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- EMDB-61118: ATP bound Arabidopsis ATP/ADP translocator AtNTT1 -

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Basic information

Entry
Database: EMDB / ID: EMD-61118
TitleATP bound Arabidopsis ATP/ADP translocator AtNTT1
Map data
Sample
  • Complex: ATP bound Arabidopsis ATP/ADP translocator AtNTT1
    • Protein or peptide: ADP,ATP carrier protein 1, chloroplastic
    • Protein or peptide: nanobody: B-D7
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
KeywordsATP/ADP translocator / non-mitochondrial / antiporter / MEMBRANE PROTEIN
Function / homologyADP/ATP carrier protein, bacterial type / TLC ATP/ADP transporter / ATP:ADP antiporter activity / chloroplast membrane / chloroplast envelope / plastid / mitochondrion / ATP binding / ADP,ATP carrier protein 1, chloroplastic
Function and homology information
Biological speciesArabidopsis (plant) / Arabidopsis thaliana (thale cress) / Vicugna pacos (alpaca)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.72 Å
AuthorsLin HJ / Huang J / Li TM / Li WJ / Su NN / Zhang JR / Wu XD / Fan MR
Funding support China, 1 items
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, 2024-
Header (metadata) releaseMar 19, 2025-
Map releaseMar 19, 2025-
UpdateMay 21, 2025-
Current statusMay 21, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_61118.png

Downloads & links

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Map

FileDownload / File: emd_61118.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.93 Å/pix.
x 256 pix.
= 238.08 Å		0.93 Å/pix.
x 256 pix.
= 238.08 Å		0.93 Å/pix.
x 256 pix.
= 238.08 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.93 Å
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Histogram (log scale)
Contour LevelBy AUTHOR: 0.28
Minimum - Maximum-3.422438 - 5.15908
Average (Standard dev.)0.000000000000654 (±0.093409546)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 238.08 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_61118_msk_1.map
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Half map: #2

Fileemd_61118_half_map_1.map
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Half map: #1

Fileemd_61118_half_map_2.map
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Sample components

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Entire : ATP bound Arabidopsis ATP/ADP translocator AtNTT1

EntireName: ATP bound Arabidopsis ATP/ADP translocator AtNTT1
Components
  • Complex: ATP bound Arabidopsis ATP/ADP translocator AtNTT1
    • Protein or peptide: ADP,ATP carrier protein 1, chloroplastic
    • Protein or peptide: nanobody: B-D7
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE

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Supramolecule #1: ATP bound Arabidopsis ATP/ADP translocator AtNTT1

SupramoleculeName: ATP bound Arabidopsis ATP/ADP translocator AtNTT1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Arabidopsis (plant)

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Macromolecule #1: ADP,ATP carrier protein 1, chloroplastic

MacromoleculeName: ADP,ATP carrier protein 1, chloroplastic / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 66.654609 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MAGAVFGEGD SAAVVASPKI FGVEVATLKK IIPLGLMFFC ILFNYTILRD TKDVLVVTAK GSSAEIIPFL KTWVNLPMAI GFMLLYTKL SNVLSKKALF YTVIVPFIIY FGAFGFVMYP LSNYIHPEAL ADKLLTTLGP RFMGPIAILR IWSFCLFYVM A ELWGSVVV ...String:
MAGAVFGEGD SAAVVASPKI FGVEVATLKK IIPLGLMFFC ILFNYTILRD TKDVLVVTAK GSSAEIIPFL KTWVNLPMAI GFMLLYTKL SNVLSKKALF YTVIVPFIIY FGAFGFVMYP LSNYIHPEAL ADKLLTTLGP RFMGPIAILR IWSFCLFYVM A ELWGSVVV SVLFWGFANQ ITTVDEAKKF YPLFGLGANV ALIFSGRTVK YFSNLRKNLG PGVDGWAVSL KAMMSIVVGM GL AICLLYW WVNRYVPLPT RSKNKKEKPK MGTMESLKFL VSSPYIRDLA TLVVAYGISI NLVEVTWKSK LKAQFPSPNE YSA FMGDFS TCTGVATFTM MLLSQYVFNK YGWGVAAKIT PTVLLLTGVA FFSLILFGGP FAPLVAKLGM TPLLAAVYVG ALQN IFSKS AKYSLFDPCK EMAYIPLDED TKVKGKAAID VVCNPLGKSG GALIQQFMIL SFGSLANSTP YLGMILLVIV TAWLA AAKS LEGQFNSLRS EEELEKEMER ASSVKIPVVS QDESGNGSLG ESPSSSPEKS APTNLVDELT SRGRGSGGLN DIFEAQ KIE WHEGSGLEVL FQGPDYKDDD DKWSHPQFEK GGGGSGGSAW SHPQFEK

UniProtKB: ADP,ATP carrier protein 1, chloroplastic

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Macromolecule #2: nanobody: B-D7

MacromoleculeName: nanobody: B-D7 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Vicugna pacos (alpaca)
Molecular weightTheoretical: 13.474857 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
EVQLVESGGG LVQAGGSLRL SCAASGFPVD EAYMTWYRQA PGKEREWVAA IYSSGYTRYA DSVKGRFTIS RDNSKNTVYL QMNSLKPED TAVYYCNVKD YVYNTYLYDY WGQGTQVTVS S

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Macromolecule #3: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 1 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*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: 6
VitrificationCryogen name: NITROGEN

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 52.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: DIFFRACTION / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 130000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.72 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 679696
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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