification / Regulation of BACH1 activity / T cell activation / B cell differentiation / nuclear estrogen receptor binding / nucleotide-excision repair / Degradation of DVL / cellular response to amino acid stimulus / Degradation of GLI1 by the proteasome / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / Recognition of DNA damage by PCNA-containing replication complex / Negative regulation of NOTCH4 signaling / Vif-mediated degradation of APOBEC3G / Hedgehog 'on' state / G1/S transition of mitotic cell cycle / negative regulation of canonical Wnt signaling pathway / 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 / regulation of circadian rhythm / DNA Damage Recognition in GG-NER / Degradation of beta-catenin by the destruction complex / RING-type E3 ubiquitin transferase / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / Evasion by RSV of host interferon responses / NOTCH1 Intracellular Domain Regulates Transcription / 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 / Regulation of expression of SLITs and ROBOs / Formation of Incision Complex in GG-NER / Wnt signaling pathway / fibrillar center / Interleukin-1 signaling / Orc1 removal from chromatin / protein polyubiquitination / Dual incision in TC-NER / Regulation of RAS by GAPs / Gap-filling DNA repair synthesis and ligation in TC-NER
Similarity search - Function
VPRBP/DCAF1 family / Lissencephaly type-1-like homology motif / Zinc finger, RING-H2-type / RING-H2 zinc finger domain / LIS1 homology (LisH) motif profile. / LIS1 homology motif / Cullin protein neddylation domain / : / Cullin, conserved site / Cullin family signature. ...VPRBP/DCAF1 family / Lissencephaly type-1-like homology motif / Zinc finger, RING-H2-type / RING-H2 zinc finger domain / LIS1 homology (LisH) motif profile. / LIS1 homology motif / Cullin protein neddylation domain / : / Cullin, conserved site / Cullin family signature. / Cullin repeat-like-containing domain superfamily / Cullin protein, neddylation domain / Cullin / Cullin protein neddylation domain / Cullin / Cullin, N-terminal / Cullin homology domain / Cullin homology domain superfamily / Cullin alpha solenoid domain / Cullin family profile. / RSE1/DDB1/CPSF1 second beta-propeller / Cleavage/polyadenylation specificity factor, A subunit, C-terminal / Cleavage/polyadenylation specificity factor, A subunit, N-terminal / : / CPSF A subunit region / RSE1/DDB1/CPSF1 first beta-propeller / Zinc finger RING-type profile. / Zinc finger, RING-type / Armadillo-like helical / Armadillo-type fold / Zinc finger, RING/FYVE/PHD-type / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
E3 ubiquitin-protein ligase RBX1 / Cullin-4A / DNA damage-binding protein 1 / DDB1- and CUL4-associated factor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 8.4 Å
AuthorsMohamed WI / Schenk AD
CitationJournal: 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
DepositionMay 18, 2021-
Header (metadata) releaseOct 13, 2021-
Map releaseOct 13, 2021-
UpdateJul 10, 2024-
Current statusJul 10, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.01
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  • Surface view with fitted model
  • Atomic models: PDB-7okq
  • Surface level: 0.01
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7okq
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_12964.png

Downloads & links

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Map

FileDownload / File: emd_12964.map.gz / Format: CCP4 / Size: 67 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.76 Å/pix.
x 260 pix.
= 457.6 Å		1.76 Å/pix.
x 260 pix.
= 457.6 Å		1.76 Å/pix.
x 260 pix.
= 457.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.76 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.00856 / Movie #1: 0.01
Minimum - Maximum-0.011189009 - 0.032275353
Average (Standard dev.)0.0003951231 (±0.0024329766)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions260260260
Spacing260260260
CellA=B=C: 457.6 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.761.761.76
M x/y/z260260260
origin x/y/z0.0000.0000.000
length x/y/z457.600457.600457.600
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ243257325
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS260260260
D min/max/mean-0.0110.0320.000

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Supplemental data

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Sample components

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Entire : CRL4(DCAF1)

EntireName: CRL4(DCAF1)
Components
  • Complex: CRL4(DCAF1)
    • Protein or peptide: DNA damage-binding protein 1
    • Protein or peptide: DDB1- and CUL4-associated factor 1
    • Protein or peptide: Cullin-4A
    • Protein or peptide: E3 ubiquitin-protein ligase RBX1

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Supramolecule #1: CRL4(DCAF1)

SupramoleculeName: CRL4(DCAF1) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: DNA damage-binding protein 1

MacromoleculeName: DNA damage-binding protein 1 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 129.394898 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: 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

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Macromolecule #2: DDB1- and CUL4-associated factor 1

MacromoleculeName: 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
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 171.279094 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: 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

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Macromolecule #3: Cullin-4A

MacromoleculeName: Cullin-4A / type: protein_or_peptide / ID: 3 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 86.702836 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: 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

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Macromolecule #4: E3 ubiquitin-protein ligase RBX1

MacromoleculeName: E3 ubiquitin-protein ligase RBX1 / type: protein_or_peptide / ID: 4 / Number of copies: 4 / Enantiomer: LEVO / EC number: RING-type E3 ubiquitin transferase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.49724 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString:
MHHHHHHVDE NLYFQGGGRG TNSGAGKKRF EVKKWNAVAL WAWDIVVDNC AICRNHIMDL CIECQANQAS ATSEECTVAW GVCNHAFHF HCISRWLKTR QVCPLDNREW EFQKYGH

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

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 45.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 8.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 14000
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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Atomic model buiding 1

Initial model
PDB IDChain

2hye

source_name: PDB, initial_model_type: experimental model

5jk7

source_name: PDB, initial_model_type: experimental model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Overall B value: 596 / Target criteria: Real-space cross-correlation
Output model

PDB-7okq:
Cryo-EM Structure of the DDB1-DCAF1-CUL4A-RBX1 Complex

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