9H76 | pdb_00009h76

Bacterial LAT transporter BASC in complex with L-Ala and NB53


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 9H76

This is version 1.2 of the entry. See complete history

Literature

The conserved lysine residue in transmembrane helix 5 is pivotal for the cytoplasmic gating of the L-amino acid transporters.

Fort, J.Nicolas-Arago, A.Maggi, L.Martinez-Molledo, M.Kapiki, D.Gonzalez-Novoa, P.Gomez-Gejo, P.Zijlstra, N.Bodoy, S.Pardon, E.Steyaert, J.Llorca, O.Orozco, M.Cordes, T.Palacin, M.

(2025) PNAS Nexus 4: pgae584-pgae584

  • DOI: https://doi.org/10.1093/pnasnexus/pgae584
  • Primary Citation Related Structures: 
    9H76

  • PubMed Abstract: 

    L-Amino acid transporters (LATs) play a key role in a wide range of physiological processes. Defects in LATs can lead to neurological disorders and aminoacidurias, while the overexpression of these transporters is related to cancer. BasC is a bacterial LAT transporter with an APC fold. In this study, to monitor the cytoplasmic motion of BasC, we developed a single-molecule Förster resonance energy transfer assay that can characterize the conformational states of the intracellular gate in solution at room temperature. Based on combined biochemical and biophysical data and molecular dynamics simulations, we propose a model in which the conserved lysine residue in TM5 supports TM1a to explore both open and closed states within the cytoplasmic gate under apo conditions. This equilibrium can be altered by substrates, mutation of conserved lysine 154 in TM5, or a transport-blocking nanobody interacting with TM1a. Overall, these findings provide insights into the transport mechanism of BasC and highlight the significance of the lysine residue in TM5 in the cytoplasmic gating of LATs.


  • Organizational Affiliation
    • Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain.

Macromolecule Content 

  • Total Structure Weight: 61.04 kDa 
  • Atom Count: 4,157 
  • Modeled Residue Count: 546 
  • Deposited Residue Count: 564 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Putative amino acid/polyamine transport protein435Carnobacterium sp. AT7Mutation(s): 0 
Gene Names: CAT7_03719
UniProt
Find proteins for A0ACD6B9K4 (Carnobacterium sp. AT7)
Explore A0ACD6B9K4 
Go to UniProtKB:  A0ACD6B9K4
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0ACD6B9K4
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Nanobody NB53129Lama glamaMutation(s): 0 

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ALA
(Subject of Investigation/LOI)

Query on ALA



Download:Ideal Coordinates CCD File
C [auth A]ALANINE
C3 H7 N O2
QNAYBMKLOCPYGJ-REOHCLBHSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARCv4.4.1
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministerio de Ciencia e Innovacion (MCIN)SpainPID2021- 122802OB-I00
Generalitat de CatalunyaSpain2021 SGR 01281

Revision History  (Full details and data files)

  • Version 1.0: 2025-01-01
    Type: Initial release
  • Version 1.1: 2025-02-19
    Changes: Data collection, Database references
  • Version 1.2: 2025-07-02
    Changes: Data collection