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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 / POZ domain binding / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF7 activity / host cytoskeleton / regulation protein catabolic process at postsynapse / negative regulation of Rho protein signal transduction / embryonic cleavage / polar microtubule / anaphase-promoting complex-dependent catabolic process / nuclear protein quality control by the ubiquitin-proteasome system ...positive regulation of mitotic cell cycle phase transition / POZ domain binding / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF7 activity / host cytoskeleton / regulation protein catabolic process at postsynapse / negative regulation of Rho protein signal transduction / embryonic cleavage / polar microtubule / anaphase-promoting complex-dependent catabolic process / nuclear protein quality control by the ubiquitin-proteasome system / COPII vesicle coat assembly / positive regulation of protein K63-linked ubiquitination / RHOBTB3 ATPase cycle / stem cell division / target-directed miRNA degradation / positive regulation of mitotic metaphase/anaphase transition / elongin complex / VCB complex / Notch binding / establishment of endothelial barrier / stress fiber assembly / RHOBTB1 GTPase cycle / positive regulation of cilium assembly / Cul5-RING ubiquitin ligase complex / ubiquitin-dependent protein catabolic process via the C-end degron rule pathway / Cul2-RING ubiquitin ligase complex / negative regulation of DNA-templated DNA replication / negative regulation of type I interferon production / Cul3-RING ubiquitin ligase complex / 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 / protein monoubiquitination / mitotic metaphase chromosome alignment / endoplasmic reticulum to Golgi vesicle-mediated transport / Tat-mediated elongation of the HIV-1 transcript / Formation of HIV-1 elongation complex containing HIV-1 Tat / RHOBTB2 GTPase cycle / sperm flagellum / 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 / kidney development / intrinsic apoptotic signaling pathway / ribosome-associated ubiquitin-dependent protein catabolic process / RNA Polymerase II Pre-transcription Events / regulation of cellular response to insulin stimulus / protein K48-linked ubiquitination / positive regulation of TORC1 signaling / integrin-mediated signaling pathway / gene expression / cyclin binding / positive regulation of protein ubiquitination / cellular response to amino acid stimulus / transcription corepressor binding / G1/S transition of mitotic cell cycle / TP53 Regulates Transcription of DNA Repair Genes / transcription initiation at RNA polymerase II promoter / protein destabilization / Degradation of DVL / transcription elongation by RNA polymerase II / Inactivation of CSF3 (G-CSF) signaling / Hedgehog 'on' state / Vif-mediated degradation of APOBEC3G / mitotic spindle / Evasion by RSV of host interferon responses / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / SPOP-mediated proteasomal degradation of PD-L1(CD274) / protein polyubiquitination / Regulation of expression of SLITs and ROBOs / Ribosome Quality Control (RQC) complex extracts and degrades nascent peptide / microtubule cytoskeleton / Regulation of RAS by GAPs / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / ubiquitin protein ligase activity / KEAP1-NFE2L2 pathway / cell migration / Antigen processing: Ubiquitination & Proteasome degradation / spindle pole / Neddylation / protein-containing complex assembly / cellular response to oxidative stress / ubiquitin-dependent protein catabolic process / 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 / proteasome-mediated ubiquitin-dependent protein catabolic process / inflammatory response / postsynapse / protein-macromolecule adaptor activity / protein ubiquitination / ubiquitin protein ligase binding / centrosome / regulation of transcription by RNA polymerase II / positive regulation of cell population proliferation / host cell cytoplasm
Similarity search - Function
Rotavirus non-structural protein 1 / Rotavirus RNA-binding Protein 53 (NS53) / Elongin-C / Elongin B / Cullin protein neddylation domain / Cullin, conserved site / Cullin family signature. / Cullin, N-terminal / Cullin repeat-like-containing domain superfamily / Cullin protein, neddylation domain ...Rotavirus non-structural protein 1 / Rotavirus RNA-binding Protein 53 (NS53) / Elongin-C / Elongin B / 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. / 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: Caleb R Glassman / Kheewoong Baek / Gaopeng Hou / Qiru Zeng / Christopher Nardone / Kate B Juergens / Eric Fujimura / Colin N O'Leary / Mamie Z Li / Joao A Paulo / Eric S Fischer / Siyuan ...Authors: Caleb R Glassman / Kheewoong Baek / Gaopeng Hou / Qiru Zeng / Christopher Nardone / Kate B Juergens / Eric Fujimura / Colin N O'Leary / Mamie Z Li / Joao A Paulo / Eric S Fischer / Siyuan Ding / J Wade Harper / Stephen J Elledge /
Abstract: Viruses are intracellular parasites that reprogram the host proteome to promote replication and evade immune recognition. We applied a virome-wide library of ~10,000 open reading frames to discover ...Viruses are intracellular parasites that reprogram the host proteome to promote replication and evade immune recognition. We applied a virome-wide library of ~10,000 open reading frames to discover viral ubiquitin ligases, mapping their mechanisms of degradation and host substrates using targeted CRISPR screens and proteomics. These viral effectors could be classified as canonical ligases that mimic host E3s, hijackers that redirect host E3s, and noncanonical ligases that rewire cullin-RING ligase machinery. These diverse strategies of virus-mediated degradation converged on immune-related substrates, including JAK1 and CUL1, underscoring immune evasion as a major driver of viral ubiquitin ligase evolution. Our findings elucidate viral strategies for exploiting the ubiquitin-proteasome system with potential for therapeutic targeting.
History
DepositionAug 18, 2025Deposition site: RCSB / Processing site: RCSB
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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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