9GRY | pdb_00009gry

Cryo-EM structure of human SLC35B1-Q113F variant with AMP-PNP


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Stepwise ATP translocation into the endoplasmic reticulum by human SLC35B1.

Gulati, A.Ahn, D.H.Suades, A.Hult, Y.Wolf, G.Iwata, S.Superti-Furga, G.Nomura, N.Drew, D.

(2025) Nature 643: 855-864

  • DOI: https://doi.org/10.1038/s41586-025-09069-w
  • Primary Citation of Related Structures:  
    9GRY, 9GRZ, 9GS3, 9GS5, 9GS7, 9GSL, 9I20

  • PubMed Abstract: 

    ATP generated in the mitochondria is exported by an ADP/ATP carrier of the SLC25 family 1 . The endoplasmic reticulum (ER) cannot synthesize ATP but must import cytoplasmic ATP to energize protein folding, quality control and trafficking 2,3 . 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 4 . 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.


  • Organizational Affiliation

    Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Stockholm, Sweden.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
human SLC35B1-Q113F329Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P78383 (Homo sapiens)
Explore P78383 
Go to UniProtKB:  P78383
PHAROS:  P78383
GTEx:  ENSG00000121073 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP78383
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Maltodextrin-binding protein612Mus musculusMutation(s): 0 
Gene Names: malEJW3994
UniProt
Find proteins for A0A4P1LXE0 (Serratia sp. (strain FS14))
Explore A0A4P1LXE0 
Go to UniProtKB:  A0A4P1LXE0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A4P1LXE0
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ANP
Query on ANP

Download Ideal Coordinates CCD File 
C [auth A]PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
C10 H17 N6 O12 P3
PVKSNHVPLWYQGJ-KQYNXXCUSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Knut and Alice Wallenberg FoundationSweden--

Revision History  (Full details and data files)

  • Version 1.0: 2025-05-21
    Type: Initial release
  • Version 1.1: 2025-08-20
    Changes: Data collection, Database references