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- EMDB-33105: Structure and mechanism of a mitochondrial AAA+ disaggregase CLPB -

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Basic information

Entry
Database: EMDB / ID: EMD-33105
TitleStructure and mechanism of a mitochondrial AAA+ disaggregase CLPB
Map data
Sample
  • Complex: cryo-EM structure of CLPB in apo-state
    • Protein or peptide: CLPB
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / negative staining / Resolution: 6.8 Å
AuthorsWu D / Liu Y / Dai Y / Wang G / Lu G / Chen Y / Li N / Lin J / Gao N
Funding support China, 1 items
OrganizationGrant numberCountry
National Science Foundation (NSF, China) China
CitationJournal: PLoS Biol / Year: 2023
Title: Comprehensive structural characterization of the human AAA+ disaggregase CLPB in the apo- and substrate-bound states reveals a unique mode of action driven by oligomerization.
Authors: Damu Wu / Yan Liu / Yuhao Dai / Guopeng Wang / Guoliang Lu / Yan Chen / Ningning Li / Jinzhong Lin / Ning Gao /
Abstract: The human AAA+ ATPase CLPB (SKD3) is a protein disaggregase in the mitochondrial intermembrane space (IMS) and functions to promote the solubilization of various mitochondrial proteins. Loss-of- ...The human AAA+ ATPase CLPB (SKD3) is a protein disaggregase in the mitochondrial intermembrane space (IMS) and functions to promote the solubilization of various mitochondrial proteins. Loss-of-function CLPB mutations are associated with a few human diseases with neutropenia and neurological disorders. Unlike canonical AAA+ proteins, CLPB contains a unique ankyrin repeat domain (ANK) at its N-terminus. How CLPB functions as a disaggregase and the role of its ANK domain are currently unclear. Herein, we report a comprehensive structural characterization of human CLPB in both the apo- and substrate-bound states. CLPB assembles into homo-tetradecamers in apo-state and is remodeled into homo-dodecamers upon substrate binding. Conserved pore-loops (PLs) on the ATPase domains form a spiral staircase to grip and translocate the substrate in a step-size of 2 amino acid residues. The ANK domain is not only responsible for maintaining the higher-order assembly but also essential for the disaggregase activity. Interactome analysis suggests that the ANK domain may directly interact with a variety of mitochondrial substrates. These results reveal unique properties of CLPB as a general disaggregase in mitochondria and highlight its potential as a target for the treatment of various mitochondria-related diseases.
History
DepositionMar 21, 2022-
Header (metadata) releaseJan 25, 2023-
Map releaseJan 25, 2023-
UpdateFeb 22, 2023-
Current statusFeb 22, 2023Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_33105.png

Downloads & links

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Map

FileDownload / File: emd_33105.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 300 pix.
= 321. Å		1.07 Å/pix.
x 300 pix.
= 321. Å		1.07 Å/pix.
x 300 pix.
= 321. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07 Å
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Histogram (log scale)
Contour LevelBy AUTHOR: 0.011
Minimum - Maximum-0.0033045476 - 0.023009738
Average (Standard dev.)0.00038334713 (±0.0019459894)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 321.00003 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_33105_half_map_1.map
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Half map: #2

Fileemd_33105_half_map_2.map
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Sample components

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Entire : cryo-EM structure of CLPB in apo-state

EntireName: cryo-EM structure of CLPB in apo-state
Components
  • Complex: cryo-EM structure of CLPB in apo-state
    • Protein or peptide: CLPB

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Supramolecule #1: cryo-EM structure of CLPB in apo-state

SupramoleculeName: cryo-EM structure of CLPB in apo-state / type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: CLPB

MacromoleculeName: CLPB / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MLGSLVLRRK ALAPRLLLRL LRSPTLRGHG GASGRNVTTG SLGEPQWLRV ATGGRPGTSP ALFSGRGAA TGGRQGGRFD TKCLAAATWG RLPGPEETLP GQDSWNGVPS RAGLGMCALA A ALVVHCYS KSPSNKDAAL LEAARANNMQ EVSRLLSEGA DVNAKHRLGW ...String:
MLGSLVLRRK ALAPRLLLRL LRSPTLRGHG GASGRNVTTG SLGEPQWLRV ATGGRPGTSP ALFSGRGAA TGGRQGGRFD TKCLAAATWG RLPGPEETLP GQDSWNGVPS RAGLGMCALA A ALVVHCYS KSPSNKDAAL LEAARANNMQ EVSRLLSEGA DVNAKHRLGW TALMVAAINR NN SVVQVLL AAGADPNLGD DFSSVYKTAK EQGIHSLEVL ITREDDFNNR LNNRASFKGC TAL HYAVLA DDYRTVKELL DGGANPLQRN EMGHTPLDYA REGEVMKLLR TSEAKYQEKQ RKRE AEERR RFPLEQRLKE HIIGQESAIA TVGAAIRRKE NGWYDEEHPL VFLFLGSSGI GKTEL AKQT AKYMHKDAKK GFIRLDMSEF QERHEVAKFI GSPPGYVGHE EGGQLTKKLK QCPNAV VLF DEVDKAHPDV LTIMLQLFDE GRLTDGKGKT IDCKDAIFIM TSNVASDEIA QHALQLR QE ALEMSRNRIA ENLGDVQISD KITISKNFKE NVIRPILKAH FRRDEFLGRI NEIVYFLP F CHSELIQLVN KELNFWAKRA KQRHNITLLW DREVADVLVD GYNVHYGARS IKHEVERRV VNQLAAAYEQ DLLPGGCTLR ITVEDSDKQL LKSPELPSPQ AEKRLPKLRL EIIDKDSKTR RLDIRAPLH PEKVCNTI

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Experimental details

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Structure determination

Methodnegative staining, cryo EM
Processingsingle particle reconstruction
Aggregation statecell

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Sample preparation

BufferpH: 6.8
StainingType: NEGATIVE / Material: Uranyl Acetate
VitrificationCryogen name: NITROGEN

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: DARK FIELD / Nominal defocus max: 5.0 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 6.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 153005
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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