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- EMDB-13616: C. thermophilum Atm1 in MSP1E3D1 nanodiscs in nucleotide-free sta... -

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Basic information

Entry
Database: EMDB / ID: EMD-13616
TitleC. thermophilum Atm1 in MSP1E3D1 nanodiscs in nucleotide-free state, class 1
Map data
Sample
  • Complex: Atm1 homodimer in MSP1E3D1 nanodiscs
    • Protein or peptide: Atm1
Function / homology
Function and homology information


iron-sulfur cluster transmembrane transport / Mitochondrial ABC transporters / iron-sulfur cluster export from the mitochondrion / mitochondrial transmembrane transport / Translocases / iron-sulfur cluster assembly / ATPase-coupled transmembrane transporter activity / ABC-type transporter activity / transmembrane transport / intracellular iron ion homeostasis ...iron-sulfur cluster transmembrane transport / Mitochondrial ABC transporters / iron-sulfur cluster export from the mitochondrion / mitochondrial transmembrane transport / Translocases / iron-sulfur cluster assembly / ATPase-coupled transmembrane transporter activity / ABC-type transporter activity / transmembrane transport / intracellular iron ion homeostasis / mitochondrial inner membrane / ATP hydrolysis activity / mitochondrion / 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 (fungus)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.1 Å
AuthorsEllinghaus TL / Kuehlbrandt W
Funding support Germany, 1 items
OrganizationGrant numberCountry
German Research Foundation (DFG)LI 415/5 & SR 113/1 Germany
CitationJournal: Sci Adv / Year: 2021
Title: Conformational changes in the yeast mitochondrial ABC transporter Atm1 during the transport cycle.
Authors: Thomas L Ellinghaus / Thomas Marcellino / Vasundara Srinivasan / Roland Lill / Werner Kühlbrandt /
Abstract: The mitochondrial inner membrane ABC transporter Atm1 exports an unknown substrate to the cytosol for iron-sulfur protein biogenesis, cellular iron regulation, and tRNA thio-modification. Mutations ...The mitochondrial inner membrane ABC transporter Atm1 exports an unknown substrate to the cytosol for iron-sulfur protein biogenesis, cellular iron regulation, and tRNA thio-modification. Mutations in the human relative ABCB7 cause the iron storage disease XLSA/A. We determined 3D structures of two complementary states of Atm1 in lipid nanodiscs by electron cryo-microscopy at 2.9- to 3.4-Å resolution. The inward-open structure resembled the known crystal structure of nucleotide-free apo-Atm1 closely. The occluded conformation with bound AMP-PNP-Mg showed a tight association of the two nucleotide-binding domains, a rearrangement of the C-terminal helices, and closure of the putative substrate-binding cavity in the homodimeric transporter. We identified a hydrophobic patch on the C-terminal helices of yeast Atm1, which is unique among type IV ABC transporters of known structure. Truncation mutants of yeast Atm1 suggest that the C-terminal helices stabilize the dimer, yet are not necessary for closure of the nucleotide-binding domains.
History
DepositionSep 23, 2021-
Header (metadata) releaseDec 29, 2021-
Map releaseDec 29, 2021-
UpdateDec 29, 2021-
Current statusDec 29, 2021Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.1704
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.1704
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_13616.png

Downloads & links

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Map

FileDownload / File: emd_13616.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 256 pix.
= 214.272 Å		0.84 Å/pix.
x 256 pix.
= 214.272 Å		0.84 Å/pix.
x 256 pix.
= 214.272 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.837 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1704 / Movie #1: 0.1704
Minimum - Maximum-0.45736918 - 0.8301306
Average (Standard dev.)0.0073596966 (±0.041838985)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 214.272 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.8370.8370.837
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z214.272214.272214.272
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ320320320
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.4570.8300.007

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Supplemental data

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Sample components

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Entire : Atm1 homodimer in MSP1E3D1 nanodiscs

EntireName: Atm1 homodimer in MSP1E3D1 nanodiscs
Components
  • Complex: Atm1 homodimer in MSP1E3D1 nanodiscs
    • Protein or peptide: Atm1

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Supramolecule #1: Atm1 homodimer in MSP1E3D1 nanodiscs

SupramoleculeName: Atm1 homodimer in MSP1E3D1 nanodiscs / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Chaetomium thermophilum (fungus)
Recombinant expressionOrganism: Escherichia coli (E. coli)
Molecular weightTheoretical: 155 KDa

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Macromolecule #1: Atm1

MacromoleculeName: Atm1 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
EC number: Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to catalyse transmembrane movement of substances
Source (natural)Organism: Chaetomium thermophilum (fungus)
SequenceString: MKKTAIAIAV ALAGFATVAQ ASTLLNPSPS PLRKAIFHTT SLRAFKNLAE IATSSKEDAS SLKPKGKPSP PGDPLATIEK TAAEQRRADW AIIKQMSRYL WPKDSWSDKA RVLLALSLLV GGKVLNVHVP FYFREIIDRL NIDVAAVGGT VSAVAGAVIF AYGASRIGAV ...String:
MKKTAIAIAV ALAGFATVAQ ASTLLNPSPS PLRKAIFHTT SLRAFKNLAE IATSSKEDAS SLKPKGKPSP PGDPLATIEK TAAEQRRADW AIIKQMSRYL WPKDSWSDKA RVLLALSLLV GGKVLNVHVP FYFREIIDRL NIDVAAVGGT VSAVAGAVIF AYGASRIGAV VSQELRNAVF SSVAQKAIRR VATQTFGHLL NLDLSFHLSK QTGGLTRAID RGTKGISYLL TSMVFHIVPT ALEIGMVCGI LTYQFGWEFA AITAATMAAY TAFTITTTAW RTKFRRQANA ADNAASTVAV DSLINYEAVK YFNNEAYEIA RYDKALQAYE RSSIKVATSL AFLNSGQNII FSSALTLMMW LGARGVLAGD LSVGDLVLIN QLVFQLSVPL NFLGSVYREL RQSLLDMETL FDLQKVNVTI REAPNAKPLA LPKGGEIRFE NVTFGYYPDR PILRNLSLTI PAGKKVAVVG PSGCGKSTLL RLLFRSYDPQ QGKIFIDDQD IKSVTLESLR KSIGVVPQDT PLFNDTVELN IRYGNVNATQ EQVIAAAQKA HIHEKIISWP HGYQTRVGER GLMISGGEKQ RLAVSRLILK DPPLLFFDEA TSALDTHTEQ ALMANINEVV KEKKRTALFV AHRLRTIYDA DLIIVLKEGV VVEQGSHREL MERDGVYAEL WMAQEMLHQG EAAEEPAEGE KAEEKKSAWS HPQFEK

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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: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 63.0 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: OTHER / Details: RELION
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 7.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.0.1) / Software - details: NU-Refinement / Number images used: 22007
Initial angle assignmentType: OTHER / Details: RELION
Final angle assignmentType: OTHER / Details: cryoSPARC
FSC plot (resolution estimation)

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