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- EMDB-26674: Human mitochondrial AAA protein ATAD1 (with a catalytic dead muta... -

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Basic information

Entry
Database: EMDB / ID: EMD-26674
TitleHuman mitochondrial AAA protein ATAD1 (with a catalytic dead mutation) in complex with a peptide substrate (closed conformation)
Map dataHuman mitochondrial AAA protein ATAD1
Sample
  • Complex: ATAD1-substrate complex in closed conformation
    • Protein or peptide: Outer mitochondrial transmembrane helix translocase
    • Protein or peptide: Unknown peptide substrate
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
KeywordsAAA protein / mitochondria / tail-anchored protein / membrane protein / PROTEIN TRANSPORT
Function / homology
Function and homology information


extraction of mislocalized protein from mitochondrial outer membrane / membrane protein dislocase activity / Class I peroxisomal membrane protein import / Translocases; Catalysing the translocation of amino acids and peptides; Linked to the hydrolysis of a nucleoside triphosphate / negative regulation of synaptic transmission, glutamatergic / regulation of postsynaptic neurotransmitter receptor internalization / peroxisomal membrane / positive regulation of receptor internalization / learning / memory ...extraction of mislocalized protein from mitochondrial outer membrane / membrane protein dislocase activity / Class I peroxisomal membrane protein import / Translocases; Catalysing the translocation of amino acids and peptides; Linked to the hydrolysis of a nucleoside triphosphate / negative regulation of synaptic transmission, glutamatergic / regulation of postsynaptic neurotransmitter receptor internalization / peroxisomal membrane / positive regulation of receptor internalization / learning / memory / postsynaptic membrane / mitochondrial outer membrane / glutamatergic synapse / ATP hydrolysis activity / ATP binding / membrane / cytosol
Similarity search - Function
AAA ATPase, AAA+ lid domain / AAA+ lid domain / ATPase, AAA-type, conserved site / AAA-protein family signature. / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Outer mitochondrial transmembrane helix translocase
Similarity search - Component
Biological speciesHomo sapiens (human) / Escherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsWang L / Toutkoushian H / Belyy V / Kokontis C / Walter P
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM032384 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)S10OD021741 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)S10OD020054 United States
CitationJournal: Elife / Year: 2022
Title: Conserved structural elements specialize ATAD1 as a membrane protein extraction machine.
Authors: Lan Wang / Hannah Toutkoushian / Vladislav Belyy / Claire Y Kokontis / Peter Walter /
Abstract: The mitochondrial AAA (TPase ssociated with diverse cellular ctivities) protein ATAD1 (in humans; Msp1 in yeast) removes mislocalized membrane proteins, as well as stuck import substrates from the ...The mitochondrial AAA (TPase ssociated with diverse cellular ctivities) protein ATAD1 (in humans; Msp1 in yeast) removes mislocalized membrane proteins, as well as stuck import substrates from the mitochondrial outer membrane, facilitating their re-insertion into their cognate organelles and maintaining mitochondria's protein import capacity. In doing so, it helps to maintain proteostasis in mitochondria. How ATAD1 tackles the energetic challenge to extract hydrophobic membrane proteins from the lipid bilayer and what structural features adapt ATAD1 for its particular function has remained a mystery. Previously, we determined the structure of Msp1 in complex with a peptide substrate (Wang et al., 2020). The structure showed that Msp1's mechanism follows the general principle established for AAA proteins while adopting several structural features that specialize it for its function. Among these features in Msp1 was the utilization of multiple aromatic amino acids to firmly grip the substrate in the central pore. However, it was not clear whether the aromatic nature of these amino acids were required, or if they could be functionally replaced by aliphatic amino acids. In this work, we determined the cryo-EM structures of the human ATAD1 in complex with a peptide substrate at near atomic resolution. The structures show that phylogenetically conserved structural elements adapt ATAD1 for its function while generally adopting a conserved mechanism shared by many AAA proteins. We developed a microscopy-based assay reporting on protein mislocalization, with which we directly assessed ATAD1's activity in live cells and showed that both aromatic amino acids in pore-loop 1 are required for ATAD1's function and cannot be substituted by aliphatic amino acids. A short α-helix at the C-terminus strongly facilitates ATAD1's oligomerization, a structural feature that distinguishes ATAD1 from its closely related proteins.
History
DepositionApr 16, 2022-
Header (metadata) releaseJun 15, 2022-
Map releaseJun 15, 2022-
UpdateFeb 14, 2024-
Current statusFeb 14, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_26674.png

Downloads & links

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Map

FileDownload / File: emd_26674.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHuman mitochondrial AAA protein ATAD1
Voxel sizeX=Y=Z: 0.832 Å
Density
Contour LevelBy AUTHOR: 0.25
Minimum - Maximum-1.2886606 - 2.6027484
Average (Standard dev.)0.0032913724 (±0.066860296)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 266.24 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Human mitochondrial AAA protein ATAD1-half map A

Fileemd_26674_half_map_1.map
AnnotationHuman mitochondrial AAA protein ATAD1-half map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Human mitochondrial AAA protein ATAD1-half map B

Fileemd_26674_half_map_2.map
AnnotationHuman mitochondrial AAA protein ATAD1-half map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : ATAD1-substrate complex in closed conformation

EntireName: ATAD1-substrate complex in closed conformation
Components
  • Complex: ATAD1-substrate complex in closed conformation
    • Protein or peptide: Outer mitochondrial transmembrane helix translocase
    • Protein or peptide: Unknown peptide substrate
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION

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Supramolecule #1: ATAD1-substrate complex in closed conformation

SupramoleculeName: ATAD1-substrate complex in closed conformation / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 200 KDa

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Macromolecule #1: Outer mitochondrial transmembrane helix translocase

MacromoleculeName: Outer mitochondrial transmembrane helix translocase / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
EC number: Translocases; Catalysing the translocation of amino acids and peptides; Linked to the hydrolysis of a nucleoside triphosphate
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 38.289855 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGSSHHHHHH SSGLVPRGSG SDPTRKQKVE AQKQAEKLMK QIGVKNVKLS EYEMSIAAHL VDPLNMHVTW SDIAGLDDVI TDLKDTVIL PIKKKHLFEN SRLLQPPKGV LLYGPPGCGK TLIAKATAKE AGCRFINLQP STLTDKWYGE SQKLAAAVFS L AIKLQPSI ...String:
MGSSHHHHHH SSGLVPRGSG SDPTRKQKVE AQKQAEKLMK QIGVKNVKLS EYEMSIAAHL VDPLNMHVTW SDIAGLDDVI TDLKDTVIL PIKKKHLFEN SRLLQPPKGV LLYGPPGCGK TLIAKATAKE AGCRFINLQP STLTDKWYGE SQKLAAAVFS L AIKLQPSI IFIDQIDSFL RNRSSSDHEA TAMMKAQFMS LWDGLDTDHS CQVIVMGATN RPQDLDSAIM RRMPTRFHIN QP ALKQREA ILKLILKNEN VDRHVDLLEV AQETDGFSGS DLKEMCRDAA LLCVREYVNS TSEESHDEDE IRPVQQQDLH RAI EKMKKS KDAAFQNVLT HVCLD

UniProtKB: Outer mitochondrial transmembrane helix translocase

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Macromolecule #2: Unknown peptide substrate

MacromoleculeName: Unknown peptide substrate / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 869.063 Da
SequenceString:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)

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Macromolecule #3: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 5 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM / Adenosine triphosphate

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Macromolecule #4: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 4 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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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

Concentration4 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: DIFFRACTION / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.6 µm
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 67.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 96577

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