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- EMDB-10936: Homodimeric structure of the rBAT complex -

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Basic information

Entry
Database: EMDB / ID: EMD-10936
TitleHomodimeric structure of the rBAT complex
Map data
Sample
  • Complex: Homodimeric complex of rBAT
    • Protein or peptide: Neutral and basic amino acid transport protein rBAT
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: CALCIUM ION
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) / basic amino acid transport / basic amino acid transmembrane transporter activity / L-cystine transmembrane transporter activity / L-cystine transport / aspartate transmembrane transport / L-glutamate transmembrane transport / Amino acid transport across the plasma membrane / amino acid transmembrane transporter activity ...Defective SLC3A1 causes cystinuria (CSNU) / Defective SLC7A9 causes cystinuria (CSNU) / basic amino acid transport / basic amino acid transmembrane transporter activity / L-cystine transmembrane transporter activity / L-cystine transport / aspartate transmembrane transport / L-glutamate transmembrane transport / Amino acid transport across the plasma membrane / amino acid transmembrane transporter activity / vacuolar membrane / amino acid transport / brush border membrane / gene expression / carbohydrate metabolic process / apical plasma membrane / protein heterodimerization activity / protein-containing complex binding / extracellular exosome / membrane / plasma membrane
Similarity search - Function
Oligo-1,6-glucosidase, domain 2 / 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 SLC3A1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.8 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-
UpdateNov 20, 2024-
Current statusNov 20, 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 cylindrical radius
  • Surface level: 0.012
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6yuz
  • Surface level: 0.012
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6yuz
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
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Supplemental images

emd_10936.png

Downloads & links

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Map

FileDownload / File: emd_10936.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-0.028816994 - 0.07374902
Average (Standard dev.)-0.00003793119 (±0.0023711107)
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-0.0290.074-0.000

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Supplemental data

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Half map: #2

Fileemd_10936_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_10936_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 : Homodimeric complex of rBAT

EntireName: Homodimeric complex of rBAT
Components
  • Complex: Homodimeric complex of rBAT
    • Protein or peptide: Neutral and basic amino acid transport protein rBAT
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: CALCIUM ION

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Supramolecule #1: Homodimeric complex of rBAT

SupramoleculeName: Homodimeric complex of rBAT / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 / Details: 2 x rBAT
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 157.704 kDa/nm

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Macromolecule #1: Neutral and basic amino acid transport protein rBAT

MacromoleculeName: Neutral and basic amino acid transport protein rBAT / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 78.937703 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MAEDKSKRDS IEMSMKGCQT NNGFVHNEDI LEQTPDPGSS TDNLKHSTRG ILGSQEPDFK GVQPYAGMPK EVLFQFSGQA RYRIPREIL FWLTVASVLV LIAATIAIIA LSPKCLDWWQ EGPMYQIYPR SFKDSNKDGN GDLKGIQDKL DYITALNIKT V WITSFYKS ...String:
MAEDKSKRDS IEMSMKGCQT NNGFVHNEDI LEQTPDPGSS TDNLKHSTRG ILGSQEPDFK GVQPYAGMPK EVLFQFSGQA RYRIPREIL FWLTVASVLV LIAATIAIIA LSPKCLDWWQ EGPMYQIYPR SFKDSNKDGN GDLKGIQDKL DYITALNIKT V WITSFYKS SLKDFRYGVE DFREVDPIFG TMEDFENLVA AIHDKGLKLI IDFIPNHTSD KHIWFQLSRT RTGKYTDYYI WH DCTHENG KTIPPNNWLS VYGNSSWHFD EVRNQCYFHQ FMKEQPDLNF RNPDVQEEIK EILRFWLTKG VDGFSLDAVK FLL EAKHLR DEIQVNKTQI PDTVTQYSEL YHDFTTTQVG MHDIVRSFRQ TMDQYSTEPG RYRFMGTEAY AESIDRTVMY YGLP FIQEA DFPFNNYLSM LDTVSGNSVY EVITSWMENM PEGKWPNWMI GGPDSSRLTS RLGNQYVNVM NMLLFTLPGT PITYY GEEI GMGNIVAANL NESYDINTLR SKSPMQWDNS SNAGFSEASN TWLPTNSDYH TVNVDVQKTQ PRSALKLYQD LSLLHA NEL LLNRGWFCHL RNDSHYVVYT RELDGIDRIF IVVLNFGEST LLNLHNMISG LPAKMRIRLS TNSADKGSKV DTSGIFL DK GEGLIFEHNT KNLLHRQTAF RDRCFVSNRA CYSSVLNILY TSC

UniProtKB: Amino acid transporter heavy chain SLC3A1

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Macromolecule #2: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 2 / Number of copies: 8 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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Macromolecule #3: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 3 / Number of copies: 2 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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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
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: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 92789
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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