Database of articles cited by EMDB/PDB/SASBDB data

Keywords
Structure methods	All X-ray diffraction NMR electron microscopy small angle scattering neutron diffraction fiber diffraction powder diffraction infrared spectroscopy EPR fluorescence transfer theoretical model Hybrid
Author
Journal
IF	>30 >20 >10 >5 all

Title	Stepwise ATP translocation into the endoplasmic reticulum by human SLC35B1.
Journal, issue, pages	Nature, Vol. 643, Issue 8072, Page 855-864, Year 2025
Publish date	May 21, 2025
Authors	Ashutosh Gulati / Do-Hwan Ahn / Albert Suades / Yurie Hult / Gernot Wolf / So Iwata / Giulio Superti-Furga / Norimichi Nomura / David Drew /
PubMed Abstract	ATP generated in the mitochondria is exported by an ADP/ATP carrier of the SLC25 family. The endoplasmic reticulum (ER) cannot synthesize ATP but must import cytoplasmic ATP to energize protein ...ATP generated in the mitochondria is exported by an ADP/ATP carrier of the SLC25 family. The endoplasmic reticulum (ER) cannot synthesize ATP but must import cytoplasmic ATP to energize protein folding, quality control and trafficking. It was recently proposed that a member of the nucleotide sugar transporter family, termed SLC35B1 (also known as AXER), is not a nucleotide sugar transporter but a long-sought-after ER importer of ATP. Here we report that human SLC35B1 does not bind nucleotide sugars but indeed executes strict ATP/ADP exchange with uptake kinetics consistent with the import of ATP into crude ER microsomes. A CRISPR-Cas9 cell-line knockout demonstrated that SLC35B1 clusters with the most essential SLC transporters for cell growth, consistent with its proposed physiological function. We have further determined seven cryogenic electron microscopy structures of human SLC35B1 in complex with an Fv fragment and either bound to an ATP analogue or ADP in all major conformations of the transport cycle. We observed that nucleotides were vertically repositioned up to approximately 6.5 Å during translocation while retaining key interactions with a flexible substrate-binding site. We conclude that SLC35B1 operates by a stepwise ATP translocation mechanism, which is a previously undescribed model for substrate translocation by an SLC transporter.
External links	Nature / PubMed:40399679 / PubMed Central
Methods	EM (single particle)
Resolution	2.85 - 3.4 Å
Structure data	51528 9gry EMDB-51528, PDB-9gry: Cryo-EM structure of human SLC35B1-Q113F variant with AMP-PNP Method: EM (single particle) / Resolution: 3.0 Å 51529 9grz EMDB-51529, PDB-9grz: Cryo-EM structure of human SLC35B1 with AMP-PNP Method: EM (single particle) / Resolution: 3.4 Å 51538 9gs3 EMDB-51538, PDB-9gs3: Cryo-EM structure of human SLC35B1-E33A variant with ADP in inward facing conformation Method: EM (single particle) / Resolution: 3.15 Å 51539 9gs5 EMDB-51539, PDB-9gs5: Cryo-EM structure of human SLC35B1-E33A variant with ADP in outward facing conformation Method: EM (single particle) / Resolution: 3.1 Å 51541 9gs7 EMDB-51541, PDB-9gs7: Cryo-EM structure of human SLC35B1-E33A variant with AMP-PNP Method: EM (single particle) / Resolution: 3.15 Å 51551 9gsl EMDB-51551, PDB-9gsl: Cryo-EM structure of human SLC35B1 in inward facing conformation Method: EM (single particle) / Resolution: 3.37 Å 52578 9i20 EMDB-52578, PDB-9i20: Cryo-EM structure of human SLC35B1 with ADP Method: EM (single particle) / Resolution: 2.85 Å
Chemicals	ChemComp-ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / AMP-PNP, energy-carrying molecule analogueYM ChemComp-ADP: ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying moleculeYM ChemComp-PEV: (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE / POPE, phospholipid*YM
Source	homo sapiens (human) mus musculus (house mouse)
Keywords	TRANSPORT PROTEIN / ATP:ADP exchanger / AXER / AMP-PNP / membrane protein / ER membrane protein / ADP