[English] 日本語
Yorodumi
- EMDB-55071: Cryo-EM structure of the ARISC(E33A)-RAP80:K63-Ub7 complex (Non-c... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-55071
TitleCryo-EM structure of the ARISC(E33A)-RAP80:K63-Ub7 complex (Non-catalytic Ub, Right Arm map)
Map dataNon-catalytic Ub, Right Arm map; Sharp Map
Sample
  • Complex: ARISC(E33A)-RAP80 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: 3.99 Å
AuthorsFoglizzo M / 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 16, 2025-
Header (metadata) releaseAug 5, 2026-
Map releaseAug 5, 2026-
UpdateAug 5, 2026-
Current statusAug 5, 2026Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_55071.png

Downloads & links

-
Map

FileDownload / File: emd_55071.map.gz / Format: CCP4 / Size: 371.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationNon-catalytic Ub, Right Arm map; Sharp Map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.74 Å/pix.
x 460 pix.
= 340.4 Å		0.74 Å/pix.
x 460 pix.
= 340.4 Å		0.74 Å/pix.
x 460 pix.
= 340.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.74 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0133
Minimum - Maximum-0.0018198222 - 1.8369994
Average (Standard dev.)0.00023429094 (±0.0112401955)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions460460460
Spacing460460460
CellA=B=C: 340.4 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_55071_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: Non-catalytic Ub, Right Arm map; Unsharp Map

Fileemd_55071_additional_1.map
AnnotationNon-catalytic Ub, Right Arm map; Unsharp Map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Non-catalytic Ub, Right Arm map; Half Map A

Fileemd_55071_half_map_1.map
AnnotationNon-catalytic Ub, Right Arm map; Half Map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Non-catalytic Ub, Right Arm map; Half Map B

Fileemd_55071_half_map_2.map
AnnotationNon-catalytic Ub, Right Arm map; Half Map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : ARISC(E33A)-RAP80 in complex with K63-linked ubiquitin chains

EntireName: ARISC(E33A)-RAP80 in complex with K63-linked ubiquitin chains
Components
  • Complex: ARISC(E33A)-RAP80 in complex with K63-linked ubiquitin chains

-
Supramolecule #1: ARISC(E33A)-RAP80 in complex with K63-linked ubiquitin chains

SupramoleculeName: ARISC(E33A)-RAP80 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: 173 KDa

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.6 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 ARISC(E33A)-RAP80 (at 0.6 mg/mL) was mixed with 1.5-fold molar excess of K63-linked heptaUb (Ub7) chains, and incubated in the presence of 0.025% (v/v) glutaraldehyde (Sigma-Aldrich) at room temperature for 4 min. The cross-linking reaction was then quenched by the addition of 100 mM Tris-HCl pH 7.5 prior to cryo-EM grids preparation.

-
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: 1 / Number real images: 10649 / Average exposure time: 3.4 sec. / Average electron dose: 45.5 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

+
Image processing

Particle selectionNumber selected: 789840
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: 3.99 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. v4.5.3) / Number images used: 214650
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)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more