7B00

Human LAT2-4F2hc complex in the apo-state


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.98 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 2.1 of the entry. See complete history


Literature

Structural basis for substrate specificity of heteromeric transporters of neutral amino acids.

Rodriguez, C.F.Escudero-Bravo, P.Diaz, L.Bartoccioni, P.Garcia-Martin, C.Gilabert, J.G.Boskovic, J.Guallar, V.Errasti-Murugarren, E.Llorca, O.Palacin, M.

(2021) Proc Natl Acad Sci U S A 118

  • DOI: https://doi.org/10.1073/pnas.2113573118
  • Primary Citation of Related Structures:  
    7B00

  • PubMed Abstract: 

    Despite having similar structures, each member of the heteromeric amino acid transporter (HAT) family shows exquisite preference for the exchange of certain amino acids. Substrate specificity determines the physiological function of each HAT and their role in human diseases. However, HAT transport preference for some amino acids over others is not yet fully understood. Using cryo-electron microscopy of apo human LAT2/CD98hc and a multidisciplinary approach, we elucidate key molecular determinants governing neutral amino acid specificity in HATs. A few residues in the substrate-binding pocket determine substrate preference. Here, we describe mutations that interconvert the substrate profiles of LAT2/CD98hc, LAT1/CD98hc, and Asc1/CD98hc. In addition, a region far from the substrate-binding pocket critically influences the conformation of the substrate-binding site and substrate preference. This region accumulates mutations that alter substrate specificity and cause hearing loss and cataracts. Here, we uncover molecular mechanisms governing substrate specificity within the HAT family of neutral amino acid transporters and provide the structural bases for mutations in LAT2/CD98hc that alter substrate specificity and that are associated with several pathologies.


  • Organizational Affiliation

    Structural Biology Programme, Spanish National Cancer Research Centre, E-28029 Madrid, Spain.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Large neutral amino acids transporter small subunit 2535Homo sapiensMutation(s): 0 
Gene Names: SLC7A8LAT2
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UHI5 (Homo sapiens)
Explore Q9UHI5 
Go to UniProtKB:  Q9UHI5
PHAROS:  Q9UHI5
GTEx:  ENSG00000092068 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UHI5
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Isoform 2 of 4F2 cell-surface antigen heavy chain529Homo sapiensMutation(s): 0 
Gene Names: SLC3A2MDU1
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P08195 (Homo sapiens)
Explore P08195 
Go to UniProtKB:  P08195
PHAROS:  P08195
GTEx:  ENSG00000168003 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP08195
Glycosylation
Glycosylation Sites: 4Go to GlyGen: P08195-1
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
C, D, E, F
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
AJP
Query on AJP

Download Ideal Coordinates CCD File 
G [auth A]Digitonin
C56 H92 O29
UVYVLBIGDKGWPX-KUAJCENISA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.98 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.1

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
La Caixa FoundationLCF/PR/HR20/52400017
Ministry of Economy and Competitiveness (MINECO)SAF2015-64869-R-FEDER
Ministry of Economy and Competitiveness (MINECO)RTI2018-094211-B-100-FEDER
Ministry of Economy and Competitiveness (MINECO)SAF2017-82632-P
Ministry of Economy and Competitiveness (MINECO)BES-2015-071348
Generalitat de Catalunya2017 SGR 961
Comunidad de MadridY2018/BIO4747

Revision History  (Full details and data files)

  • Version 1.0: 2021-10-27
    Type: Initial release
  • Version 2.0: 2022-02-23
    Type: Coordinate replacement
    Reason: Chirality error
    Changes: Advisory, Atomic model, Author supporting evidence, Data collection, Database references, Source and taxonomy, Structure summary
  • Version 2.1: 2024-10-16
    Changes: Data collection, Structure summary