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- EMDB-58935: CryoEM structure of DDB1-VprBP complex in "ARM-down" conformation -

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Basic information

Entry
Database: EMDB / ID: EMD-58935
TitleCryoEM structure of DDB1-VprBP complex in "ARM-down" conformation
Map data
Sample
  • Complex: DDB1-VprBP
KeywordsE3 ligase / Complex / Ubiquitination / LIGASE
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 9.6 Å
AuthorsWang D / Xu J
Funding support China, 5 items
OrganizationGrant numberCountry
Other government2021YFA1300204 China
National Natural Science Foundation of China (NSFC)31925023 China
National Natural Science Foundation of China (NSFC)21827810 China
National Natural Science Foundation of China (NSFC)31861143027 China
National Natural Science Foundation of China (NSFC)31470721 China
CitationJournal: PLoS Pathog / Year: 2026
Title: Structural basis of diverse substrate recruitment by the HIV-1 Vpr-hijacked CRL4(VprBP) E3 ligase.
Authors: Dianhong Wang / Weijia Ding / Jingwei Xu / Ruofan Li / Tamino Cairoli / Qi Liu / Yiying Zhu / Ye Xiang /
Abstract: HIV-1 hijacks the host CUL4-RING E3 ligase (CRL4) complex to trigger the degradation of various restriction factors. The viral accessory protein Vpr is the key protein that recruits diverse ...HIV-1 hijacks the host CUL4-RING E3 ligase (CRL4) complex to trigger the degradation of various restriction factors. The viral accessory protein Vpr is the key protein that recruits diverse substrates to the receptor VprBP for proteasomal degradation. However, the underlying molecular mechanism remains poorly understood. Here, we characterize the molecular architecture of the DDB1-VprBP substrate recognition unit alone and in complex with different Vpr-substrates. Our results pinpoint that the LisH domain of VprBP mediates the DDB1-VprBP dimerization. Of note, the Armadillo-like (ARM-like) domains of VprBP adopt either an "up" or "down" conformation that may assist in accommodating Vpr-substrates of divergent stoichiometries and sizes. When bound to the small Vpr substrate UNG2, the two "up" ARM-like domains wrap around and directly interact with two symmetrical UNG2 molecules. Intriguingly, the ARM-like domains adopt a "down" conformation when bound to the larger TET2 fragment. Our structures highlight that the conformational dynamics of VprBP could enable the DDB1-VprBP complex to mediate the degradation of diverse Vpr-bound host factors. These findings could facilitate the structure-guided development of CRL4(VprBP)-based targeted protein degradation.
History
DepositionJul 12, 2026-
Header (metadata) releaseOct 14, 2026-
Map releaseOct 14, 2026-
UpdateOct 14, 2026-
Current statusOct 14, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_58935.png

Downloads & links

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Map

FileDownload / File: emd_58935.map.gz / Format: CCP4 / Size: 15.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
2.18 Å/pix.
x 160 pix.
= 349.12 Å		2.18 Å/pix.
x 160 pix.
= 349.12 Å		2.18 Å/pix.
x 160 pix.
= 349.12 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 2.182 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02
Minimum - Maximum-0.020940084 - 0.062117007
Average (Standard dev.)-0.000056005512 (±0.004190294)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions160160160
Spacing160160160
CellA=B=C: 349.12 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_58935_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_58935_half_map_2.map
Projections & Slices
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Sample components

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Entire : DDB1-VprBP

EntireName: DDB1-VprBP
Components
  • Complex: DDB1-VprBP

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Supramolecule #1: DDB1-VprBP

SupramoleculeName: DDB1-VprBP / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 593 KDa

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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
Component:
ConcentrationFormulaName
20.0 mMHEPES-NaOH4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid
150.0 mMNaClSodium Chloride
GridModel: EMS Lacey Carbon / Mesh: 400 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 45 sec. / Pretreatment - Pressure: 0.39 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 281.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 9.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 127356
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)

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