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- EMDB-52577: Membrane Protein Transporter -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-52577
TitleMembrane Protein Transporter
Map data
Sample
  • Cell: Y+LAT1/4F2 Heteromeric Aminoacid Transporter
    • Protein or peptide: Y+L amino acid transporter 1
    • Protein or peptide: 4F2 cell-surface antigen heavy chain
  • Ligand: GLUTAMINE
  • Ligand: water
KeywordsMembrane Protein Transporter / TRANSPORT PROTEIN
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
Amino acid transporter heavy chain SLC3A2 / Y+L amino acid transporter 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.45 Å
AuthorsAparicio D / Martinez M / Llorca O / Palacin M
Funding support Spain, 1 items
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, 2025-
Header (metadata) releaseJul 29, 2026-
Map releaseJul 29, 2026-
UpdateJul 29, 2026-
Current statusJul 29, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_52577.png

Downloads & links

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Map

FileDownload / File: emd_52577.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 256 pix.
= 210.893 Å		0.82 Å/pix.
x 256 pix.
= 210.893 Å		0.82 Å/pix.
x 256 pix.
= 210.893 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8238 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.245
Minimum - Maximum-1.0928547 - 1.4221652
Average (Standard dev.)0.002154584 (±0.036436267)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 210.8928 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_52577_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_52577_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Y+LAT1/4F2 Heteromeric Aminoacid Transporter

EntireName: Y+LAT1/4F2 Heteromeric Aminoacid Transporter
Components
  • Cell: Y+LAT1/4F2 Heteromeric Aminoacid Transporter
    • Protein or peptide: Y+L amino acid transporter 1
    • Protein or peptide: 4F2 cell-surface antigen heavy chain
  • Ligand: GLUTAMINE
  • Ligand: water

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Supramolecule #1: Y+LAT1/4F2 Heteromeric Aminoacid Transporter

SupramoleculeName: Y+LAT1/4F2 Heteromeric Aminoacid Transporter / type: cell / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Y+L amino acid transporter 1

MacromoleculeName: Y+L amino acid transporter 1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 56.025281 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MVDSTEYEVA SQPEVETSPL GDGASPGPEQ VKLKKEISLL NGVCLIVGNM IGSGIFVSPK GVLIYSASFG LSLVIWAVGG LFSVFGALC YAELGTTIKK SGASYAYILE AFGGFLAFIR LWTSLLIIEP TSQAIIAITF ANYMVQPLFP SCFAPYAASR L LAAACICL ...String:
MVDSTEYEVA SQPEVETSPL GDGASPGPEQ VKLKKEISLL NGVCLIVGNM IGSGIFVSPK GVLIYSASFG LSLVIWAVGG LFSVFGALC YAELGTTIKK SGASYAYILE AFGGFLAFIR LWTSLLIIEP TSQAIIAITF ANYMVQPLFP SCFAPYAASR L LAAACICL LTFINCAYVK WGTLVQDIFT YAKVLALIAV IVAGIVRLGQ GASTHFENSF EGSSFAVGDI ALALYSALFS YS GWDTLNY VTEEIKNPER NLPLSIGISM PIVTIIYILT NVAYYTVLDM RDILASDAVA VTFADQIFGI FNWIIPLSVA LSC FGGLNA SIVAASRLFF VGSREGHLPD AICMIHVERF TPVPSLLFNG IMALIYLCVE DIFQLINYYS FSYWFFVGLS IVGQ LYLRW KEPDRPRPLK LSVFFPIVFC LCTIFLVAVP LYSDTINSLI GIAIALSGLP FYFLIIRVPE HKRPLYLRRI VGSAT RYLQ VLCMSVAAEM DLEDGGEMPK QRDPKSN

UniProtKB: Y+L amino acid transporter 1

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Macromolecule #2: 4F2 cell-surface antigen heavy chain

MacromoleculeName: 4F2 cell-surface antigen heavy chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 68.056688 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MELQPPEASI AVVSIPRQLP GSHSEAGVQG LSAGDDSELG SHCVAQTGLE LLASGDPLPS ASQNAEMIET GSDCVTQAGL QLLASSDPP ALASKNAEVT GTMSQDTEVD MKEVELNELE PEKQPMNAAS GAAMSLAGAE KNGLVKIKVA EDEAEAAAAA K FTGLSKEE ...String:
MELQPPEASI AVVSIPRQLP GSHSEAGVQG LSAGDDSELG SHCVAQTGLE LLASGDPLPS ASQNAEMIET GSDCVTQAGL QLLASSDPP ALASKNAEVT GTMSQDTEVD MKEVELNELE PEKQPMNAAS GAAMSLAGAE KNGLVKIKVA EDEAEAAAAA K FTGLSKEE LLKVAGSPGW VRTRWALLLL FWLGWLGMLA GAVVIIVRAP RCRELPAQKW WHTGALYRIG DLQAFQGHGA GN LAGLKGR LDYLSSLKVK GLVLGPIHKN QKDDVAQTDL LQIDPNFGSK EDFDSLLQSA KKKSIRVILD LTPNYRGENS WFS TQVDTV ATKVKDALEF WLQAGVDGFQ VRDIENLKDA SSFLAEWQNI TKGFSEDRLL IAGTNSSDLQ QILSLLESNK DLLL TSSYL SDSGSTGEHT KSLVTQYLNA TGNRWCSWSL SQARLLTSFL PAQLLRLYQL MLFTLPGTPV FSYGDEIGLD AAALP GQPM EAPVMLWDES SFPDIPGAVS ANMTVKGQSE DPGSLLSLFR RLSDQRSKER SLLHGDFHAF SAGPGLFSYI RHWDQN ERF LVVLNFGDVG LSAGLQASDL PASASLPAKA DLLLSTQPGR EEGSPLELER LKLEPHEGLL LRFPYAA

UniProtKB: Amino acid transporter heavy chain SLC3A2

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Macromolecule #3: GLUTAMINE

MacromoleculeName: GLUTAMINE / type: ligand / ID: 3 / Number of copies: 1 / Formula: GLN
Molecular weightTheoretical: 146.144 Da
Chemical component information

ChemComp-GLN:
GLUTAMINE

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Macromolecule #4: water

MacromoleculeName: water / type: ligand / ID: 4 / Number of copies: 4 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statecell

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Sample preparation

Concentration3.3 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormulaName
150.0 mMNaClSodium chloride
20.0 mMTrisTris
2.0 CMCGDNGDN

Details: 20mM Tris ph7.4, 150mM NaCl, 2CMC GDN
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOCONTINUUM (6k x 4k) / Average electron dose: 43.1 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.7 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.45 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 125878
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
Details: The initial model consisted of an alphafold for Y+LAT1
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-9i1z:
Membrane Protein Transporter

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