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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 / 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)
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: Glassman CR / Baek K / Nardone C / Juergens KB / Fujimura E / OLeary CN / Li MZ / Paulo JA / Fischer ES / Harper JW / Elledge SJ
History
DepositionAug 18, 2025-
Header (metadata) releaseJul 8, 2026-
Map releaseJul 8, 2026-
UpdateJul 8, 2026-
Current statusJul 8, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_72190.png

Downloads & links

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Map

FileReleased
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
Density

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
Projections & Slices
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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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Histogram

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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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