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- EMDB-13607: Structure of CtAtm1 in the occluded conformation with ATP bound -

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Basic information

Entry
Database: EMDB / ID: EMD-13607
TitleStructure of CtAtm1 in the occluded conformation with ATP bound
Map data
Sample
  • Complex: atm1
    • Protein or peptide: Putative iron-sulfur protein
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
KeywordsABC exporter / MEMBRANE PROTEIN
Function / homology
Function and homology information


ABC-type transporter activity / mitochondrial inner membrane / ATP hydrolysis activity / ATP binding
Similarity search - Function
Type 1 protein exporter / ABC transporter transmembrane region / ABC transporter type 1, transmembrane domain / ABC transporter integral membrane type-1 fused domain profile. / ABC transporter type 1, transmembrane domain superfamily / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. ...Type 1 protein exporter / ABC transporter transmembrane region / ABC transporter type 1, transmembrane domain / ABC transporter integral membrane type-1 fused domain profile. / ABC transporter type 1, transmembrane domain superfamily / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Iron-sulfur clusters transporter ATM1, mitochondrial
Similarity search - Component
Biological speciesChaetomium thermophilum var. thermophilum DSM 1495 (fungus) / Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.81 Å
AuthorsLi P / Wang KT
Funding support Denmark, 3 items
OrganizationGrant numberCountry
LundbeckfondenR313-2019-774 Denmark
Swedish Research Council2016-04474 Denmark
Danish Council for Independent Research9039-00273 Denmark
CitationJournal: Nat Commun / Year: 2022
Title: Structures of Atm1 provide insight into [2Fe-2S] cluster export from mitochondria.
Authors: Ping Li / Amber L Hendricks / Yong Wang / Rhiza Lyne E Villones / Karin Lindkvist-Petersson / Gabriele Meloni / J A Cowan / Kaituo Wang / Pontus Gourdon /
Abstract: In eukaryotes, iron-sulfur clusters are essential cofactors for numerous physiological processes, but these clusters are primarily biosynthesized in mitochondria. Previous studies suggest ...In eukaryotes, iron-sulfur clusters are essential cofactors for numerous physiological processes, but these clusters are primarily biosynthesized in mitochondria. Previous studies suggest mitochondrial ABCB7-type exporters are involved in maturation of cytosolic iron-sulfur proteins. However, the molecular mechanism for how the ABCB7-type exporters participate in this process remains elusive. Here, we report a series of cryo-electron microscopy structures of a eukaryotic homolog of human ABCB7, CtAtm1, determined at average resolutions ranging from 2.8 to 3.2 Å, complemented by functional characterization and molecular docking in silico. We propose that CtAtm1 accepts delivery from glutathione-complexed iron-sulfur clusters. A partially occluded state links cargo-binding to residues at the mitochondrial matrix interface that line a positively charged cavity, while the binding region becomes internalized and is partially divided in an early occluded state. Collectively, our findings substantially increase the understanding of the transport mechanism of eukaryotic ABCB7-type proteins.
History
DepositionSep 20, 2021-
Header (metadata) releaseAug 10, 2022-
Map releaseAug 10, 2022-
UpdateJul 17, 2024-
Current statusJul 17, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_13607.png

Downloads & links

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Map

FileDownload / File: emd_13607.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 320 pix.
= 266.24 Å		0.83 Å/pix.
x 320 pix.
= 266.24 Å		0.83 Å/pix.
x 320 pix.
= 266.24 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.832 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.7
Minimum - Maximum-3.1827703 - 5.8892283
Average (Standard dev.)0.00011889104 (±0.123700984)
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: #2

Fileemd_13607_half_map_1.map
Projections & Slices
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Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_13607_half_map_2.map
Projections & Slices
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Histogram (log scale)

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Sample components

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Entire : atm1

EntireName: atm1
Components
  • Complex: atm1
    • Protein or peptide: Putative iron-sulfur protein
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION

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Supramolecule #1: atm1

SupramoleculeName: atm1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)

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Macromolecule #1: Putative iron-sulfur protein

MacromoleculeName: Putative iron-sulfur protein / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719
Molecular weightTheoretical: 77.199812 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MSPRSRLLAS SLRGGLLLRP CSARRSTLLN PSPSPLRKAI FHTTSLRAFK NLAEIATSSK EDASSLKPKG KPSPPGDPLA TIEKTAAEQ RRADWAIIKQ MSRYLWPKDS WSDKARVLLA LSLLVGGKVL NVHVPFYFRE IIDRLNIDVA AVGGTVSAVA G AVIFAYGA ...String:
MSPRSRLLAS SLRGGLLLRP CSARRSTLLN PSPSPLRKAI FHTTSLRAFK NLAEIATSSK EDASSLKPKG KPSPPGDPLA TIEKTAAEQ RRADWAIIKQ MSRYLWPKDS WSDKARVLLA LSLLVGGKVL NVHVPFYFRE IIDRLNIDVA AVGGTVSAVA G AVIFAYGA SRIGAVVSQE LRNAVFSSVA QKAIRRVATQ TFGHLLNLDL SFHLSKQTGG LTRAIDRGTK GISYLLTSMV FH IVPTALE IGMVCGILTY QFGWEFAAIT AATMAAYTAF TITTTAWRTK FRRQANAADN AASTVAVDSL INYEAVKYFN NEA YEIARY DKALQAYERS SIKVATSLAF LNSGQNIIFS SALTLMMWLG ARGVLAGDLS VGDLVLINQL VFQLSVPLNF LGSV YRELR QSLLDMETLF DLQKVNVTIR EAPNAKPLAL PKGGEIRFEN VTFGYYPDRP ILRNLSLTIP AGKKVAVVGP SGCGK STLL RLLFRSYDPQ QGKIFIDDQD IKSVTLESLR KSIGVVPQDT PLFNDTVELN IRYGNVNATQ EQVIAAAQKA HIHEKI ISW PHGYQTRVGE RGLMISGGEK QRLAVSRLIL KDPPLLFFDQ ATSALDTHTE QALMANINEV VKEKKRTALF VAHRLRT IY DADLIIVLKE GVVVEQGSHR ELMERDGVYA ELWMAQEMLH QGEAAEEPAE GEKAEEKK

UniProtKB: Iron-sulfur clusters transporter ATM1, mitochondrial

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Macromolecule #2: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 2 / Number of copies: 2 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

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

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Macromolecule #3: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 3 / Number of copies: 2 / 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

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.81 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 117631
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: RANDOM ASSIGNMENT

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Atomic model buiding 1

Initial modelPDB ID:

7pqx


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementProtocol: RIGID BODY FIT
Output model

PDB-7pr1:
Structure of CtAtm1 in the occluded conformation with ATP bound

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