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- EMDB-13614: S. cerevisiae Atm1 in MSP1D1 nanodiscs with bound AMP-PNP and Mg2+ -

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Basic information

Entry
Database: EMDB / ID: EMD-13614
TitleS. cerevisiae Atm1 in MSP1D1 nanodiscs with bound AMP-PNP and Mg2+
Map data
Sample
  • Complex: Atm1 homodimer in MSP1D1 nanodiscs
    • Protein or peptide: Iron-sulfur clusters transporter ATM1, mitochondrial
  • Ligand: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
  • Ligand: MAGNESIUM ION
  • Ligand: (1R)-2-{[(R)-(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(DODECANOYLOXY)METHYL]ETHYL (9Z)-OCTADEC-9-ENOATE
KeywordsABC transporter / TRANSPORT PROTEIN
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 speciesSaccharomyces cerevisiae (brewer's yeast) / Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 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-
UpdateJul 17, 2024-
Current statusJul 17, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.7
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.7
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7psm
  • Surface level: 0.7
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_13614.png

Downloads & links

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Map

FileDownload / File: emd_13614.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.
= 266.56 Å		0.83 Å/pix.
x 320 pix.
= 266.56 Å		0.83 Å/pix.
x 320 pix.
= 266.56 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.833 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.7 / Movie #1: 0.7
Minimum - Maximum-2.7353876 - 3.8097975
Average (Standard dev.)-0.0001277876 (±0.095953435)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 266.56 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.8330.8330.833
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z266.560266.560266.560
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ320320320
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-2.7353.810-0.000

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Supplemental data

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Sample components

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Entire : Atm1 homodimer in MSP1D1 nanodiscs

EntireName: Atm1 homodimer in MSP1D1 nanodiscs
Components
  • Complex: Atm1 homodimer in MSP1D1 nanodiscs
    • Protein or peptide: Iron-sulfur clusters transporter ATM1, mitochondrial
  • Ligand: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
  • Ligand: MAGNESIUM ION
  • Ligand: (1R)-2-{[(R)-(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(DODECANOYLOXY)METHYL]ETHYL (9Z)-OCTADEC-9-ENOATE

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Supramolecule #1: Atm1 homodimer in MSP1D1 nanodiscs

SupramoleculeName: Atm1 homodimer in MSP1D1 nanodiscs / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 137 KDa

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Macromolecule #1: Iron-sulfur clusters transporter ATM1, mitochondrial

MacromoleculeName: Iron-sulfur clusters transporter ATM1, mitochondrial / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: Translocases
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 68.392969 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: LKDLFRYIWP KGNNKVRIRV LIALGLLISA KILNVQVPFF FKQTIDSMNI AWDDPTVALP AAIGLTILCY GVARFGSVLF GELRNAVFA KVAQNAIRTV SLQTFQHLMK LDLGWHLSRQ TGGLTRAMDR GTKGISQVLT AMVFHIIPIS FEISVVCGIL T YQFGASFA ...String:
LKDLFRYIWP KGNNKVRIRV LIALGLLISA KILNVQVPFF FKQTIDSMNI AWDDPTVALP AAIGLTILCY GVARFGSVLF GELRNAVFA KVAQNAIRTV SLQTFQHLMK LDLGWHLSRQ TGGLTRAMDR GTKGISQVLT AMVFHIIPIS FEISVVCGIL T YQFGASFA AITFSTMLLY SIFTIKTTAW RTHFRRDANK ADNKAASVAL DSLINFEAVK YFNNEKYLAD KYNGSLMNYR DS QIKVSQS LAFLNSGQNL IFTTALTAMM YMGCTGVIGG NLTVGDLVLI NQLVFQLSVP LNFLGSVYRD LKQSLIDMET LFK LRKNEV KIKNAERPLM LPENVPYDIT FENVTFGYHP DRKILKNASF TIPAGWKTAI VGSSGSGKST ILKLVFRFYD PESG RILIN GRDIKEYDID ALRKVIGVVP QDTPLFNDTI WENVKFGRID ATDEEVITVV EKAQLAPLIK KLPQGFDTIV GERGL MISG GEKQRLAIAR VLLKNARIMF FDEATSALDT HTEQALLRTI RDNFTSGSRT SVYIAHRLRT IADADKIIVL DNGRVR EEG KHLELLAMPG SLYRELWTIQ EDLDHLENEL KDQQELWSHP QFEK

UniProtKB: Iron-sulfur clusters transporter ATM1, mitochondrial

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Macromolecule #2: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER

MacromoleculeName: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / type: ligand / ID: 2 / Number of copies: 2 / Formula: ANP
Molecular weightTheoretical: 506.196 Da
Chemical component information

ChemComp-ANP:
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / AMP-PNP, energy-carrying molecule analogue*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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Macromolecule #4: (1R)-2-{[(R)-(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(DODECANO...

MacromoleculeName: (1R)-2-{[(R)-(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(DODECANOYLOXY)METHYL]ETHYL (9Z)-OCTADEC-9-ENOATE
type: ligand / ID: 4 / Number of copies: 2 / Formula: LOP
Molecular weightTheoretical: 661.89 Da
Chemical component information

ChemComp-LOP:
(1R)-2-{[(R)-(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(DODECANOYLOXY)METHYL]ETHYL (9Z)-OCTADEC-9-ENOATE / phospholipid*YM

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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: 50.0 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: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 2.15.0) / Software - details: NU-Refinement / Number images used: 178134
Initial angle assignmentType: OTHER / Details: RELION
Final angle assignmentType: OTHER / Details: cryoSPARC
FSC plot (resolution estimation)

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