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- EMDB-13000: Structure of Neddylated CRL5Vif-CBFbeta-ARIH2*-APOBEC3C (A3C cons... -

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Basic information

Entry
Database: EMDB / ID: EMD-13000
TitleStructure of Neddylated CRL5Vif-CBFbeta-ARIH2*-APOBEC3C (A3C consensus )
Map data
Sample
  • Complex: Neddylated CUL5 C-terminal region-RBX2-ARIH2
    • Complex: Cullin-5
    • Complex: ARIH2
    • Complex: RBX2
    • Complex: NEDD8
Function / homology
Function and homology information


developmental cell growth / RBR-type E3 ubiquitin transferase / ERBB2 signaling pathway / NEDD8 transferase activity / regulation of proteolysis / protein neddylation / ubiquitin conjugating enzyme binding / NEDD8 ligase activity / Cul5-RING ubiquitin ligase complex / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process ...developmental cell growth / RBR-type E3 ubiquitin transferase / ERBB2 signaling pathway / NEDD8 transferase activity / regulation of proteolysis / protein neddylation / ubiquitin conjugating enzyme binding / NEDD8 ligase activity / Cul5-RING ubiquitin ligase complex / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / response to redox state / positive regulation of protein targeting to mitochondrion / SCF ubiquitin ligase complex / hematopoietic stem cell proliferation / TGF-beta receptor signaling activates SMADs / protein K63-linked ubiquitination / site of DNA damage / cullin family protein binding / anatomical structure morphogenesis / protein K48-linked ubiquitination / ubiquitin ligase complex / post-translational protein modification / intrinsic apoptotic signaling pathway / Iron uptake and transport / Vif-mediated degradation of APOBEC3G / G1/S transition of mitotic cell cycle / protein modification process / modification-dependent protein catabolic process / calcium channel activity / protein localization / Inactivation of CSF3 (G-CSF) signaling / protein tag activity / Downregulation of ERBB2 signaling / protein polyubiquitination / ubiquitin-protein transferase activity / UCH proteinases / ubiquitin protein ligase activity / protein-macromolecule adaptor activity / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / Antigen processing: Ubiquitination & Proteasome degradation / Cargo recognition for clathrin-mediated endocytosis / signaling receptor activity / Neddylation / ubiquitin-dependent protein catabolic process / protein ubiquitination / copper ion binding / ubiquitin protein ligase binding / regulation of transcription by RNA polymerase II / proteolysis / extracellular exosome / zinc ion binding / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
E3 ubiquitin-protein ligase ARIH2 / Ariadne domain / Ariadne domain / E3 ubiquitin ligase RBR family / Nedd8-like ubiquitin / IBR domain, a half RING-finger domain / IBR domain / In Between Ring fingers / TRIAD supradomain / TRIAD supradomain profile. ...E3 ubiquitin-protein ligase ARIH2 / Ariadne domain / Ariadne domain / E3 ubiquitin ligase RBR family / Nedd8-like ubiquitin / IBR domain, a half RING-finger domain / IBR domain / In Between Ring fingers / TRIAD supradomain / TRIAD supradomain profile. / Zinc finger, RING-H2-type / RING-H2 zinc finger domain / Cullin protein neddylation domain / Cullin, conserved site / Cullin family signature. / Cullin / Cullin repeat-like-containing domain superfamily / Cullin protein, neddylation domain / Cullin protein neddylation domain / Cullin / Cullin, N-terminal / Cullin homology domain / Cullin homology domain superfamily / Cullin family / Cullin family profile. / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Ring finger / Ubiquitin conserved site / Ubiquitin domain / Zinc finger RING-type profile. / Zinc finger, RING-type / Ubiquitin domain signature. / Ubiquitin family / Ubiquitin homologues / Ubiquitin-like domain / Ubiquitin domain profile. / Ubiquitin-like domain superfamily / Zinc finger, RING/FYVE/PHD-type / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
E3 ubiquitin-protein ligase ARIH2 / NEDD8 / Cullin-5 / RING-box protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsKostrhon SP / Prabu JR / Schulman BA
Funding support Germany, 3 items
OrganizationGrant numberCountry
Max Planck Society Germany
European Research Council (ERC)H2020 789016-NEDD8Activate Germany
German Research Foundation (DFG)SCHU 3196/1-1 Germany
CitationJournal: Nat Chem Biol / Year: 2021
Title: CUL5-ARIH2 E3-E3 ubiquitin ligase structure reveals cullin-specific NEDD8 activation.
Authors: Sebastian Kostrhon / J Rajan Prabu / Kheewoong Baek / Daniel Horn-Ghetko / Susanne von Gronau / Maren Klügel / Jérôme Basquin / Arno F Alpi / Brenda A Schulman /
Abstract: An emerging mechanism of ubiquitylation involves partnering of two distinct E3 ligases. In the best-characterized E3-E3 pathways, ARIH-family RING-between-RING (RBR) E3s ligate ubiquitin to ...An emerging mechanism of ubiquitylation involves partnering of two distinct E3 ligases. In the best-characterized E3-E3 pathways, ARIH-family RING-between-RING (RBR) E3s ligate ubiquitin to substrates of neddylated cullin-RING E3s. The E3 ARIH2 has been implicated in ubiquitylation of substrates of neddylated CUL5-RBX2-based E3s, including APOBEC3-family substrates of the host E3 hijacked by HIV-1 virion infectivity factor (Vif). However, the structural mechanisms remained elusive. Here structural and biochemical analyses reveal distinctive ARIH2 autoinhibition, and activation on assembly with neddylated CUL5-RBX2. Comparison to structures of E3-E3 assemblies comprising ARIH1 and neddylated CUL1-RBX1-based E3s shows cullin-specific regulation by NEDD8. Whereas CUL1-linked NEDD8 directly recruits ARIH1, CUL5-linked NEDD8 does not bind ARIH2. Instead, the data reveal an allosteric mechanism. NEDD8 uniquely contacts covalently linked CUL5, and elicits structural rearrangements that unveil cryptic ARIH2-binding sites. The data reveal how a ubiquitin-like protein induces protein-protein interactions indirectly, through allostery. Allosteric specificity of ubiquitin-like protein modifications may offer opportunities for therapeutic targeting.
History
DepositionMay 25, 2021-
Header (metadata) releaseSep 15, 2021-
Map releaseSep 15, 2021-
UpdateOct 6, 2021-
Current statusOct 6, 2021Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0105
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.0105
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_13000.png

Downloads & links

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Map

FileDownload / File: emd_13000.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.8512 Å
Density
Contour LevelBy AUTHOR: 0.0105 / Movie #1: 0.0105
Minimum - Maximum-0.023768498 - 0.06598283
Average (Standard dev.)7.914731e-05 (±0.0011120867)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 408.576 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.85120.85120.8512
M x/y/z480480480
origin x/y/z0.0000.0000.000
length x/y/z408.576408.576408.576
α/β/γ90.00090.00090.000
start NX/NY/NZ29290
NX/NY/NZ140137200
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS480480480
D min/max/mean-0.0240.0660.000

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Supplemental data

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Mask #1

Fileemd_13000_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
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Histogram

Histogram (log scale)

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Additional map: DeepEMhancer sharpened Map

Fileemd_13000_additional_1.map
AnnotationDeepEMhancer sharpened Map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Half map: #1

Fileemd_13000_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Half map: #2

Fileemd_13000_half_map_2.map
Projections & Slices
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Histogram (log scale)

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Sample components

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Entire : Neddylated CUL5 C-terminal region-RBX2-ARIH2

EntireName: Neddylated CUL5 C-terminal region-RBX2-ARIH2
Components
  • Complex: Neddylated CUL5 C-terminal region-RBX2-ARIH2
    • Complex: Cullin-5
    • Complex: ARIH2
    • Complex: RBX2
    • Complex: NEDD8

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Supramolecule #1: Neddylated CUL5 C-terminal region-RBX2-ARIH2

SupramoleculeName: Neddylated CUL5 C-terminal region-RBX2-ARIH2 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4

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Supramolecule #2: Cullin-5

SupramoleculeName: Cullin-5 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)

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Supramolecule #3: ARIH2

SupramoleculeName: ARIH2 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)

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Supramolecule #4: RBX2

SupramoleculeName: RBX2 / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #3
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)

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Supramolecule #5: NEDD8

SupramoleculeName: NEDD8 / type: complex / ID: 5 / Parent: 1 / Macromolecule list: #4
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)

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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

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 14.9 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1.1)
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 191538
FSC plot (resolution estimation)

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