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- PDB-7pru: Structure of CtAtm1 in the inward-facing partially occluded with ... -

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Basic information

Entry
Database: PDB / ID: 7pru
TitleStructure of CtAtm1 in the inward-facing partially occluded with cargo bound
ComponentsPutative iron-sulfur protein
KeywordsMEMBRANE PROTEIN / ABC exporter
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
GLUTATHIONE / Iron-sulfur clusters transporter ATM1, mitochondrial
Similarity search - Component
Biological speciesChaetomium thermophilum (fungus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsLi, P. / Wang, K.T. / Gourdon, P.E.
Funding support Denmark, 3items
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 22, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 10, 2022Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_3d_fitting_list / em_admin / pdbx_initial_refinement_model
Item: _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id ..._em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative iron-sulfur protein
B: Putative iron-sulfur protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)155,0144
Polymers154,4002
Non-polymers6152
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "A"
d_2ens_1chain "B"

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1ALAMETA1 - 582
d_21ens_1ALAMETB1 - 582

NCS oper: (Code: givenMatrix: (-0.999986794561, -0.00462888859354, 0.00223250855368), (0.00463107130333, -0.999988802659, 0.000973517302293), (0.00222797725239, 0.000983843352867, 0.99999703408) ...NCS oper: (Code: given
Matrix: (-0.999986794561, -0.00462888859354, 0.00223250855368), (0.00463107130333, -0.999988802659, 0.000973517302293), (0.00222797725239, 0.000983843352867, 0.99999703408)
Vector: 266.609738387, 265.582014418, -0.540634617762)

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Components

#1: Protein Putative iron-sulfur protein


Mass: 77199.812 Da / Num. of mol.: 2 / Mutation: E603Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0050000 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: G0SBE6
#2: Chemical ChemComp-GSH / GLUTATHIONE


Mass: 307.323 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N3O6S / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: atm1 / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
Source (recombinant)Organism: Saccharomyces cerevisiae (brewer's yeast)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 40 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON III (4k x 4k)

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Processing

Software
NameVersionClassificationNB
phenix.real_space_refine1.18.2_3874refinement
PHENIX1.18.2_3874refinement
EM software
IDNameCategory
4cryoSPARCCTF correction
7UCSF Chimeramodel fitting
9PHENIXmodel refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 60113 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT
Atomic model buildingPDB-ID: 7PQX

7pqx


Accession code: 7PQX / Source name: PDB / Type: experimental model
RefinementHighest resolution: 3.2 Å / Cross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 97.74 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00929284
ELECTRON MICROSCOPYf_angle_d0.982812588
ELECTRON MICROSCOPYf_chiral_restr0.06021472
ELECTRON MICROSCOPYf_plane_restr0.00661600
ELECTRON MICROSCOPYf_dihedral_angle_d29.19711280
Refine LS restraints NCSType: NCS constraints / Rms dev position: 0.000708079012739 Å

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