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- EMDB-0903: Heteromeric amino acid transporter b0,+AT-rBAT complex bound with... -

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Basic information

Entry
Database: EMDB / ID: EMD-0903
TitleHeteromeric amino acid transporter b0,+AT-rBAT complex bound with Arginine
Map datacryo EM map of b0, AT-rBAT complex bound with Arginine
Sample
  • Complex: b0,+AT-rBAT complex bound with Arginine
    • Protein or peptide: Neutral and basic amino acid transport protein rBAT
    • Protein or peptide: b(0,+)-type amino acid transporter 1
  • Ligand: CALCIUM ION
  • Ligand: ARGININE
  • Ligand: 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE
  • Ligand: water
Keywordstransporter / MEMBRANE PROTEIN
Function / homology
Function and homology information


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 / basic amino acid transmembrane transporter activity / L-cystine transmembrane transporter activity / L-cystine transport / amino acid transmembrane transport / aspartate transmembrane transport / L-glutamate transmembrane transport ...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 / basic amino acid transmembrane transporter activity / L-cystine transmembrane transporter activity / L-cystine transport / amino acid transmembrane transport / aspartate transmembrane transport / L-glutamate transmembrane transport / neutral amino acid transport / neutral L-amino acid transmembrane transporter activity / Amino acid transport across the plasma membrane / amino acid transmembrane transporter activity / vacuolar membrane / antiporter activity / Basigin interactions / amino acid transport / brush border membrane / peptide antigen binding / protein-containing complex assembly / gene expression / 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: 2.3 Å
AuthorsYan RH / Li YN
Funding support China, 7 items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2016YFA0500402 China
Ministry of Science and Technology (MoST, China)2016YFA0501100 China
Ministry of Science and Technology (MoST, China)2015CB910101 China
National Natural Science Foundation of China (NSFC)31621092 China
National Natural Science Foundation of China (NSFC)31630017 China
National Natural Science Foundation of China (NSFC)81861138009 China
National Natural Science Foundation of China (NSFC)31971123 China
CitationJournal: Sci Adv / Year: 2020
Title: Cryo-EM structure of the human heteromeric amino acid transporter bAT-rBAT.
Authors: Renhong Yan / Yaning Li / Yi Shi / Jiayao Zhou / Jianlin Lei / Jing Huang / Qiang Zhou /
Abstract: Heteromeric amino acid transporters (HATs) catalyze the transmembrane movement of amino acids, comprising two subunits, a heavy chain and a light chain, linked by a disulfide bridge. The bAT (SLC7A9) ...Heteromeric amino acid transporters (HATs) catalyze the transmembrane movement of amino acids, comprising two subunits, a heavy chain and a light chain, linked by a disulfide bridge. The bAT (SLC7A9) is a representative light chain of HATs, forming heterodimer with rBAT, a heavy chain which mediates the membrane trafficking of bAT. The bAT-rBAT complex is an obligatory exchanger, which mediates the influx of cystine and cationic amino acids and the efflux of neutral amino acids in kidney and small intestine. Here, we report the cryo-EM structure of the human bAT-rBAT complex alone and in complex with arginine substrate at resolution of 2.7 and 2.3 Å, respectively. The overall structure of bAT-rBAT exists as a dimer of heterodimer consistent with the previous study. A ligand molecule is bound to the substrate binding pocket, near which an occluded pocket is identified, to which we found that it is important for substrate transport.
History
DepositionDec 10, 2019-
Header (metadata) releaseApr 29, 2020-
Map releaseApr 29, 2020-
UpdateOct 23, 2024-
Current statusOct 23, 2024Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.06
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.06
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6li9
  • Surface level: 0.06
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_0903.png

Downloads & links

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Map

FileDownload / File: emd_0903.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationcryo EM map of b0, AT-rBAT complex bound with Arginine
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.09 Å/pix.
x 320 pix.
= 349.12 Å		1.09 Å/pix.
x 320 pix.
= 349.12 Å		1.09 Å/pix.
x 320 pix.
= 349.12 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.091 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.06 / Movie #1: 0.06
Minimum - Maximum-0.2435733 - 0.35580352
Average (Standard dev.)0.00009970616 (±0.0063319085)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 349.12 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0911.0911.091
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z349.120349.120349.120
α/β/γ90.00090.00090.000
start NX/NY/NZ-31-35-52
NX/NY/NZ11798209
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-0.2440.3560.000

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Supplemental data

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Additional map: cryo EM map of b0, AT-rBAT complex bound...

Fileemd_0903_additional_1.map
Annotationcryo EM map of b0, AT-rBAT complex bound with Arginine, focused refined on TM domain
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: cryo EM map of b0, AT-rBAT complex bound...

Fileemd_0903_additional_2.map
Annotationcryo EM map of b0, AT-rBAT complex bound with Arginine, focused refined on soluble domain
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : b0,+AT-rBAT complex bound with Arginine

EntireName: b0,+AT-rBAT complex bound with Arginine
Components
  • Complex: b0,+AT-rBAT complex bound with Arginine
    • Protein or peptide: Neutral and basic amino acid transport protein rBAT
    • Protein or peptide: b(0,+)-type amino acid transporter 1
  • Ligand: CALCIUM ION
  • Ligand: ARGININE
  • Ligand: 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE
  • Ligand: water

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Supramolecule #1: b0,+AT-rBAT complex bound with Arginine

SupramoleculeName: b0,+AT-rBAT complex bound with Arginine / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 120 KDa

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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: 80.691586 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MAHHHHHHHH HHSGRAEDKS KRDSIEMSMK GCQTNNGFVH NEDILEQTPD PGSSTDNLKH STRGILGSQE PDFKGVQPYA GMPKEVLFQ FSGQARYRIP REILFWLTVA SVLVLIAATI AIIALSPKCL DWWQEGPMYQ IYPRSFKDSN KDGNGDLKGI Q DKLDYITA ...String:
MAHHHHHHHH HHSGRAEDKS KRDSIEMSMK GCQTNNGFVH NEDILEQTPD PGSSTDNLKH STRGILGSQE PDFKGVQPYA GMPKEVLFQ FSGQARYRIP REILFWLTVA SVLVLIAATI AIIALSPKCL DWWQEGPMYQ IYPRSFKDSN KDGNGDLKGI Q DKLDYITA LNIKTVWITS FYKSSLKDFR YGVEDFREVD PIFGTMEDFE NLVAAIHDKG LKLIIDFIPN HTSDKHIWFQ LS RTRTGKY TDYYIWHDCT HENGKTIPPN NWLSVYGNSS WHFDEVRNQC YFHQFMKEQP DLNFRNPDVQ EEIKEILRFW LTK GVDGFS LDAVKFLLEA KHLRDEIQVN KTQIPDTVTQ YSELYHDFTT TQVGMHDIVR SFRQTMDQYS TEPGRYRFMG TEAY AESID RTVMYYGLPF IQEADFPFNN YLSMLDTVSG NSVYEVITSW MENMPEGKWP NWMIGGPDSS RLTSRLGNQY VNVMN MLLF TLPGTPITYY GEEIGMGNIV AANLNESYDI NTLRSKSPMQ WDNSSNAGFS EASNTWLPTN SDYHTVNVDV QKTQPR SAL KLYQDLSLLH ANELLLNRGW FCHLRNDSHY VVYTRELDGI DRIFIVVLNF GESTLLNLHN MISGLPAKMR IRLSTNS AD KGSKVDTSGI FLDKGEGLIF EHNTKNLLHR QTAFRDRCFV SNRACYSSVL NILYTSC

UniProtKB: Amino acid transporter heavy chain SLC3A1

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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: 55.656105 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MADYKDDDDK SGPDEVDASG RGDTGLRKRR EDEKSIQSQE PKTTSLQKEL GLISGISIIV GTIIGSGIFV SPKSVLSNTE AVGPCLIIW AACGVLATLG ALCFAELGTM ITKSGGEYPY LMEAYGPIPA YLFSWASLIV IKPTSFAIIC LSFSEYVCAP F YVGCKPPQ ...String:
MADYKDDDDK SGPDEVDASG RGDTGLRKRR EDEKSIQSQE PKTTSLQKEL GLISGISIIV GTIIGSGIFV SPKSVLSNTE AVGPCLIIW AACGVLATLG ALCFAELGTM ITKSGGEYPY LMEAYGPIPA YLFSWASLIV IKPTSFAIIC LSFSEYVCAP F YVGCKPPQ IVVKCLAAAA ILFISTVNSL SVRLGSYVQN IFTAAKLVIV AIIIISGLVL LAQGNTKNFD NSFEGAQLSV GA ISLAFYN GLWAYDGWNQ LNYITEELRN PYRNLPLAII IGIPLVTACY ILMNVSYFTV MTATELLQSQ AVAVTFGDRV LYP ASWIVP LFVAFSTIGA ANGTCFTAGR LIYVAGREGH MLKVLSYISV RRLTPAPAII FYGIIATIYI IPGDINSLVN YFSF AAWLF YGLTILGLIV MRFTRKELER PIKVPVVIPV LMTLISVFLV LAPIISKPTW EYLYCVLFIL SGLLFYFLFV HYKFG WAQK ISKPITMHLQ MLMEVVPPEE DPE

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

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Macromolecule #4: CALCIUM ION

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

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Macromolecule #5: ARGININE

MacromoleculeName: ARGININE / type: ligand / ID: 5 / Number of copies: 2 / Formula: ARG
Molecular weightTheoretical: 175.209 Da
Chemical component information

ChemComp-ARG:
ARGININE

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Macromolecule #6: 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE

MacromoleculeName: 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE / type: ligand / ID: 6 / Number of copies: 4 / Formula: 3PH
Molecular weightTheoretical: 704.998 Da
Chemical component information

ChemComp-3PH:
1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE

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Macromolecule #7: water

MacromoleculeName: water / type: ligand / ID: 7 / Number of copies: 246 / 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 stateparticle

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Sample preparation

BufferpH: 8
VitrificationCryogen name: NITROGEN

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3) / Number images used: 665827
Initial angle assignmentType: OTHER
Final angle assignmentType: MAXIMUM LIKELIHOOD

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