[English] 日本語
Yorodumi
- EMDB-10933: Heterotetrameric structure of the rBAT-b(0,+)AT1 complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-10933
TitleHeterotetrameric structure of the rBAT-b(0,+)AT1 complex
Map data
Sample
  • Complex: Heterotetrameric complex of rBAT and b(0,+)AT1
    • Protein or peptide: Neutral and basic amino acid transport protein rBAT
    • Protein or peptide: b(0,+)-type amino acid transporter 1
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: CALCIUM IONCalcium
Function / homology
Function and homology information


basic amino acid transmembrane transporter activity / broad specificity neutral L-amino acid:basic L-amino acid antiporter activity / Defective SLC3A1 causes cystinuria (CSNU) / Defective SLC7A9 causes cystinuria (CSNU) / basic amino acid transport / L-cystine transmembrane transporter activity / L-cystine transport / amino acid transmembrane transport / neutral amino acid transport / L-glutamate transmembrane transport ...basic amino acid transmembrane transporter activity / broad specificity neutral L-amino acid:basic L-amino acid antiporter activity / Defective SLC3A1 causes cystinuria (CSNU) / Defective SLC7A9 causes cystinuria (CSNU) / basic amino acid transport / L-cystine transmembrane transporter activity / L-cystine transport / amino acid transmembrane transport / neutral amino acid transport / L-glutamate transmembrane transport / amino acid transmembrane transporter activity / aspartate transmembrane transport / Amino acid transport across the plasma membrane / neutral L-amino acid transmembrane transporter activity / amino acid transport / antiporter activity / Basigin interactions / vacuolar membrane / brush border membrane / peptide antigen binding / gene expression / protein-containing complex assembly / carbohydrate metabolic process / apical plasma membrane / protein heterodimerization activity / protein-containing complex binding / extracellular exosome / membrane / plasma membrane
Similarity search - Function
Amino acid/polyamine transporter I / Amino acid permease / 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
b(0,+)-type amino acid transporter 1 / Amino acid transporter heavy chain SLC3A1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsWu D / Safarian S / Michel H
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-
UpdateJan 20, 2021-
Current statusJan 20, 2021Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.011
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.011
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6yup
  • Surface level: 0.011
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10933.png

Downloads & links

-
Map

FileDownload / File: emd_10933.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.837 Å
Density
Contour LevelBy AUTHOR: 0.01 / Movie #1: 0.011
Minimum - Maximum-0.0330811 - 0.07284846
Average (Standard dev.)9.8896735e-06 (±0.0022957383)
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-0.0330.0730.000

-
Supplemental data

-
Half map: #2

Fileemd_10933_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_10933_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Heterotetrameric complex of rBAT and b(0,+)AT1

EntireName: Heterotetrameric complex of rBAT and b(0,+)AT1
Components
  • Complex: Heterotetrameric complex of rBAT and b(0,+)AT1
    • Protein or peptide: Neutral and basic amino acid transport protein rBAT
    • Protein or peptide: b(0,+)-type amino acid transporter 1
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: CALCIUM IONCalcium

-
Supramolecule #1: Heterotetrameric complex of rBAT and b(0,+)AT1

SupramoleculeName: Heterotetrameric complex of rBAT and b(0,+)AT1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 / Details: 2 x rBAT 2 x b(0,+)AT1
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human) / Recombinant strain: HEK293 / Recombinant plasmid: pcDNA5.1/pACMV-teto
Molecular weightExperimental: 264.666 kDa/nm

-
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

-
Macromolecule #2: b(0,+)-type amino acid transporter 1

MacromoleculeName: b(0,+)-type amino acid transporter 1 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / 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

-
Macromolecule #3: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 3 / Number of copies: 8 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine

-
Macromolecule #4: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 4 / Number of copies: 2 / Formula: CA
Molecular weightTheoretical: 40.078 Da

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration2.5 mg/mL
BufferpH: 7.5
Component:
ConcentrationName
25.0 mMTris
150.0 mMNaClSodium chloride
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
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 283.15 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

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

-
Image processing

CTF correctionSoftware - Name: Gctf (ver. 1.06)
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 92789
FSC plot (resolution estimation)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more