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- EMDB-0905: cryo EM map of b0,+AT-rBAT complex, focused refined on soluble domain -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-0905 | ||||||||||||||||||||||||
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Title | cryo EM map of b0,+AT-rBAT complex, focused refined on soluble domain | ||||||||||||||||||||||||
![]() | Cryo EM map of b0, AT-rBAT complex, focused refined on soluble domain | ||||||||||||||||||||||||
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Biological species | ![]() | ||||||||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.5 Å | ||||||||||||||||||||||||
![]() | 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) | ![]() ![]() | 12.5 KB 12.5 KB | Display Display | ![]() |
Images | ![]() | 49.1 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 78.9 KB | Display | ![]() |
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Full document | ![]() | 78 KB | Display | |
Data in XML | ![]() | 493 B | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 0903C ![]() 0904C ![]() 0906C ![]() 0907C ![]() 0908C ![]() 6li9C ![]() 6lidC C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Cryo EM map of b0, AT-rBAT complex, focused refined on soluble domain | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
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Sample components
-Entire : b0,+AT-rBAT complex
Entire | Name: b0,+AT-rBAT complex |
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Components |
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-Supramolecule #1: b0,+AT-rBAT complex
Supramolecule | Name: b0,+AT-rBAT complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: ![]() |
Recombinant expression | Organism: ![]() |
Molecular weight | Theoretical: 120 KDa |
-Macromolecule #1: rBAT
Macromolecule | Name: rBAT / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Recombinant expression | Organism: ![]() |
Sequence | String: MAHHHHHHHH HHSGRAEDKS KRDSIEMSMK GCQTNNGFVH NEDILEQTPD PGSSTDNLKH STRGILGSQE PDFKGVQPYA GMPKEVLFQF SGQARYRIPR EILFWLTVAS VLVLIAATIA IIALSPKCLD WWQEGPMYQI YPRSFKDSNK DGNGDLKGIQ DKLDYITALN ...String: MAHHHHHHHH HHSGRAEDKS KRDSIEMSMK GCQTNNGFVH NEDILEQTPD PGSSTDNLKH STRGILGSQE PDFKGVQPYA GMPKEVLFQF SGQARYRIPR EILFWLTVAS VLVLIAATIA IIALSPKCLD WWQEGPMYQI YPRSFKDSNK DGNGDLKGIQ DKLDYITALN IKTVWITSFY KSSLKDFRYG VEDFREVDPI FGTMEDFENL VAAIHDKGLK LIIDFIPNHT SDKHIWFQLS RTRTGKYTDY YIWHDCTHEN GKTIPPNNWL SVYGNSSWHF DEVRNQCYFH QFMKEQPDLN FRNPDVQEEI KEILRFWLTK GVDGFSLDAV KFLLEAKHLR DEIQVNKTQI PDTVTQYSEL YHDFTTTQVG MHDIVRSFRQ TMDQYSTEPG RYRFMGTEAY AESIDRTVMY YGLPFIQEAD FPFNNYLSML DTVSGNSVYE VITSWMENMP EGKWPNWMIG GPDSSRLTSR LGNQYVNVMN MLLFTLPGTP ITYYGEEIGM GNIVAANLNE SYDINTLRSK SPMQWDNSSN AGFSEASNTW LPTNSDYHTV NVDVQKTQPR SALKLYQDLS LLHANELLLN RGWFCHLRND SHYVVYTREL DGIDRIFIVV LNFGESTLLN LHNMISGLPA KMRIRLSTNS ADKGSKVDTS GIFLDKGEGL IFEHNTKNLL HRQTAFRDRC FVSNRACYSS VLNILYTSC |
-Macromolecule #2: b0,+AT
Macromolecule | Name: b0,+AT / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Recombinant expression | Organism: ![]() |
Sequence | String: MADYKDDDDK SGPDEVDASG RGDTGLRKRR EDEKSIQSQE PKTTSLQKEL GLISGISIIV GTIIGSGIFV SPKSVLSNTE AVGPCLIIWA ACGVLATLGA LCFAELGTMI TKSGGEYPYL MEAYGPIPAY LFSWASLIVI KPTSFAIICL SFSEYVCAPF YVGCKPPQIV ...String: MADYKDDDDK SGPDEVDASG RGDTGLRKRR EDEKSIQSQE PKTTSLQKEL GLISGISIIV GTIIGSGIFV SPKSVLSNTE AVGPCLIIWA ACGVLATLGA LCFAELGTMI TKSGGEYPYL MEAYGPIPAY LFSWASLIVI KPTSFAIICL SFSEYVCAPF YVGCKPPQIV VKCLAAAAIL FISTVNSLSV RLGSYVQNIF TAAKLVIVAI IIISGLVLLA QGNTKNFDNS FEGAQLSVGA ISLAFYNGLW AYDGWNQLNY ITEELRNPYR NLPLAIIIGI PLVTACYILM NVSYFTVMTA TELLQSQAVA VTFGDRVLYP ASWIVPLFVA FSTIGAANGT CFTAGRLIYV AGREGHMLKV LSYISVRRLT PAPAIIFYGI IATIYIIPGD INSLVNYFSF AAWLFYGLTI LGLIVMRFTR KELERPIKVP VVIPVLMTLI SVFLVLAPII SKPTWEYLYC VLFILSGLLF YFLFVHYKFG WAQKISKPIT MHLQMLMEVV PPEEDPE |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
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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Image recording | Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 50.0 e/Å2 |
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 |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Final reconstruction | Applied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3) / Number images used: 127377 |
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Initial angle assignment | Type: OTHER |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |