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- EMDB-0903: Heteromeric amino acid transporter b0,+AT-rBAT complex bound with... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-0903 | ||||||||||||||||||||||||
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Title | Heteromeric amino acid transporter b0,+AT-rBAT complex bound with Arginine | ||||||||||||||||||||||||
![]() | cryo EM map of b0, AT-rBAT complex bound with Arginine | ||||||||||||||||||||||||
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Function / homology | ![]() 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 / aspartate transmembrane transport / amino acid transmembrane transporter activity / Amino acid transport across the plasma membrane / neutral L-amino acid transmembrane transporter activity / ![]() ![]() ![]() ![]() Similarity search - Function | ||||||||||||||||||||||||
Biological species | ![]() ![]() | ||||||||||||||||||||||||
Method | ![]() ![]() | ||||||||||||||||||||||||
![]() | Yan RH / Li YN / Lei JL / Zhou Q | ||||||||||||||||||||||||
Funding support | ![]()
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![]() | ![]() 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 |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 116.6 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 19 KB 19 KB | Display Display | ![]() |
Images | ![]() | 40.5 KB | ||
Others | ![]() ![]() | 116.9 MB 116.6 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6li9MC ![]() 0904C ![]() 0905C ![]() 0906C ![]() 0907C ![]() 0908C ![]() 6lidC M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | cryo EM map of b0, AT-rBAT complex bound with Arginine | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.091 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: cryo EM map of b0, AT-rBAT complex bound...
File | emd_0903_additional_1.map | ||||||||||||
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Annotation | cryo EM map of b0, AT-rBAT complex bound with Arginine, focused refined on TM domain | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: cryo EM map of b0, AT-rBAT complex bound...
File | emd_0903_additional_2.map | ||||||||||||
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Annotation | cryo EM map of b0, AT-rBAT complex bound with Arginine, focused refined on soluble domain | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
-Entire : b0,+AT-rBAT complex bound with Arginine
Entire | Name: b0,+AT-rBAT complex bound with Arginine |
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Components |
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-Supramolecule #1: b0,+AT-rBAT complex bound with Arginine
Supramolecule | Name: b0,+AT-rBAT complex bound with Arginine / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 |
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Source (natural) | Organism: ![]() ![]() |
Recombinant expression | Organism: ![]() ![]() |
Molecular weight | Theoretical: 120 KDa |
-Macromolecule #1: Neutral and basic amino acid transport protein rBAT
Macromolecule | Name: Neutral and basic amino acid transport protein rBAT / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 80.691586 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: 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 |
-Macromolecule #2: b(0,+)-type amino acid transporter 1
Macromolecule | Name: b(0,+)-type amino acid transporter 1 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 55.656105 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: 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 |
-Macromolecule #4: CALCIUM ION
Macromolecule | Name: CALCIUM ION / type: ligand / ID: 4 / Number of copies: 2 / Formula: CA |
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Molecular weight | Theoretical: 40.078 Da |
-Macromolecule #5: ARGININE
Macromolecule | Name: ARGININE / type: ligand / ID: 5 / Number of copies: 2 / Formula: ARG |
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Molecular weight | Theoretical: 175.209 Da |
Chemical component information | ![]() ChemComp-ARG: |
-Macromolecule #6: 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE
Macromolecule | Name: 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE / type: ligand / ID: 6 / Number of copies: 4 / Formula: 3PH |
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Molecular weight | Theoretical: 704.998 Da |
Chemical component information | ![]() ChemComp-3PH: |
-Macromolecule #7: water
Macromolecule | Name: water / type: ligand / ID: 7 / Number of copies: 246 / Formula: HOH |
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Molecular weight | Theoretical: 18.015 Da |
Chemical component information | ![]() ChemComp-HOH: |
-Experimental details
-Structure determination
Method | ![]() |
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Aggregation state | particle |
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Sample preparation
Buffer | pH: 8 |
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Vitrification | Cryogen name: NITROGEN |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD![]() |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 50.0 e/Å2 |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Initial angle assignment | Type: OTHER |
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Final angle assignment | Type: MAXIMUM LIKELIHOOD |
Final reconstruction | Applied symmetry - Point group: C2 (2 fold cyclic![]() |