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- PDB-9q3e: Cryo-EM structure of RotavirusA NSP1-ELOB-ELOC-CUL3 -

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Basic information

Entry
Database: PDB / ID: 9q3e
TitleCryo-EM structure of RotavirusA NSP1-ELOB-ELOC-CUL3
Components
  • Cullin-3
  • Elongin-B
  • Elongin-C
  • Non-structural protein 1
KeywordsVIRAL PROTEIN / Viral effector / E3 ligase / NSP1 / CUL3
Function / homology
Function and homology information


positive regulation of mitotic cell cycle phase transition / trophectodermal cellular morphogenesis / liver morphogenesis / POZ domain binding / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF7 activity / host cytoskeleton / polar microtubule / regulation protein catabolic process at postsynapse / anaphase-promoting complex-dependent catabolic process / nuclear protein quality control by the ubiquitin-proteasome system ...positive regulation of mitotic cell cycle phase transition / trophectodermal cellular morphogenesis / liver morphogenesis / POZ domain binding / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF7 activity / host cytoskeleton / polar microtubule / regulation protein catabolic process at postsynapse / anaphase-promoting complex-dependent catabolic process / nuclear protein quality control by the ubiquitin-proteasome system / COPII vesicle coat assembly / RHOBTB3 ATPase cycle / embryonic cleavage / target-directed miRNA degradation / positive regulation of mitotic metaphase/anaphase transition / elongin complex / fibroblast apoptotic process / Notch binding / cell projection organization / negative regulation of Rho protein signal transduction / RHOBTB1 GTPase cycle / VCB complex / Cul5-RING ubiquitin ligase complex / stem cell division / mitotic metaphase chromosome alignment / ubiquitin-dependent protein catabolic process via the C-end degron rule pathway / Cul2-RING ubiquitin ligase complex / stress fiber assembly / Cul3-RING ubiquitin ligase complex / negative regulation of type I interferon production / positive regulation of cytokinesis / ubiquitin ligase complex scaffold activity / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / endoplasmic reticulum to Golgi vesicle-mediated transport / protein monoubiquitination / Tat-mediated elongation of the HIV-1 transcript / sperm flagellum / Formation of HIV-1 elongation complex containing HIV-1 Tat / RHOBTB2 GTPase cycle / Formation of HIV elongation complex in the absence of HIV Tat / protein autoubiquitination / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / protein K48-linked ubiquitination / RNA Polymerase II Pre-transcription Events / regulation of cellular response to insulin stimulus / positive regulation of TORC1 signaling / gastrulation / intrinsic apoptotic signaling pathway / cyclin binding / transcription corepressor binding / positive regulation of protein ubiquitination / integrin-mediated signaling pathway / TP53 Regulates Transcription of DNA Repair Genes / kidney development / cellular response to amino acid stimulus / transcription initiation at RNA polymerase II promoter / transcription elongation by RNA polymerase II / G1/S transition of mitotic cell cycle / Degradation of DVL / Inactivation of CSF3 (G-CSF) signaling / Hedgehog 'on' state / Vif-mediated degradation of APOBEC3G / protein destabilization / Evasion by RSV of host interferon responses / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / Wnt signaling pathway / Regulation of expression of SLITs and ROBOs / spindle pole / protein polyubiquitination / mitotic spindle / Regulation of RAS by GAPs / ubiquitin protein ligase activity / KEAP1-NFE2L2 pathway / cell migration / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / Antigen processing: Ubiquitination & Proteasome degradation / Neddylation / cellular response to oxidative stress / protein-containing complex assembly / gene expression / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / Potential therapeutics for SARS / symbiont-mediated suppression of host NF-kappaB cascade / ubiquitin-dependent protein catabolic process / host cell cytoplasm / proteasome-mediated ubiquitin-dependent protein catabolic process / protein-macromolecule adaptor activity / postsynapse / protein ubiquitination / inflammatory response / positive regulation of cell population proliferation / ubiquitin protein ligase binding / regulation of transcription by RNA polymerase II / centrosome / glutamatergic synapse / negative regulation of transcription by RNA polymerase II
Similarity search - Function
Rotavirus non-structural protein 1 / Rotavirus RNA-binding Protein 53 (NS53) / Cullin protein neddylation domain / Cullin, N-terminal / Elongin-C / Elongin B / Cullin, conserved site / Cullin family signature. / Cullin repeat-like-containing domain superfamily / Cullin protein, neddylation domain ...Rotavirus non-structural protein 1 / Rotavirus RNA-binding Protein 53 (NS53) / Cullin protein neddylation domain / Cullin, N-terminal / Elongin-C / Elongin B / Cullin, conserved site / Cullin family signature. / Cullin repeat-like-containing domain superfamily / Cullin protein, neddylation domain / Cullin / Cullin alpha solenoid domain / Cullin protein neddylation domain / Cullin / : / Cullin alpha+beta domain / Cullin homology domain / Cullin homology domain superfamily / Cullin family profile. / S-phase kinase-associated protein 1-like / SKP1 component, POZ domain / Skp1 family, tetramerisation domain / Found in Skp1 protein family / SKP1/BTB/POZ domain superfamily / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
Non-structural protein 1 / Cullin-3 / Elongin-C / Elongin-B
Similarity search - Component
Biological speciesRotavirus A
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsBaek, K. / Glassman, C.R. / Fischer, E.S.
Funding support United States, 1items
OrganizationGrant numberCountry
Damon Runyon Cancer Research FoundationDRG-2514-24 United States
CitationJournal: Science / Year: 2026
Title: Virome-wide ubiquitin ligase discovery reveals diverse mechanisms of immune evasion
Authors: Glassman, C.R. / Baek, K. / Nardone, C. / Juergens, K.B. / Fujimura, E. / OLeary, C.N. / Li, M.Z. / Paulo, J.A. / Fischer, E.S. / Harper, J.W. / Elledge, S.J.
History
DepositionAug 18, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 8, 2026Provider: repository / Type: Initial release
Revision 1.0Jul 8, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 8, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Jul 8, 2026Data content type: Additional map / Part number: 2 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Jul 8, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jul 8, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 8, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 8, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 8, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Jul 8, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
N: Non-structural protein 1
B: Elongin-B
C: Elongin-C
L: Cullin-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)172,9087
Polymers172,7124
Non-polymers1963
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Non-structural protein 1 / NSP1 / NCVP2 / Non-structural RNA-binding protein 53 / NS53


Mass: 57744.199 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rotavirus A / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: B3SRV2
#2: Protein Elongin-B / EloB / Elongin 18 kDa subunit / RNA polymerase II transcription factor SIII subunit B / SIII p18 / ...EloB / Elongin 18 kDa subunit / RNA polymerase II transcription factor SIII subunit B / SIII p18 / Transcription elongation factor B polypeptide 2


Mass: 13147.781 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ELOB, TCEB2 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q15370
#3: Protein Elongin-C / EloC / Elongin 15 kDa subunit / RNA polymerase II transcription factor SIII subunit C / SIII p15 / ...EloC / Elongin 15 kDa subunit / RNA polymerase II transcription factor SIII subunit C / SIII p15 / Transcription elongation factor B polypeptide 1


Mass: 12485.135 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ELOC, TCEB1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q15369
#4: Protein Cullin-3 / CUL-3


Mass: 89334.625 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: N-terminal fraction of CUL3 used for local refinement based structure.
Source: (gene. exp.) Homo sapiens (human) / Gene: CUL3, KIAA0617 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q13618
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
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: RotavirusA NSP1-ELOB-ELOC-CUL3 / Type: COMPLEX / Entity ID: #1-#4 / Source: RECOMBINANT
Source (natural)Organism: Rotavirus A / Strain: B3SRV2.0.1
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

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 50.6 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 173093 / Symmetry type: POINT

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