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- EMDB-55088: Cryo-EM structure of the ARISCdC(E33A):K63-Ub4 complex (Right Arm map) -

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Basic information

Entry
Database: EMDB / ID: EMD-55088
TitleCryo-EM structure of the ARISCdC(E33A):K63-Ub4 complex (Right Arm map)
Map data
Sample
  • Complex: ARISCdC(E33A) in complex with K63-linked ubiquitin chains
KeywordsDeubiquitylating enzymes / JAMM/MPN family / ubiquitin chains / DNA damage repair / HYDROLASE
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.88 Å
AuthorsFoglizzo M / Degtjarik O / Zeqiraj E
Funding support United Kingdom, 4 items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/Z51522X/1 United Kingdom
Wellcome Trust222531/Z/21/Z United Kingdom
Medical Research Council (MRC, United Kingdom)MR/T029471/1 United Kingdom
Wellcome Trust221524/Z/20/Z United Kingdom
CitationJournal: To Be Published
Title: Mechanism of K63-linked polyubiquitin recognition and cleavage by the BRCA1-A complex
Authors: Foglizzo M / Datta A / Degtjarik O / Perera H / Liburd J / Sykora UM / Ganji RS / Wildsmith G / Chandler F / Campbell LJ / Calabrese AN / Greenberg RA / Zeqiraj E
History
DepositionSep 17, 2025-
Header (metadata) releaseAug 5, 2026-
Map releaseAug 5, 2026-
UpdateAug 5, 2026-
Current statusAug 5, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_55088.png

Downloads & links

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Map

FileDownload / File: emd_55088.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.74 Å/pix.
x 400 pix.
= 296. Å		0.74 Å/pix.
x 400 pix.
= 296. Å		0.74 Å/pix.
x 400 pix.
= 296. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.74 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0135
Minimum - Maximum-0.001814488 - 1.8646029
Average (Standard dev.)0.000087711975 (±0.0072101974)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 296.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_55088_msk_1.map
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AxesZYX

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Additional map: #1

Fileemd_55088_additional_1.map
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Half map: #1

Fileemd_55088_half_map_1.map
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Half map: #2

Fileemd_55088_half_map_2.map
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Sample components

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Entire : ARISCdC(E33A) in complex with K63-linked ubiquitin chains

EntireName: ARISCdC(E33A) in complex with K63-linked ubiquitin chains
Components
  • Complex: ARISCdC(E33A) in complex with K63-linked ubiquitin chains

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Supramolecule #1: ARISCdC(E33A) in complex with K63-linked ubiquitin chains

SupramoleculeName: ARISCdC(E33A) in complex with K63-linked ubiquitin chains
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 131 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

Concentration0.8 mg/mL
BufferpH: 7.3
Component:
ConcentrationFormulaName
25.0 mMHEPES2-[4-(2-hydroxyethyl)piperazin-1-yl]ethanesulfonic acid
150.0 mMNaClsodium chloride
1.0 mMTCEPtris(2-carboxyethyl)phosphine
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 3.8e-07 kPa
Details: UltrAuFoil R1.2/1.3 300-mesh grids (Quantifoil Micro Tools GmbH) were glow-discharged for 1 min at 12 mA and 0.38 mBar pressure using a PELCO easiGlow system (Ted Pella).
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
Details: blot force = 1 N; blot time = 6 s; waiting time = 27 s.
DetailsFreshly purified ARISCdC(E33A) (at 0.8 mg/mL) was mixed with 1.5-fold molar excess of K63-linked tetraUb (Ub4) chains, and incubated in the presence of 0.025% (v/v) glutaraldehyde (Sigma-Aldrich) at room temperature for 4 min. Cross-linking reactions were then quenched by the addition of 100 mM Tris-HCl pH 7.5 prior to cryo-EM grids preparation.

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsPhase plate: VOLTA PHASE PLATE / Energy filter - Name: TFS Selectris / Energy filter - Slit width: 10 eV
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Number grids imaged: 2 / Number real images: 58037 / Average exposure time: 3.4 sec. / Average electron dose: 45.8 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.9 µm / Nominal magnification: 165000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 2194750
CTF correctionSoftware - Name: cryoSPARC (ver. v4.5.3) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Details: A previously determined 3D volume was used as the startup model
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.88 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. v4.5.3) / Number images used: 54452
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. v4.5.3)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. v4.5.3)
Final 3D classificationNumber classes: 3 / Software - Name: cryoSPARC (ver. v4.5.3)
FSC plot (resolution estimation)

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Atomic model buiding 1

SoftwareName: UCSF ChimeraX (ver. v1.6.1)

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