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- PDB-9j3n: ATP bound Chlamydia pneumoniae ATP/ADP translocator NTT1(Inward o... -

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Basic information

Entry
Database: PDB / ID: 9j3n
TitleATP bound Chlamydia pneumoniae ATP/ADP translocator NTT1(Inward open state)
Components
  • 1D10
  • ADP,ATP carrier protein 1
KeywordsMEMBRANE PROTEIN / ATP/ADP translocator / non-mitochondrial / antiporter
Function / homologyADP/ATP carrier protein, bacterial type / TLC ATP/ADP transporter / ATP:ADP antiporter activity / MFS transporter superfamily / ATP binding / plasma membrane / ADENOSINE-5'-TRIPHOSPHATE / ADP,ATP carrier protein 1
Function and homology information
Biological speciesVicugna pacos (alpaca)
Chlamydia pneumoniae (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.72 Å
AuthorsLin, H.J. / Huang, J. / Li, T.M. / Li, W.J. / Su, N.N. / Zhang, J.R. / Wu, X.D. / Fan, M.R.
Funding support China, 1items
OrganizationGrant numberCountry
Chinese Academy of SciencesXDB0630101 China
CitationJournal: Nature / Year: 2025
Title: Structure and mechanism of the plastid/parasite ATP/ADP translocator.
Authors: Huajian Lin / Jian Huang / Tianming Li / Wenjuan Li / Yutong Wu / Tianjiao Yang / Yuwei Nian / Xiang Lin / Jiangqin Wang / Ruiying Wang / Xiaohui Zhao / Nannan Su / Jinru Zhang / Xudong Wu / Minrui Fan /
Abstract: Adenosine triphosphate (ATP) is the principal energy currency of all living cells. Metabolically impaired obligate intracellular parasites, such as the human pathogens Chlamydia trachomatis and ...Adenosine triphosphate (ATP) is the principal energy currency of all living cells. Metabolically impaired obligate intracellular parasites, such as the human pathogens Chlamydia trachomatis and Rickettsia prowazekii, can acquire ATP from their host cells through a unique ATP/adenosine diphosphate (ADP) translocator, which mediates the import of ATP into and the export of ADP and phosphate out of the parasite cells, thus allowing the exploitation of the energy reserves of host cells (also known as energy parasitism). This type of ATP/ADP translocator also exists in the obligate intracellular endosymbionts of protists and the plastids of plants and algae and has been implicated to play an important role in endosymbiosis. The plastid/parasite type of ATP/ADP translocator is phylogenetically and functionally distinct from the mitochondrial ATP/ADP translocator, and its structure and transport mechanism are still unknown. Here we report the cryo-electron microscopy structures of two plastid/parasite types of ATP/ADP translocators in the apo and substrate-bound states. The ATP/ADP-binding pocket is located at the interface between the N and C domains of the translocator, and a conserved asparagine residue within the pocket is critical for substrate specificity. The translocator operates through a rocker-switch alternating access mechanism involving the relative rotation of the two domains as rigid bodies. Our results provide critical insights for understanding ATP translocation across membranes in energy parasitism and endosymbiosis and offer a structural basis for developing drugs against obligate intracellular parasites.
History
DepositionAug 8, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Mar 19, 2025Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: 1D10
A: ADP,ATP carrier protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,0133
Polymers78,5062
Non-polymers5071
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Antibody 1D10


Mass: 13474.846 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vicugna pacos (alpaca) / Production host: Escherichia coli (E. coli)
#2: Protein ADP,ATP carrier protein 1 / ADP/ATP translocase 1


Mass: 65031.344 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlamydia pneumoniae (bacteria) / Gene: tlcA, adt_1, CPn_0351, CP_0408, CpB0359 / Production host: Homo sapiens (human) / References: UniProt: Q9Z8J2
#3: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
Has ligand of interestY
Has protein modificationY

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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: Chlamydia pneumoniae ATP/ADP translocator NTT1(Inward open state)
Type: COMPLEX / Entity ID: #1-#2 / Source: MULTIPLE SOURCES
Source (natural)Organism: Chlamydia pneumoniae (bacteria)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: NITROGEN

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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: DIFFRACTION / Nominal magnification: 130000 X / Nominal defocus max: 2200 nm / Nominal defocus min: 1100 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.72 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 119152 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0044934
ELECTRON MICROSCOPYf_angle_d0.5696707
ELECTRON MICROSCOPYf_dihedral_angle_d3.5542855
ELECTRON MICROSCOPYf_chiral_restr0.04766
ELECTRON MICROSCOPYf_plane_restr0.004814

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