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- PDB-8b3g: C(N)RL4CSA-UVSSA-E2-ubiquitin complex. -

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Basic information

Entry
Database: PDB / ID: 8b3g
TitleC(N)RL4CSA-UVSSA-E2-ubiquitin complex.
Components
  • Cullin-4A
  • DNA damage-binding protein 1
  • DNA excision repair protein ERCC-8
  • E3 ubiquitin-protein ligase RBX1
  • NEDD8
  • UV-stimulated scaffold protein A
  • Ubiquitin
  • ubiquitin-conjugating enzyme E2 D2 isoform X3
KeywordsTRANSCRIPTION / DNA repair / ubiquitin / cryo-EM
Function / homology
Function and homology information


RNA polymerase inhibitor activity / regulation of transcription-coupled nucleotide-excision repair / response to auditory stimulus / cellular response to camptothecin / negative regulation of beige fat cell differentiation / cullin-RING-type E3 NEDD8 transferase / NEDD8 transferase activity / cullin-RING ubiquitin ligase complex / negative regulation of mitophagy / regulation of xenophagy ...RNA polymerase inhibitor activity / regulation of transcription-coupled nucleotide-excision repair / response to auditory stimulus / cellular response to camptothecin / negative regulation of beige fat cell differentiation / cullin-RING-type E3 NEDD8 transferase / NEDD8 transferase activity / cullin-RING ubiquitin ligase complex / negative regulation of mitophagy / regulation of xenophagy / double-strand break repair via classical nonhomologous end joining / cellular response to chemical stress / Loss of Function of FBXW7 in Cancer and NOTCH1 Signaling / Cul7-RING ubiquitin ligase complex / single strand break repair / regulation of cell cycle process / neural crest cell differentiation / RNA polymerase II transcription initiation surveillance / positive regulation by virus of viral protein levels in host cell / positive regulation of protein autoubiquitination / protein neddylation / regulation of BMP signaling pathway / chromatin-protein adaptor activity / NEDD8 ligase activity / spindle assembly involved in female meiosis / epigenetic programming in the zygotic pronuclei / regulation of mitophagy / negative regulation of response to oxidative stress / regulation of centrosome duplication / UV-damage excision repair / protein K27-linked ubiquitination / positive regulation of cilium assembly / Cul5-RING ubiquitin ligase complex / ubiquitin-ubiquitin ligase activity / regulation of TOR signaling / ubiquitin-dependent protein catabolic process via the C-end degron rule pathway / Cul2-RING ubiquitin ligase complex / negative regulation of DNA-templated DNA replication / biological process involved in interaction with symbiont / SCF ubiquitin ligase complex / regulation of DNA damage checkpoint / regulation of mitotic cytokinesis / negative regulation of type I interferon production / Cul3-RING ubiquitin ligase complex / regulation of mitotic cell cycle phase transition / regulation of miRNA-mediated gene silencing / regulation of natural killer cell activation / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / WD40-repeat domain binding / Prolactin receptor signaling / nucleotide-excision repair complex / regulation of cell cycle phase transition / Cul4-RING E3 ubiquitin ligase complex / regulation of stem cell population maintenance / Cul4A-RING E3 ubiquitin ligase complex / TGF-beta receptor signaling activates SMADs / response to UV / ubiquitin ligase complex scaffold activity / RNA polymerase II complex binding / negative regulation of adipose tissue development / ubiquitin conjugating enzyme activity / regulation of proteolysis / Cul4B-RING E3 ubiquitin ligase complex / regulation of cellular response to stress / limb development / viral release from host cell / regulation of postsynapse assembly / protein monoubiquitination / anatomical structure morphogenesis / cullin family protein binding / centrosome duplication / regulation of DNA-templated DNA replication initiation / positive regulation of viral genome replication / cilium assembly / protein autoubiquitination / ubiquitin-like ligase-substrate adaptor activity / positive regulation of gluconeogenesis / intrinsic apoptotic signaling pathway / ribosome-associated ubiquitin-dependent protein catabolic process / signal transduction in response to DNA damage / negative regulation of insulin receptor signaling pathway / protein K63-linked ubiquitination / Nuclear events stimulated by ALK signaling in cancer / regulation of cellular response to insulin stimulus / protein K48-linked ubiquitination / in utero embryonic development / transcription-coupled nucleotide-excision repair / post-translational protein modification / Maturation of protein E / positive regulation of TORC1 signaling / Maturation of protein E / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / regulation of embryonic development / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / Glycogen synthesis / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation
Similarity search - Function
UV-stimulated scaffold protein A / : / : / Uncharacterized conserved protein (DUF2043) / UVSSA N-terminal domain / Zinc finger UVSSA-type profile. / DNA excision repair protein Rad28/ERCC8/Ckn1/ATCSA-1 / Nedd8-like ubiquitin / ENTH/VHS / Zinc finger, RING-H2-type ...UV-stimulated scaffold protein A / : / : / Uncharacterized conserved protein (DUF2043) / UVSSA N-terminal domain / Zinc finger UVSSA-type profile. / DNA excision repair protein Rad28/ERCC8/Ckn1/ATCSA-1 / Nedd8-like ubiquitin / ENTH/VHS / Zinc finger, RING-H2-type / RING-H2 zinc finger domain / : / Cullin protein neddylation domain / Cullin, conserved site / Cullin family signature. / Cullin, N-terminal / Cullin repeat-like-containing domain superfamily / Cullin protein, neddylation domain / Cullin / Cullin protein neddylation domain / Cullin alpha solenoid domain / Cullin / : / Cullin alpha+beta domain / Cullin homology domain / Cullin homology domain superfamily / 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 / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Ubiquitin-conjugating enzyme/RWD-like / Zinc finger RING-type profile. / Zinc finger, RING-type / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / WD domain, G-beta repeat / Zinc finger, RING/FYVE/PHD-type / Ubiquitin-like domain superfamily / Winged helix DNA-binding domain superfamily / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / Winged helix-like DNA-binding domain superfamily / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Ubiquitin-conjugating enzyme E2 D2 / Polyubiquitin-C / E3 ubiquitin-protein ligase RBX1 / DNA excision repair protein ERCC-8 / Cullin-4A / Ubiquitin-like protein NEDD8 / DNA damage-binding protein 1 / UV-stimulated scaffold protein A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.4 Å
AuthorsKokic, G. / Cramer, P.
Funding support Germany, European Union, 2items
OrganizationGrant numberCountry
German Research Foundation (DFG)EXC 2067/1-390729940 Germany
European Research Council (ERC)Advanced Investigator Grant CHROMATRANS (grant agreement No. 882357)European Union
CitationJournal: Nat Struct Mol Biol / Year: 2024
Title: Structural basis for RNA polymerase II ubiquitylation and inactivation in transcription-coupled repair.
Authors: Goran Kokic / George Yakoub / Diana van den Heuvel / Annelotte P Wondergem / Paula J van der Meer / Yana van der Weegen / Aleksandar Chernev / Isaac Fianu / Thornton J Fokkens / Sonja Lorenz ...Authors: Goran Kokic / George Yakoub / Diana van den Heuvel / Annelotte P Wondergem / Paula J van der Meer / Yana van der Weegen / Aleksandar Chernev / Isaac Fianu / Thornton J Fokkens / Sonja Lorenz / Henning Urlaub / Patrick Cramer / Martijn S Luijsterburg /
Abstract: During transcription-coupled DNA repair (TCR), RNA polymerase II (Pol II) transitions from a transcriptionally active state to an arrested state that allows for removal of DNA lesions. This ...During transcription-coupled DNA repair (TCR), RNA polymerase II (Pol II) transitions from a transcriptionally active state to an arrested state that allows for removal of DNA lesions. This transition requires site-specific ubiquitylation of Pol II by the CRL4 ubiquitin ligase, a process that is facilitated by ELOF1 in an unknown way. Using cryogenic electron microscopy, biochemical assays and cell biology approaches, we found that ELOF1 serves as an adaptor to stably position UVSSA and CRL4 on arrested Pol II, leading to ligase neddylation and activation of Pol II ubiquitylation. In the presence of ELOF1, a transcription factor IIS (TFIIS)-like element in UVSSA gets ordered and extends through the Pol II pore, thus preventing reactivation of Pol II by TFIIS. Our results provide the structural basis for Pol II ubiquitylation and inactivation in TCR.
History
DepositionSep 16, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 4, 2024Provider: repository / Type: Initial release
Revision 1.0Sep 4, 2024Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Sep 4, 2024Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Sep 4, 2024Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Sep 4, 2024Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Sep 4, 2024Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Jul 9, 2025Group: Data collection / Structure summary / Category: em_admin / em_software / pdbx_entry_details
Item: _em_admin.last_update / _em_software.name / _pdbx_entry_details.has_protein_modification
Revision 1.1Jul 9, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Data processing / Experimental summary / Data content type: EM metadata / EM metadata / Category: em_admin / em_software / Data content type: EM metadata / EM metadata / Item: _em_admin.last_update / _em_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: ubiquitin-conjugating enzyme E2 D2 isoform X3
N: NEDD8
R: E3 ubiquitin-protein ligase RBX1
U: Ubiquitin
a: DNA excision repair protein ERCC-8
c: UV-stimulated scaffold protein A
d: DNA damage-binding protein 1
e: Cullin-4A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)386,13311
Polymers385,9378
Non-polymers1963
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 8 types, 8 molecules DNRUacde

#1: Protein ubiquitin-conjugating enzyme E2 D2 isoform X3


Mass: 16755.227 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBE2D2 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A6P5C4T4
#2: Protein NEDD8 / Neddylin / Neural precursor cell expressed developmentally down-regulated protein 8 / NEDD-8 / ...Neddylin / Neural precursor cell expressed developmentally down-regulated protein 8 / NEDD-8 / Ubiquitin-like protein Nedd8


Mass: 8573.978 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NEDD8 / Production host: Escherichia coli (E. coli) / References: UniProt: Q15843
#3: Protein E3 ubiquitin-protein ligase RBX1 / E3 ubiquitin-protein transferase RBX1 / Protein ZYP / RING finger protein 75 / RING-box protein 1 / ...E3 ubiquitin-protein transferase RBX1 / Protein ZYP / RING finger protein 75 / RING-box protein 1 / Rbx1 / Regulator of cullins 1 / ROC1


Mass: 12289.977 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RBX1, RNF75, ROC1 / Production host: Trichoplusia ni (cabbage looper)
References: UniProt: P62877, RING-type E3 ubiquitin transferase, cullin-RING-type E3 NEDD8 transferase
#4: Protein Ubiquitin / Polyubiquitin-C


Mass: 8576.831 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBC / Production host: Escherichia coli (E. coli) / References: UniProt: P0CG48
#5: Protein DNA excision repair protein ERCC-8 / Cockayne syndrome WD repeat protein CSA


Mass: 44107.160 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ERCC8, CKN1, CSA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q13216
#6: Protein UV-stimulated scaffold protein A


Mass: 80721.680 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UVSSA, KIAA1530 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q2YD98
#7: Protein DNA damage-binding protein 1 / DDB p127 subunit / DNA damage-binding protein a / DDBa / Damage-specific DNA-binding protein 1 / ...DDB p127 subunit / DNA damage-binding protein a / DDBa / Damage-specific DNA-binding protein 1 / HBV X-associated protein 1 / XAP-1 / UV-damaged DNA-binding factor / UV-damaged DNA-binding protein 1 / UV-DDB 1 / XPE-binding factor / XPE-BF / Xeroderma pigmentosum group E-complementing protein / XPCe


Mass: 127097.469 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DDB1, XAP1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q16531
#8: Protein Cullin-4A / CUL-4A


Mass: 87814.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CUL4A / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q13619

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Non-polymers , 1 types, 3 molecules

#9: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn

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Details

Has ligand of interestN
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: C(N)RL4CSA-UVSSA-E2-ubiquitin complex. / Type: COMPLEX / Entity ID: #1-#8 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Trichoplusia ni (cabbage looper)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

MicroscopyModel: TFS GLACIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3550 nm / Nominal defocus min: 400 nm
Image recordingElectron dose: 40.2 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.18.2_3874: / Classification: refinement
EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 67365 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00521825
ELECTRON MICROSCOPYf_angle_d0.68129480
ELECTRON MICROSCOPYf_dihedral_angle_d6.4212894
ELECTRON MICROSCOPYf_chiral_restr0.0443316
ELECTRON MICROSCOPYf_plane_restr0.0053789

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