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- EMDB-72190: Cryo-EM structure of RotavirusA NSP1-ELOB-ELOC-CUL3 -

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Basic information

Entry
Database: EMDB / ID: EMD-72190
TitleCryo-EM structure of RotavirusA NSP1-ELOB-ELOC-CUL3
Map datadeepEMhancer
Sample
  • Complex: RotavirusA NSP1-ELOB-ELOC-CUL3
    • Protein or peptide: Non-structural protein 1
    • Protein or peptide: Elongin-B
    • Protein or peptide: Elongin-C
    • Protein or peptide: Cullin-3
  • Ligand: ZINC ION
KeywordsViral effector / E3 ligase / NSP1 / CUL3 / VIRAL PROTEIN
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 / 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 / regulation protein catabolic process at postsynapse ...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 / 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 / regulation protein catabolic process at postsynapse / COPII vesicle coat assembly / cell projection organization / RHOBTB3 ATPase cycle / stem cell division / target-directed miRNA degradation / positive regulation of mitotic metaphase/anaphase transition / elongin complex / Notch binding / stress fiber assembly / RHOBTB1 GTPase cycle / VCB complex / 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 / 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 / protein monoubiquitination / mitotic metaphase chromosome alignment / endoplasmic reticulum to Golgi vesicle-mediated transport / Tat-mediated elongation of the HIV-1 transcript / RHOBTB2 GTPase cycle / Formation of HIV-1 elongation complex containing HIV-1 Tat / 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 / protein K48-linked ubiquitination / RNA Polymerase II Pre-transcription Events / regulation of cellular response to insulin stimulus / positive regulation of TORC1 signaling / gene expression / integrin-mediated signaling pathway / cellular response to amino acid stimulus / cyclin binding / positive regulation of protein ubiquitination / transcription corepressor binding / TP53 Regulates Transcription of DNA Repair Genes / G1/S transition of mitotic cell cycle / transcription initiation at RNA polymerase II promoter / protein destabilization / Degradation of DVL / transcription elongation by RNA polymerase II / Hedgehog 'on' state / Inactivation of CSF3 (G-CSF) signaling / 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) / spindle pole / Regulation of expression of SLITs and ROBOs / protein polyubiquitination / microtubule cytoskeleton / Ribosome Quality Control (RQC) complex extracts and degrades nascent peptide / 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 / 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 / host cell cytoplasm / protein-macromolecule adaptor activity / postsynapse / protein ubiquitination / inflammatory response / ubiquitin protein ligase binding / centrosome / positive regulation of cell population proliferation / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / glutamatergic synapse
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsBaek K / Glassman CR / Fischer ES
Funding support United States, 1 items
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 non-canonical 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, 2025-
Header (metadata) releaseJul 8, 2026-
Map releaseJul 8, 2026-
UpdateJul 22, 2026-
Current statusJul 22, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_72190.png

Downloads & links

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Map

FileDownload / File: emd_72190.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationdeepEMhancer
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.74 Å/pix.
x 384 pix.
= 283.008 Å		0.74 Å/pix.
x 384 pix.
= 283.008 Å		0.74 Å/pix.
x 384 pix.
= 283.008 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.737 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.00180659 - 2.0513484
Average (Standard dev.)0.00064352853 (±0.018982792)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 283.008 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_72190_msk_1.map
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Additional map: sharpened

Fileemd_72190_additional_1.map
Annotationsharpened
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Additional map: unsharpened

Fileemd_72190_additional_2.map
Annotationunsharpened
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Half map: halfmap1

Fileemd_72190_half_map_1.map
Annotationhalfmap1
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Half map: halfmap2

Fileemd_72190_half_map_2.map
Annotationhalfmap2
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Sample components

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Entire : RotavirusA NSP1-ELOB-ELOC-CUL3

EntireName: RotavirusA NSP1-ELOB-ELOC-CUL3
Components
  • Complex: RotavirusA NSP1-ELOB-ELOC-CUL3
    • Protein or peptide: Non-structural protein 1
    • Protein or peptide: Elongin-B
    • Protein or peptide: Elongin-C
    • Protein or peptide: Cullin-3
  • Ligand: ZINC ION

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Supramolecule #1: RotavirusA NSP1-ELOB-ELOC-CUL3

SupramoleculeName: RotavirusA NSP1-ELOB-ELOC-CUL3 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Rotavirus A / Strain: B3SRV2.0.1

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Macromolecule #1: Non-structural protein 1

MacromoleculeName: Non-structural protein 1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rotavirus A
Molecular weightTheoretical: 57.744199 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MATFKDACYH YKRINKLNHT VLKLGVNDTW RSSPPTKYKG WCLDCCQHTD LTYCRGCTMY HVCQWCSQYG RCFLDNEPHL LRMRTFKNE VTKDDLKNLI DMYEILFPMN QKIVCRFINN TRQHKCRNEC MTQWYNHLLL PITLQSMSIE LDGDVYYVFG Y YDNMNSIN ...String:
MATFKDACYH YKRINKLNHT VLKLGVNDTW RSSPPTKYKG WCLDCCQHTD LTYCRGCTMY HVCQWCSQYG RCFLDNEPHL LRMRTFKNE VTKDDLKNLI DMYEILFPMN QKIVCRFINN TRQHKCRNEC MTQWYNHLLL PITLQSMSIE LDGDVYYVFG Y YDNMNSIN QTPFSFTNLV DIYDKLLLDD VNFARMSFLP ASLQQEYALR YFSKSRFISE QRKCVNDSHF SINVLENLHN PS FKVQITR NCSELSFDWN EACKLVKNVS AYFDMLKTSH IEFYSVSTRC RIFTQCKLKM ASKLIKPNYI TSNHKTLATE VHN CKWCSV NNSYTVWNDF RIKKIYDNIF NFLRALVKSN VNIGHCSSQE KIYEYVEDVL NVCDDERWKT SIMEIFNCLE PVEL DDVKY VLFNHEINWD VINVLVHSIG KVPQILTLEN VITIMQSIIY EWFDIRYMRN TPMVTFTIDK LRRLHTGLKT VEYDS GISD IE

UniProtKB: Non-structural protein 1

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Macromolecule #2: Elongin-B

MacromoleculeName: Elongin-B / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.147781 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString:
MDVFLMIRRH KTTIFTDAKE SSTVFELKRI VEGILKRPPD EQRLYKDDQL LDDGKTLGEC GFTSQTARPQ APATVGLAFR ADDTFEALC IEPFSSPPEL PDVMKPQDSG SSANEQAVQ

UniProtKB: Elongin-B

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Macromolecule #3: Elongin-C

MacromoleculeName: Elongin-C / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 12.485135 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString:
MDGEEKTYGG CEGPDAMYVK LISSDGHEFI VKREHALTSG TIKAMLSGPG QFAENETNEV NFREIPSHVL SKVCMYFTYK VRYTNSSTE IPEFPIAPEI ALELLMAANF LDC

UniProtKB: Elongin-C

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Macromolecule #4: Cullin-3

MacromoleculeName: Cullin-3 / type: protein_or_peptide / ID: 4
Details: N-terminal fraction of CUL3 used for local refinement based structure.
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 89.334625 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: GGRMSNLSKG TGSRKDTKMR IRAFPMTMDE KYVNSIWDLL KNAIQEIQRK NNSGLSFEEL YRNAYTMVLH KHGEKLYTGL REVVTEHLI NKVREDVLNS LNNNFLQTLN QAWNDHQTAM VMIRDILMYM DRVYVQQNNV ENVYNLGLII FRDQVVRYGC I RDHLRQTL ...String:
GGRMSNLSKG TGSRKDTKMR IRAFPMTMDE KYVNSIWDLL KNAIQEIQRK NNSGLSFEEL YRNAYTMVLH KHGEKLYTGL REVVTEHLI NKVREDVLNS LNNNFLQTLN QAWNDHQTAM VMIRDILMYM DRVYVQQNNV ENVYNLGLII FRDQVVRYGC I RDHLRQTL LDMIARERKG EVVDRGAIRN ACQMLMILGL EGRSVYEEDF EAPFLEMSAE FFQMESQKFL AENSASVYIK KV EARINEE IERVMHCLDK STEEPIVKVV ERELISKHMK TIVEMENSGL VHMLKNGKTE DLGCMYKLFS RVPNGLKTMC ECM SSYLRE QGKALVSEEG EGKNPVDYIQ GLLDLKSRFD RFLLESFNND RLFKQTIAGD FEYFLNLNSR SPEYLSLFID DKLK KGVKG LTEQEVETIL DKAMVLFRFM QEKDVFERYY KQHLARRLLT NKSVSDDSEK NMISKLKTEC GCQFTSKLEG MFRDM SISN TTMDEFRQHL QATGVSLGGV DLTVRVLTTG YWPTQSATPK CNIPPAPRHA FEIFRRFYLA KHSGRQLTLQ HHMGSA DLN ATFYGPVKKE DGSEVGVGGA QVTGSNTRKH ILQVSTFQMT ILMLFNNREK YTFEEIQQET DIPERELVRA LQSLACG KP TQRVLTKEPK SKEIENGHIF TVNDQFTSKL HRVKIQTVAA KQGESDPERK ETRQKVDDDR KHEIEAAIVR IMKSRKKM Q HNVLVAEVTQ QLKARFLPSP VVIKKRIEGL IEREYLARTP EDRKVYTYVA

UniProtKB: Cullin-3

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Macromolecule #5: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 5 / Number of copies: 3 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.6 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 173093
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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