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- PDB-9ldr: Overall structure of the y+LAT2-4F2hc bound with Leu -

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Basic information

Entry
Database: PDB / ID: 9ldr
TitleOverall structure of the y+LAT2-4F2hc bound with Leu
Components
  • Amino acid transporter heavy chain SLC3A2
  • Y+L amino acid transporter 2
KeywordsMEMBRANE PROTEIN / Amino acid / transporter / complex
Function / homology
Function and homology information


ornithine transport / L-lysine:L-arginine antiporter activity / basic amino acid transmembrane transporter activity / L-arginine transmembrane transport / L-arginine transmembrane transporter activity / glycine betaine transport / apical pole of neuron / tyrosine transport / L-histidine transport / amino acid transport complex ...ornithine transport / L-lysine:L-arginine antiporter activity / basic amino acid transmembrane transporter activity / L-arginine transmembrane transport / L-arginine transmembrane transporter activity / glycine betaine transport / apical pole of neuron / tyrosine transport / L-histidine transport / amino acid transport complex / L-leucine import across plasma membrane / L-alanine transmembrane transporter activity / L-alanine import across plasma membrane / Defective SLC7A7 causes lysinuric protein intolerance (LPI) / aromatic amino acid transmembrane transporter activity / phenylalanine transport / methionine transport / L-leucine transmembrane transporter activity / amino acid transmembrane transport / isoleucine transport / valine transport / proline transport / L-amino acid transmembrane transporter activity / L-leucine transport / thyroid hormone transport / neutral amino acid transport / neutral L-amino acid transmembrane transporter activity / Tryptophan catabolism / Amino acid transport across the plasma membrane / amino acid transmembrane transporter activity / exogenous protein binding / arginine binding / anchoring junction / Basigin interactions / response to exogenous dsRNA / amino acid transport / tryptophan transport / nitric oxide biosynthetic process / basal plasma membrane / calcium ion transport / melanosome / double-stranded RNA binding / virus receptor activity / basolateral plasma membrane / carbohydrate metabolic process / apical plasma membrane / cadherin binding / protein heterodimerization activity / lysosomal membrane / synapse / symbiont entry into host cell / cell surface / protein homodimerization activity / RNA binding / extracellular exosome / nucleoplasm / membrane / plasma membrane
Similarity search - Function
Solute carrier family 3 member 2, N-terminal domain / 4F2 cell-surface antigen heavy chain / Solute carrier family 3 member 2 N-terminus / : / Amino acid/polyamine transporter I / Amino acid permease / Alpha amylase, catalytic domain / Glycosyl hydrolase, family 13, catalytic domain / Alpha-amylase domain / Glycosyl hydrolase, all-beta / Glycoside hydrolase superfamily
Similarity search - Domain/homology
LEUCINE / Amino acid transporter heavy chain SLC3A2 / Y+L amino acid transporter 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.58 Å
AuthorsYan, R.H. / Dai, I. / Zhang, T.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Overall structure of the y+LAT2-4F2hc bound with Leu
Authors: Yan, R.H. / Dai, I. / Zhang, T.
History
DepositionJan 6, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 23, 2025Provider: repository / Type: Initial release
Revision 1.0Apr 23, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Apr 23, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 23, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 23, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Apr 23, 2025Data content type: Primary map / Data content type: Primary map / Provider: 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 2
B: Amino acid transporter heavy chain SLC3A2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,9033
Polymers128,7722
Non-polymers1311
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 2 / Cationic amino acid transporter / y+ system / Solute carrier family 7 member 6 / y(+)L-type amino ...Cationic amino acid transporter / y+ system / Solute carrier family 7 member 6 / y(+)L-type amino acid transporter 2 / Y+LAT2 / y+LAT-2


Mass: 58934.102 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SLC7A6, KIAA0245 / Production host: Homo sapiens (human) / References: UniProt: Q92536
#2: Protein Amino acid transporter heavy chain SLC3A2 / 4F2 cell-surface antigen heavy chain / 4F2hc / 4F2 heavy chain antigen / Lymphocyte activation ...4F2 cell-surface antigen heavy chain / 4F2hc / 4F2 heavy chain antigen / Lymphocyte activation antigen 4F2 large subunit / Solute carrier family 3 member 2


Mass: 69837.523 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SLC3A2, MDU1 / Production host: Homo sapiens (human) / References: UniProt: P08195
#3: Chemical ChemComp-LEU / LEUCINE


Type: L-peptide linking / Mass: 131.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO2
Has ligand of interestN
Has protein modificationY

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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: Overall structure of the y+LAT2-4F2hc bound with Leu / Type: COMPLEX / Entity ID: #1-#2 / 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: TFS 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

EM softwareName: PHENIX / Version: 1.17.1_3660 / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.58 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 370341 / Symmetry type: POINT
RefinementStereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0067456
ELECTRON MICROSCOPYf_angle_d0.70410143
ELECTRON MICROSCOPYf_dihedral_angle_d14.984999
ELECTRON MICROSCOPYf_chiral_restr0.0441163
ELECTRON MICROSCOPYf_plane_restr0.0051274

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