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- EMDB-62640: Structure of y+LAT2 bound with Arg -

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Basic information

Entry
Database: EMDB / ID: EMD-62640
TitleStructure of y+LAT2 bound with Arg
Map data
Sample
  • Complex: Structure of the y+LAT2 bound with Arg
    • Protein or peptide: Y+L amino acid transporter 2
    • Protein or peptide: Amino acid transporter heavy chain SLC3A2
  • Ligand: ARGININE
Keywordscomplex / membrane protein / amino acid
Function / homology
Function and homology information


ornithine transport / L-lysine:L-arginine antiporter activity / L-arginine transmembrane transporter activity / basic amino acid transmembrane transporter activity / L-arginine transmembrane transport / glycine betaine transport / apical pole of neuron / tyrosine transport / L-histidine transport / amino acid transport complex ...ornithine transport / L-lysine:L-arginine antiporter activity / L-arginine transmembrane transporter activity / basic amino acid transmembrane transporter activity / L-arginine transmembrane transport / 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 / amino acid transmembrane transport / L-leucine transmembrane transporter activity / isoleucine transport / valine transport / L-amino acid transmembrane transporter activity / proline transport / L-leucine transport / thyroid hormone transport / neutral amino acid transport / neutral L-amino acid transmembrane transporter activity / amino acid transmembrane transporter activity / Amino acid transport across the plasma membrane / Tryptophan catabolism / exogenous protein binding / arginine binding / anchoring junction / Basigin interactions / amino acid transport / response to exogenous dsRNA / 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 / cadherin binding / apical plasma membrane / protein heterodimerization activity / symbiont entry into host cell / lysosomal membrane / synapse / 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
Amino acid transporter heavy chain SLC3A2 / Y+L amino acid transporter 2
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsYan RH / Dai L / Zhang T
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Structure of y+LAT2 bound with Arg
Authors: Yan RH / Dai L / Zhang T
History
DepositionDec 8, 2024-
Header (metadata) releaseApr 23, 2025-
Map releaseApr 23, 2025-
UpdateApr 23, 2025-
Current statusApr 23, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_62640.png

Downloads & links

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Map

FileDownload / File: emd_62640.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.)
0.83 Å/pix.
x 256 pix.
= 211.712 Å		0.83 Å/pix.
x 256 pix.
= 211.712 Å		0.83 Å/pix.
x 256 pix.
= 211.712 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.827 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.33
Minimum - Maximum-2.2676349 - 3.067388
Average (Standard dev.)0.0040354813 (±0.06678302)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 211.712 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_62640_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_62640_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 : Structure of the y+LAT2 bound with Arg

EntireName: Structure of the y+LAT2 bound with Arg
Components
  • Complex: Structure of the y+LAT2 bound with Arg
    • Protein or peptide: Y+L amino acid transporter 2
    • Protein or peptide: Amino acid transporter heavy chain SLC3A2
  • Ligand: ARGININE

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Supramolecule #1: Structure of the y+LAT2 bound with Arg

SupramoleculeName: Structure of the y+LAT2 bound with Arg / type: complex / 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 2

MacromoleculeName: Y+L amino acid transporter 2 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 58.934102 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DYKDDDDKSG PDEVDASGRM EAREPGRPTP TYHLVPNTSQ SQVEEDVSSP PQRSSETMQL KKEISLLNGV SLVVGNMIGS GIFVSPKGV LVHTASYGMS LIVWAIGGLF SVVGALCYAE LGTTITKSGA SYAYILEAFG GFIAFIRLWV SLLVVEPTGQ A IIAITFAN ...String:
DYKDDDDKSG PDEVDASGRM EAREPGRPTP TYHLVPNTSQ SQVEEDVSSP PQRSSETMQL KKEISLLNGV SLVVGNMIGS GIFVSPKGV LVHTASYGMS LIVWAIGGLF SVVGALCYAE LGTTITKSGA SYAYILEAFG GFIAFIRLWV SLLVVEPTGQ A IIAITFAN YIIQPSFPSC DPPYLACRLL AAACICLLTF VNCAYVKWGT RVQDTFTYAK VVALIAIIVM GLVKLCQGHS EH FQDAFEG SSWDMGNLSL ALYSALFSYS GWDTLNFVTE EIKNPERNLP LAIGISMPIV TLIYILTNVA YYTVLNISDV LSS DAVAVT FADQTFGMFS WTIPIAVALS CFGGLNASIF ASSRLFFVGS REGHLPDLLS MIHIERFTPI PALLFNCTMA LIYL IVEDV FQLINYFSFS YWFFVGLSVV GQLYLRWKEP KRPRPLKLSV FFPIVFCICS VFLVIVPLFT DTINSLIGIG IALSG VPFY FMGVYLPESR RPLFIRNVLA AITRGTQQLC FCVLTELDVA EEKKDERKTD

UniProtKB: Y+L amino acid transporter 2

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Macromolecule #2: Amino acid transporter heavy chain SLC3A2

MacromoleculeName: Amino acid transporter heavy chain SLC3A2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 69.837523 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: HHHHHHHHHH SGRELQPPEA SIAVVSIPRQ LPGSHSEAGV QGLSAGDDSE LGSHCVAQTG LELLASGDPL PSASQNAEMI ETGSDCVTQ AGLQLLASSD PPALASKNAE VTGTMSQDTE VDMKEVELNE LEPEKQPMNA ASGAAMSLAG AEKNGLVKIK V AEDEAEAA ...String:
HHHHHHHHHH SGRELQPPEA SIAVVSIPRQ LPGSHSEAGV QGLSAGDDSE LGSHCVAQTG LELLASGDPL PSASQNAEMI ETGSDCVTQ AGLQLLASSD PPALASKNAE VTGTMSQDTE VDMKEVELNE LEPEKQPMNA ASGAAMSLAG AEKNGLVKIK V AEDEAEAA AAAKFTGLSK EELLKVAGSP GWVRTRWALL LLFWLGWLGM LAGAVVIIVR APRCRELPAQ KWWHTGALYR IG DLQAFQG HGAGNLAGLK GRLDYLSSLK VKGLVLGPIH KNQKDDVAQT DLLQIDPNFG SKEDFDSLLQ SAKKKSIRVI LDL TPNYRG ENSWFSTQVD TVATKVKDAL EFWLQAGVDG FQVRDIENLK DASSFLAEWQ NITKGFSEDR LLIAGTNSSD LQQI LSLLE SNKDLLLTSS YLSDSGSTGE HTKSLVTQYL NATGNRWCSW SLSQARLLTS FLPAQLLRLY QLMLFTLPGT PVFSY GDEI GLDAAALPGQ PMEAPVMLWD ESSFPDIPGA VSANMTVKGQ SEDPGSLLSL FRRLSDQRSK ERSLLHGDFH AFSAGP GLF SYIRHWDQNE RFLVVLNFGD VGLSAGLQAS DLPASASLPA KADLLLSTQP GREEGSPLEL ERLKLEPHEG LLLRFPY AA TGA

UniProtKB: Amino acid transporter heavy chain SLC3A2

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Macromolecule #3: ARGININE

MacromoleculeName: ARGININE / type: ligand / ID: 3 / Number of copies: 1 / Formula: ARG
Molecular weightTheoretical: 175.209 Da
Chemical component information

ChemComp-ARG:
ARGININE

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 5.0 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 175906
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER

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