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- PDB-7n5a: Structure of AtAtm3 in the closed conformation -

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Basic information

Entry
Database: PDB / ID: 7n5a
TitleStructure of AtAtm3 in the closed conformation
ComponentsABC transporter B family member 25, mitochondrial
KeywordsMEMBRANE PROTEIN / ABC transporter / ATPase
Function / homology
Function and homology information


regulation of chlorophyll biosynthetic process / regulation of catalytic activity / chloroplast organization / root development / pollen development / Mo-molybdopterin cofactor biosynthetic process / chloroplast envelope / plastid / chromosome organization / response to cadmium ion ...regulation of chlorophyll biosynthetic process / regulation of catalytic activity / chloroplast organization / root development / pollen development / Mo-molybdopterin cofactor biosynthetic process / chloroplast envelope / plastid / chromosome organization / response to cadmium ion / ABC-type transporter activity / chloroplast / iron ion transport / response to lead ion / 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
ADENOSINE-5'-DIPHOSPHATE / VANADATE ION / ABC transporter B family member 25, mitochondrial
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.95 Å
AuthorsFan, C. / Rees, D.C.
Funding support United States, 1items
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, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 13, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 20, 2022Group: Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2May 29, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_3d_fitting_list / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ABC transporter B family member 25, mitochondrial
B: ABC transporter B family member 25, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)164,7208
Polymers163,5872
Non-polymers1,1336
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area16580 Å2
ΔGint-112 kcal/mol
Surface area49720 Å2
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_1ALASERA1 - 589
d_12ens_1ADPADPB
d_13ens_1VO4VO4C
d_21ens_1ALASERE1 - 589
d_22ens_1ADPADPF
d_23ens_1VO4VO4G

NCS oper: (Code: givenMatrix: (-0.999999642496, -0.000458256284585, -0.000710640404987), (0.000457931560355, -0.999999790706, 0.000457041324744), (-0.000710849698313, 0.000456715736681, 0. ...NCS oper: (Code: given
Matrix: (-0.999999642496, -0.000458256284585, -0.000710640404987), (0.000457931560355, -0.999999790706, 0.000457041324744), (-0.000710849698313, 0.000456715736681, 0.999999643052)
Vector: 246.205673551, 245.823860525, 0.099187809021)

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Components

#1: Protein ABC transporter B family member 25, mitochondrial / ABC transporter ABCB.25 / AtABCB25 / ABC transporter of the mitochondrion 3 / AtATM3 / Iron-sulfur ...ABC transporter ABCB.25 / AtABCB25 / ABC transporter of the mitochondrion 3 / AtATM3 / Iron-sulfur clusters transporter ATM3 / Protein STARIK 1


Mass: 81793.344 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: ABCB25, ATM3, STA1, At5g58270, MCK7.14 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9LVM1
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-VO4 / VANADATE ION


Mass: 114.939 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: VO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / 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: AtAtm3 in MSP nanodiscs / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 0.14 MDa / Experimental value: NO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria) / Strain: BL21(DE3)
Buffer solutionpH: 7.5
Buffer component
IDConc.NameFormulaBuffer-ID
1100 mMSodium ChlorideNaCl1
220 mMTris1
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid type: UltrAuFoil R2/2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 295 K

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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 / Nominal defocus max: 2100 nm / Nominal defocus min: 1500 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 1.5 sec. / Electron dose: 48 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of real images: 23125

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Processing

Software
NameVersionClassificationNB
phenix.real_space_refine1.19_4092refinement
PHENIX1.19_4092refinement
EM software
IDNameVersionCategory
1cryoSPARC2.15particle selection
2EPUimage acquisition
4cryoSPARC2.15CTF correction
7PHENIX1.19model fitting
9PHENIX1.19model refinement
10cryoSPARC2.15initial Euler assignment
12cryoSPARC2.15classification
13cryoSPARC2.153D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 4230125
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 3.95 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 140569 / Symmetry type: POINT
Atomic model buildingB value: 119 / Protocol: RIGID BODY FIT / Space: REAL
Atomic model buildingPDB-ID: 6PAR

6par


Pdb chain-ID: A / Accession code: 6PAR / Source name: PDB / Type: experimental model
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 118.29 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00259414
ELECTRON MICROSCOPYf_angle_d0.595912746
ELECTRON MICROSCOPYf_chiral_restr0.0391490
ELECTRON MICROSCOPYf_plane_restr0.00291606
ELECTRON MICROSCOPYf_dihedral_angle_d5.80691296
Refine LS restraints NCSType: NCS constraints / Rms dev position: 0.000705040983529 Å

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