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- PDB-8xxi: Structure of y+LAT1 bound with Leu -

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Basic information

Entry
Database: PDB / ID: 8xxi
TitleStructure of y+LAT1 bound with Leu
ComponentsY+L amino acid transporter 1
KeywordsMEMBRANE PROTEIN / complex / amino acid
Function / homology
Function and homology information


basic amino acid transmembrane transport / basic amino acid transmembrane transporter activity / L-arginine transmembrane transporter activity / L-arginine transmembrane transport / regulation of arginine metabolic process / Defective SLC7A7 causes lysinuric protein intolerance (LPI) / L-amino acid transmembrane transporter activity / L-leucine transport / amino acid transmembrane transport / Amino acid transport across the plasma membrane ...basic amino acid transmembrane transport / basic amino acid transmembrane transporter activity / L-arginine transmembrane transporter activity / L-arginine transmembrane transport / regulation of arginine metabolic process / Defective SLC7A7 causes lysinuric protein intolerance (LPI) / L-amino acid transmembrane transporter activity / L-leucine transport / amino acid transmembrane transport / Amino acid transport across the plasma membrane / Basigin interactions / basolateral plasma membrane / plasma membrane
Similarity search - Function
: / Amino acid/polyamine transporter I / Amino acid permease
Similarity search - Domain/homology
LEUCINE / Y+L amino acid transporter 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.04 Å
AuthorsYan, R.H. / Dai, L. / Zhang, T.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Structure of y+LAT1 bound with Leu
Authors: Yan, R.H. / Dai, L. / Zhang, T.
History
DepositionJan 18, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 22, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Y+L amino acid transporter 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,1173
Polymers57,9631
Non-polymers1542
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Y+L amino acid transporter 1 / Monocyte amino acid permease 2 / MOP-2 / Solute carrier family 7 member 7 / y(+)L-type amino acid ...Monocyte amino acid permease 2 / MOP-2 / Solute carrier family 7 member 7 / y(+)L-type amino acid transporter 1 / Y+LAT1 / y+LAT-1


Mass: 57963.137 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SLC7A7 / Production host: Homo sapiens (human) / References: UniProt: Q9UM01
#2: Chemical ChemComp-LEU / LEUCINE


Type: L-peptide linking / Mass: 131.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Structure of the y+LAT1 bound with Leu / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 5000 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.04 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 427472 / Symmetry type: POINT

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