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- EMDB-24185: Structure of AtAtm3 in the outward-facing conformation -

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Basic information

Entry
Database: EMDB / ID: EMD-24185
TitleStructure of AtAtm3 in the outward-facing conformation
Map dataAtAtm3 in the outward-facing conformation
Sample
  • Complex: AtAtm3 in detergent
    • Protein or peptide: ABC transporter B family member 25, mitochondrial
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: VANADATE ION
  • Ligand: MAGNESIUM ION
KeywordsABC transporter / ATPase / MEMBRANE PROTEIN
Function / homology
Function and homology information


regulation of chlorophyll biosynthetic process / chloroplast organization / pollen development / root development / regulation of catalytic activity / Mo-molybdopterin cofactor biosynthetic process / chloroplast envelope / plastid / chromosome organization / ABC-type transporter activity ...regulation of chlorophyll biosynthetic process / chloroplast organization / pollen development / root development / regulation of catalytic activity / Mo-molybdopterin cofactor biosynthetic process / chloroplast envelope / plastid / chromosome organization / ABC-type transporter activity / response to cadmium ion / chloroplast / response to lead ion / iron ion 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
ABC transporter B family member 25, mitochondrial
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsFan C / Rees DC
Funding support United States, 1 items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Elife / Year: 2022
Title: Glutathione binding to the plant Atm3 transporter and implications for the conformational coupling of ABC transporters.
Authors: Chengcheng Fan / Douglas C Rees /
Abstract: The ATP binding cassette (ABC) transporter of mitochondria (Atm) from (Atm3) has been implicated in the maturation of cytosolic iron-sulfur proteins and heavy metal detoxification, plausibly by ...The ATP binding cassette (ABC) transporter of mitochondria (Atm) from (Atm3) has been implicated in the maturation of cytosolic iron-sulfur proteins and heavy metal detoxification, plausibly by exporting glutathione derivatives. Using single-particle cryo-electron microscopy, we have determined four structures of Atm3 in three different conformational states: two inward-facing conformations (with and without bound oxidized glutathione [GSSG]), together with closed and outward-facing states stabilized by MgADP-VO. These structures not only provide a structural framework for defining the alternating access transport cycle, but also reveal the paucity of cysteine residues in the glutathione binding site that could potentially form inhibitory mixed disulfides with GSSG. Despite extensive efforts, we were unable to prepare the ternary complex of Atm3 containing both GSSG and MgATP. A survey of structurally characterized type IV ABC transporters that includes Atm3 establishes that while nucleotides are found associated with all conformational states, they are effectively required to stabilize occluded, closed, and outward-facing conformations. In contrast, transport substrates have only been observed associated with inward-facing conformations. The absence of structures with dimerized nucleotide binding domains containing both nucleotide and transport substrate suggests that this form of the ternary complex exists only transiently during the transport cycle.
History
DepositionJun 5, 2021-
Header (metadata) releaseApr 13, 2022-
Map releaseApr 13, 2022-
UpdateMay 29, 2024-
Current statusMay 29, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_24185.png

Downloads & links

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Map

FileDownload / File: emd_24185.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationAtAtm3 in the outward-facing conformation
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 300 pix.
= 256.5 Å		0.86 Å/pix.
x 300 pix.
= 256.5 Å		0.86 Å/pix.
x 300 pix.
= 256.5 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.855 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.11
Minimum - Maximum-0.4671436 - 0.7121018
Average (Standard dev.)0.001353221 (±0.018869994)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 256.5 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: AtAtm3 in the outward-facing conformation

Fileemd_24185_half_map_1.map
AnnotationAtAtm3 in the outward-facing conformation
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: AtAtm3 in the outward-facing conformation

Fileemd_24185_half_map_2.map
AnnotationAtAtm3 in the outward-facing conformation
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : AtAtm3 in detergent

EntireName: AtAtm3 in detergent
Components
  • Complex: AtAtm3 in detergent
    • Protein or peptide: ABC transporter B family member 25, mitochondrial
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: VANADATE ION
  • Ligand: MAGNESIUM ION

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Supramolecule #1: AtAtm3 in detergent

SupramoleculeName: AtAtm3 in detergent / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 140 KDa

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Macromolecule #1: ABC transporter B family member 25, mitochondrial

MacromoleculeName: ABC transporter B family member 25, mitochondrial / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 81.793344 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MSRGSRFVRA PGLLLCRVNL QPQPKIPSFS YSLRSDYRLH NGFSNYIRRN SIRTSPVINA FLSDNSPSPS PSPSPIRFVQ RSSMLNGRL FSTSTPNPDQ TTTKTKEIKT TSSDSDSAMA DMKILRTLAG YLWMRDNPEF RFRVIAALGF LVGAKVLNVQ V PFLFKLAV ...String:
MSRGSRFVRA PGLLLCRVNL QPQPKIPSFS YSLRSDYRLH NGFSNYIRRN SIRTSPVINA FLSDNSPSPS PSPSPIRFVQ RSSMLNGRL FSTSTPNPDQ TTTKTKEIKT TSSDSDSAMA DMKILRTLAG YLWMRDNPEF RFRVIAALGF LVGAKVLNVQ V PFLFKLAV DWLASATGTG ASLTTFAATN PTLLTVFATP AAVLIGYGIA RTGSSAFNEL RTAVFSKVAL RTIRSVSRKV FS HLHDLDL RYHLSRETGG LNRIIDRGSR AINFILSAMV FNVVPTILEI SMVSGILAYK FGAAFAWITS LSVGSYIVFT LAV TQWRTK FRKAMNKADN DASTRAIDSL INYETVKYFN NEGYEAEKYD QFLKKYEDAA LQTQRSLAFL NFGQSIIFST ALST AMVLC SQGIMNGQMT VGDLVMVNGL LFQLSLPLNF LGSVYRETIQ SLVDMKSMFQ LLEEKSDITN TSDAKPLVLK GGNIE FENV HFSYLPERKI LDGISFVVPA GKSVAIVGTS GSGKSTILRM LFRFFDTDSG NIRIDGQDIK EVRLDSLRSS IGVVPQ DTV LFNDTIFHNI HYGRLSATEE EVYEAARRAA IHETISNFPD KYSTIVGERG LKLSGGEKQR VALARTFLKS PAILLCD EA TSALDSTTEA EILNALKALA SNRTSIFIAH RLTTAMQCDE IVVLENGKVV EQGPHDELLG KSGRYAQLWT QQNSSVDM L DAAIKLEAAA LEHHHHHH

UniProtKB: ABC transporter B family member 25, mitochondrial

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Macromolecule #2: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 2 / Number of copies: 2 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

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Macromolecule #3: VANADATE ION

MacromoleculeName: VANADATE ION / type: ligand / ID: 3 / Number of copies: 2 / Formula: VO4
Molecular weightTheoretical: 114.939 Da
Chemical component information

ChemComp-VN3:
VANADATE ION

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Macromolecule #4: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 4 / 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

Concentration1 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
100.0 mMNaClSodium Chloride
20.0 mMTris
GridModel: UltrAuFoil R1.2/1.3 / Support film - Material: GOLD / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number real images: 5631 / Average exposure time: 2.7 sec. / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1675302
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6par

Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 2.15) / Number images used: 103161
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 2.15)
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final 3D classificationNumber classes: 100 / Software - Name: cryoSPARC (ver. 2.15)

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Atomic model buiding 1

Initial modelPDB ID:

6par


Chain - Chain ID: A / Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Overall B value: 49
Output model

PDB-7n5b:
Structure of AtAtm3 in the outward-facing conformation

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