8XPU

Overall structure of the LAT1-4F2hc bound with JPH203

• PDB DOI: https://doi.org/10.2210/pdb8XPU/pdb
• EM Map EMD-38561: EMDB EMDataResource

• Classification: TRANSPORT PROTEIN
• Organism(s): Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): No 
• Membrane Protein: Yes  PDBTMmpstruc


• Deposited: 2024-01-04 Released: 2024-07-17 
• Deposition Author(s): Hu, Z., Yan, R.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.30 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structural basis for the inhibition mechanism of LAT1-4F2hc complex by JPH203.

Hu, Z., Yan, R.

(2024) Cell Discov 10: 73-73

• PubMed: 38956038 
• DOI: https://doi.org/10.1038/s41421-024-00697-6
• Primary Citation of Related Structures:  
  8XPU

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Organizational Affiliation: 

Department of Biochemistry, School of Medicine, Key University Laboratory of Metabolism and Health of Guangdong, Institute for Biological Electron Microscopy, Southern University of Science and Technology, Shenzhen, Guangdong, China.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content

• Total Structure Weight: 129.52 kDa 
• Atom Count: 7,391 
• Modelled Residue Count: 934 
• Deposited Residue Count: 1,174 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Isoform 5 of Amino acid transporter heavy chain SLC3A2	A	647	Homo sapiens	Mutation(s): 0  Gene Names: SLC3A2, MDU1 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
Glycosylation
Glycosylation Sites: 3		Go to GlyGen: P08195-1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Large neutral amino acids transporter small subunit 1	B	527	Homo sapiens	Mutation(s): 0  Gene Names: SLC7A5, CD98LC, LAT1, MPE16 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for Q01650 (Homo sapiens) Explore Q01650  Go to UniProtKB:  Q01650
PHAROS:  Q01650 GTEx:  ENSG00000103257

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C, D, E, F	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
VRW	G [auth B]	Nanvuranlat C23 H19 Cl2 N3 O4 XNRZJPQTMQZBCE-SFHVURJKSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
VRW	BindingDB:  8XPU	IC50: min: 60, max: 790 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.30 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-07-17 
Deposition Author(s): Hu, Z., Yan, R.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	32371267

Revision History  

• Version 1.0: 2024-07-17
  Type: Initial release
  
• Version 1.1: 2024-07-24
  Changes: Data collection
• Version 1.2: 2024-07-31
  Changes: Data collection, Structure summary
• Version 1.3: 2024-11-13
  Changes: Data collection, Structure summary
• Version 1.4: 2024-11-20
  Changes: Data collection, Derived calculations, Structure summary