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- PDB-9i1z: Membrane Protein Transporter -

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Basic information

Entry
Database: PDB / ID: 9i1z
TitleMembrane Protein Transporter
Components
  • 4F2 cell-surface antigen heavy chain
  • Y+L amino acid transporter 1
KeywordsTRANSPORT PROTEIN / Membrane Protein Transporter
Function / homology
Function and homology information


basic amino acid transmembrane transport / basic amino acid transmembrane transporter activity / L-arginine transmembrane transport / L-arginine transmembrane transporter activity / apical pole of neuron / tyrosine transport / L-histidine transport / amino acid transport complex / L-leucine import across plasma membrane / L-alanine import across plasma membrane ...basic amino acid transmembrane transport / basic amino acid transmembrane transporter activity / L-arginine transmembrane transport / L-arginine transmembrane transporter activity / apical pole of neuron / tyrosine transport / L-histidine transport / amino acid transport complex / L-leucine import across plasma membrane / L-alanine import across plasma membrane / Defective amino acid transport by SLC7A7 causes lysinuric protein intolerance (LPI) / aromatic amino acid transmembrane transporter activity / L-alanine transmembrane transporter activity / phenylalanine transport / methionine transport / valine transport / L-leucine transmembrane transporter activity / isoleucine transport / amino acid transmembrane transport / L-amino acid transmembrane transporter activity / L-leucine transport / proline transport / thyroid hormone transport / neutral L-amino acid transmembrane transporter activity / Tryptophan catabolism / exogenous protein binding / Amino acid transport across the plasma membrane / anchoring junction / Basigin interactions / response to exogenous dsRNA / tryptophan transport / amino acid transport / amino acid import across plasma membrane / transport across blood-brain barrier / basal plasma membrane / calcium ion transport / melanosome / double-stranded RNA binding / virus receptor activity / carbohydrate metabolic process / basolateral plasma membrane / apical plasma membrane / cadherin binding / protein heterodimerization activity / lysosomal membrane / symbiont entry into host cell / synapse / cell surface / protein homodimerization activity / RNA binding / extracellular exosome / 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
GLUTAMINE / Amino acid transporter heavy chain SLC3A2 / Y+L amino acid transporter 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.45 Å
AuthorsAparicio, D. / Martinez, M. / Llorca, O. / Palacin, M.
Funding support Spain, 1items
OrganizationGrant numberCountry
Ministerio de Ciencia e Innovacion (MCIN)PID2021-122802OB-I00 Spain
CitationJournal: To Be Published
Title: Membrane Protein Transporter
Authors: Aparicio, D. / Palacin, M. / Llorca, O. / Martinez, M.
History
DepositionJan 17, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 29, 2026Provider: repository / Type: Initial release
Revision 1.0Jul 29, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 29, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jul 29, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 29, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 29, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 29, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Y+L amino acid transporter 1
C: 4F2 cell-surface antigen heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,2283
Polymers124,0822
Non-polymers1461
Water724
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: 56025.281 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line: HEK293 / Gene: SLC7A7 / Cell (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: Q9UM01
#2: Protein 4F2 cell-surface antigen heavy chain / 4F2hc / 4F2 heavy chain antigen / Lymphocyte activation antigen 4F2 large subunit / Solute carrier ...4F2hc / 4F2 heavy chain antigen / Lymphocyte activation antigen 4F2 large subunit / Solute carrier family 3 member 2


Mass: 68056.688 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line: HEK293 / Gene: SLC3A2, MDU1 / Cell (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: P08195
#3: Chemical ChemComp-GLN / GLUTAMINE


Type: L-peptide linking / Mass: 146.144 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H10N2O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: Y+LAT1/4F2 Heteromeric Aminoacid Transporter / Type: CELL / Entity ID: #1-#2 / Source: NATURAL
Source (natural)Organism: Homo sapiens (human)
Buffer solutionpH: 7.4 / Details: 20mM Tris ph7.4, 150mM NaCl, 2CMC GDN
Buffer component
IDConc.NameFormulaBuffer-ID
1150 mMSodium chlorideNaCl1
220 mMTrisTris1
32 CMCGDNGDN1
SpecimenConc.: 3.3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen 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: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1700 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 43.1 e/Å2 / Film or detector model: GATAN K3 BIOCONTINUUM (6k x 4k)

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Processing

EM software
IDNameCategory
2EPUimage acquisition
7UCSF ChimeraXmodel fitting
9PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.45 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 125878 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Atomic model buildingDetails: The initial model consisted of an alphafold for Y+LAT1
Source name: AlphaFold / Type: in silico model
RefinementHighest resolution: 3.45 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0027294
ELECTRON MICROSCOPYf_angle_d0.4159921
ELECTRON MICROSCOPYf_dihedral_angle_d5.223997
ELECTRON MICROSCOPYf_chiral_restr0.0351140
ELECTRON MICROSCOPYf_plane_restr0.0031242

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