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- EMDB-10940: Structure of human b(0,+)AT1 -

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Basic information

Entry
Database: EMDB / ID: EMD-10940
TitleStructure of human b(0,+)AT1
Map data
Sample
  • Complex: human b(0,+)AT1
    • Protein or peptide: b(0,+)-type amino acid transporter 1
KeywordsMembrane transporter Heteromeric amino acid transporter Human transporter / MEMBRANE PROTEIN
Function / homology
Function and homology information


Defective SLC3A1 causes cystinuria (CSNU) / Defective SLC7A9 causes cystinuria (CSNU) / broad specificity neutral L-amino acid:basic L-amino acid antiporter activity / L-cystine transmembrane transporter activity / L-cystine transport / amino acid transmembrane transport / neutral amino acid transport / Amino acid transport across the plasma membrane / neutral L-amino acid transmembrane transporter activity / antiporter activity ...Defective SLC3A1 causes cystinuria (CSNU) / Defective SLC7A9 causes cystinuria (CSNU) / broad specificity neutral L-amino acid:basic L-amino acid antiporter activity / L-cystine transmembrane transporter activity / L-cystine transport / amino acid transmembrane transport / neutral amino acid transport / Amino acid transport across the plasma membrane / neutral L-amino acid transmembrane transporter activity / antiporter activity / Basigin interactions / brush border membrane / peptide antigen binding / protein-containing complex assembly / protein heterodimerization activity / apical plasma membrane / plasma membrane
Similarity search - Function
: / Amino acid/polyamine transporter I / Amino acid permease
Similarity search - Domain/homology
b(0,+)-type amino acid transporter 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsWu D / Safarian S
Funding support Germany, 2 items
OrganizationGrant numberCountry
German Federal Ministry for Education and Research Germany
Max Planck Society Germany
CitationJournal: Proc Natl Acad Sci U S A / Year: 2020
Title: Structural basis for amino acid exchange by a human heteromeric amino acid transporter.
Authors: Di Wu / Tamara N Grund / Sonja Welsch / Deryck J Mills / Max Michel / Schara Safarian / Hartmut Michel /
Abstract: Heteromeric amino acid transporters (HATs) comprise a group of membrane proteins that belong to the solute carrier (SLC) superfamily. They are formed by two different protein components: a light ...Heteromeric amino acid transporters (HATs) comprise a group of membrane proteins that belong to the solute carrier (SLC) superfamily. They are formed by two different protein components: a light chain subunit from an SLC7 family member and a heavy chain subunit from the SLC3 family. The light chain constitutes the transport subunit whereas the heavy chain mediates trafficking to the plasma membrane and maturation of the functional complex. Mutation, malfunction, and dysregulation of HATs are associated with a wide range of pathologies or represent the direct cause of inherited and acquired disorders. Here we report the cryogenic electron microscopy structure of the neutral and basic amino acid transport complex (bAT1-rBAT) which reveals a heterotetrameric protein assembly composed of two heavy and light chain subunits, respectively. The previously uncharacterized interaction between two HAT units is mediated via dimerization of the heavy chain subunits and does not include participation of the light chain subunits. The bAT1 transporter adopts a LeuT fold and is captured in an inward-facing conformation. We identify an amino-acid-binding pocket that is formed by transmembrane helices 1, 6, and 10 and conserved among SLC7 transporters.
History
DepositionApr 27, 2020-
Header (metadata) releaseJan 20, 2021-
Map releaseJan 20, 2021-
UpdateMay 22, 2024-
Current statusMay 22, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.012
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.012
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6yv1
  • Surface level: 0.012
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6yv1
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10940.png

Downloads & links

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Map

FileDownload / File: emd_10940.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 320 pix.
= 267.84 Å		0.84 Å/pix.
x 320 pix.
= 267.84 Å		0.84 Å/pix.
x 320 pix.
= 267.84 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.837 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.012 / Movie #1: 0.012
Minimum - Maximum-0.008013819 - 0.032865796
Average (Standard dev.)0.0001058033 (±0.00092629815)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 267.84 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.8370.8370.837
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z267.840267.840267.840
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-0.0080.0330.000

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Supplemental data

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Half map: #2

Fileemd_10940_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_10940_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : human b(0,+)AT1

EntireName: human b(0,+)AT1
Components
  • Complex: human b(0,+)AT1
    • Protein or peptide: b(0,+)-type amino acid transporter 1

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Supramolecule #1: human b(0,+)AT1

SupramoleculeName: human b(0,+)AT1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 106.962 kDa/nm

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Macromolecule #1: b(0,+)-type amino acid transporter 1

MacromoleculeName: b(0,+)-type amino acid transporter 1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 53.515992 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGDTGLRKRR EDEKSIQSQE PKTTSLQKEL GLISGISIIV GTIIGSGIFV SPKSVLSNTE AVGPCLIIWA ACGVLATLGA LCFAELGTM ITKSGGEYPY LMEAYGPIPA YLFSWASLIV IKPTSFAIIC LSFSEYVCAP FYVGCKPPQI VVKCLAAAAI L FISTVNSL ...String:
MGDTGLRKRR EDEKSIQSQE PKTTSLQKEL GLISGISIIV GTIIGSGIFV SPKSVLSNTE AVGPCLIIWA ACGVLATLGA LCFAELGTM ITKSGGEYPY LMEAYGPIPA YLFSWASLIV IKPTSFAIIC LSFSEYVCAP FYVGCKPPQI VVKCLAAAAI L FISTVNSL SVRLGSYVQN IFTAAKLVIV AIIIISGLVL LAQGNTKNFD NSFEGAQLSV GAISLAFYNG LWAYDGWNQL NY ITEELRN PYRNLPLAII IGIPLVTACY ILMNVSYFTV MTATELLQSQ AVAVTFGDRV LYPASWIVPL FVAFSTIGAA NGT CFTAGR LIYVAGREGH MLKVLSYISV RRLTPAPAII FYGIIATIYI IPGDINSLVN YFSFAAWLFY GLTILGLIVM RFTR KELER PIKVPVVIPV LMTLISVFLV LAPIISKPTW EYLYCVLFIL SGLLFYFLFV HYKFGWAQKI SKPITMHLQM LMEVV PPEE DPE

UniProtKB: b(0,+)-type amino acid transporter 1

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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

Concentration2.5 mg/mL
BufferpH: 7.5
Component:
ConcentrationName
25.0 mMTris
150.0 mMNaCl
0.1 % (w/V)Digitonin
GridModel: C-flat-1.2/1.3 4C / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 283.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 104202
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
FSC plot (resolution estimation)

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