[English] 日本語
Yorodumi
- EMDB-26728: PARL-cleaved Skd3 (human ClpB) E455Q dodecamer bound to ATPgammaS -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-26728
TitlePARL-cleaved Skd3 (human ClpB) E455Q dodecamer bound to ATPgammaS
Map dataPARL-cleaved Skd3 (human ClpB) E455Q Nucleotide Binding Domain in the dodecameric state, half map 2
Sample
  • Complex: PARL-cleaved Skd3
    • Protein or peptide: PARL-cleaved Skd3
KeywordsAAA+ ATPase / Chaperone / Mitochondria / Protein Folding
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.8 Å
AuthorsGupta A / Lentzsch AM / Siegel AS / Yu Z / Lu C / Chio US / Cheng Y / Shan S
Funding support United States, 6 items
OrganizationGrant numberCountry
National Institutes of Health/Office of the DirectorOD021741 United States
National Institutes of Health/Office of the DirectorOD026881 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM129541 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM136321 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM137463 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM140847 United States
CitationJournal: Sci Adv / Year: 2023
Title: Dodecamer assembly of a metazoan AAA chaperone couples substrate extraction to refolding.
Authors: Arpit Gupta / Alfred M Lentzsch / Alex Siegel / Zanlin Yu / Un Seng Chio / Yifan Cheng / Shu-Ou Shan /
Abstract: Ring-forming AAA chaperones solubilize protein aggregates and protect organisms from proteostatic stress. In metazoans, the AAA chaperone Skd3 in the mitochondrial intermembrane space (IMS) is ...Ring-forming AAA chaperones solubilize protein aggregates and protect organisms from proteostatic stress. In metazoans, the AAA chaperone Skd3 in the mitochondrial intermembrane space (IMS) is critical for human health and efficiently refolds aggregated proteins, but its underlying mechanism is poorly understood. Here, we show that Skd3 harbors both disaggregase and protein refolding activities enabled by distinct assembly states. High-resolution structures of Skd3 hexamers in distinct conformations capture ratchet-like motions that mediate substrate extraction. Unlike previously described disaggregases, Skd3 hexamers further assemble into dodecameric cages in which solubilized substrate proteins can attain near-native states. Skd3 mutants defective in dodecamer assembly retain disaggregase activity but are impaired in client refolding, linking the disaggregase and refolding activities to the hexameric and dodecameric states of Skd3, respectively. We suggest that Skd3 is a combined disaggregase and foldase, and this property is particularly suited to meet the complex proteostatic demands in the mitochondrial IMS.
History
DepositionApr 23, 2022-
Header (metadata) releaseApr 26, 2023-
Map releaseApr 26, 2023-
UpdateNov 8, 2023-
Current statusNov 8, 2023Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_26728.png

Downloads & links

-
Map

FileDownload / File: emd_26728.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPARL-cleaved Skd3 (human ClpB) E455Q Nucleotide Binding Domain in the dodecameric state, half map 2
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.39 Å/pix.
x 288 pix.
= 400.435 Å		1.39 Å/pix.
x 288 pix.
= 400.435 Å		1.39 Å/pix.
x 288 pix.
= 400.435 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.3904 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02
Minimum - Maximum-0.017665446 - 0.08778833
Average (Standard dev.)0.00021343623 (±0.004176119)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions288288288
Spacing288288288
CellA=B=C: 400.4352 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: PARL-cleaved Skd3 (human ClpB) E455Q Nucleotide Binding Domain...

Fileemd_26728_half_map_1.map
AnnotationPARL-cleaved Skd3 (human ClpB) E455Q Nucleotide Binding Domain in the dodecameric state, half map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: PARL-cleaved Skd3 (human ClpB) E455Q Nucleotide Binding Domain...

Fileemd_26728_half_map_2.map
AnnotationPARL-cleaved Skd3 (human ClpB) E455Q Nucleotide Binding Domain in the dodecameric state, half map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : PARL-cleaved Skd3

EntireName: PARL-cleaved Skd3
Components
  • Complex: PARL-cleaved Skd3
    • Protein or peptide: PARL-cleaved Skd3

-
Supramolecule #1: PARL-cleaved Skd3

SupramoleculeName: PARL-cleaved Skd3 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 792 KDa

-
Macromolecule #1: PARL-cleaved Skd3

MacromoleculeName: PARL-cleaved Skd3 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: YSKSPSNKDA ALLEAARANN MQEVSRLLSE GADVNAKHRL GWTALMVAAI NRNNSVVQVL LAAGADPNLG DDFSSVYKTA KEQGIHSLED GGQDGASRHI TNQWTSALEF RRWLGLPAGV LITREDDFNN RLNNRASFKG CTALHYAVLA DDYRTVKELL DGGANPLQRN ...String:
YSKSPSNKDA ALLEAARANN MQEVSRLLSE GADVNAKHRL GWTALMVAAI NRNNSVVQVL LAAGADPNLG DDFSSVYKTA KEQGIHSLED GGQDGASRHI TNQWTSALEF RRWLGLPAGV LITREDDFNN RLNNRASFKG CTALHYAVLA DDYRTVKELL DGGANPLQRN EMGHTPLDYA REGEVMKLLR TSEAKYQEKQ RKREAEERRR FPLEQRLKEH IIGQESAIAT VGAAIRRKEN GWYDEEHPLV FLFLGSSGIG KTELAKQTAK YMHKDAKKGF IRLDMSEFQE RHEVAKFIGS PPGYVGHEEG GQLTKKLKQC PNAVVLFDQV DKAHPDVLTI MLQLFDEGRL TDGKGKTIDC KDAIFIMTSN VASDEIAQHA LQLRQEALEM SRNRIAENLG DVQISDKITI SKNFKENVIR PILKAHFRRD EFLGRINEIV YFLPFCHSEL IQLVNKELNF WAKRAKQRHN ITLLWDREVA DVLVDGYNVH YGARSIKHEV ERRVVNQLAA AYEQDLLPGG CTLRITVEDS DKQLLKSPEL PSPQAEKRLP KLRLEIIDKD SKTRRLDIRA PLHPEKVCNT I

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.1 mg/mL
BufferpH: 7.4
VitrificationCryogen name: ETHANE / Chamber humidity: 100 %

-
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 / Nominal defocus max: -2.0 µm / Nominal defocus min: -1.0 µm
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 60.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Startup modelType of model: NONE
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
Final reconstructionResolution.type: BY AUTHOR / Resolution: 6.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 521193
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