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)

Experimental Data Snapshot

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

wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

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 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1038/s41421-024-00697-6
Primary Citation of Related Structures:
8XPU

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.

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

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P08195
Glycosylation
Glycosylation Sites: 3	Glycosylation Focus chain A	Go to GlyGen: P08195-1
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q01650
Sequence Annotations Expand
Reference Sequence

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	Interactions Focus chain C Focus chain D Focus chain E Focus chain F Interactions & Density Focus chain C Focus chain D Focus chain E Focus chain F
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
VRW Query on VRW Download Ideal Coordinates CCD File SDF format, chain G [auth B] MOL2 format, chain G [auth B] mmCIF format, chain G [auth B]	G [auth B]	Nanvuranlat C₂₃ H₁₉ Cl₂ N₃ O₄ XNRZJPQTMQZBCE-SFHVURJKSA-N		Interactions Focus chain G [auth B] Interactions & Density Focus chain G [auth B]

Experimental Data & Validation

Experimental Data

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

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2024-07-17

Deposition Author(s):

Hu, Z.

Yan, R.

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

Revision History (Full details and data files)

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