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- EMDB-0908: Cryo EM map of b0,+ AT-rBAT complex bound with Arginine, focused ... -

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Basic information

Entry
Database: EMDB / ID: EMD-0908
TitleCryo EM map of b0,+ AT-rBAT complex bound with Arginine, focused refined on TM domain
Map dataCryo EM map of b0, AT-rBAT complex bound with Arginine, focused refined on TM domain
Sample
  • Complex: b0,+AT-rBAT complex bound with Arginine, focused refined on TM domain
    • Protein or peptide: rBAT
  • Protein or peptide: b0,+AT
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.6 Å
AuthorsYan RH / Li YN / Lei JL / Zhou Q
Funding support China, 7 items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2016YFA0500402 China
Ministry of Science and Technology (MoST, China)2015CB910101 China
Ministry of Science and Technology (MoST, China)2016YFA0501100 China
National Natural Science Foundation of China (NSFC)31630017 China
National Natural Science Foundation of China (NSFC)31621092 China
National Natural Science Foundation of China (NSFC)31971123 China
National Natural Science Foundation of China (NSFC)81861138009 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-
UpdateJun 17, 2020-
Current statusJun 17, 2020Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.08
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.08
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_0908.png

Downloads & links

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Map

FileDownload / File: emd_0908.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, focused refined on TM domain
Voxel sizeX=Y=Z: 1.091 Å
Density
Contour LevelBy AUTHOR: 0.08 / Movie #1: 0.08
Minimum - Maximum-0.27154845 - 0.39657843
Average (Standard dev.)0.0000757140 (±0.008130251)
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
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-0.2720.3970.000

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Supplemental data

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Sample components

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Entire : b0,+AT-rBAT complex bound with Arginine, focused refined on TM domain

EntireName: b0,+AT-rBAT complex bound with Arginine, focused refined on TM domain
Components
  • Complex: b0,+AT-rBAT complex bound with Arginine, focused refined on TM domain
    • Protein or peptide: rBAT
  • Protein or peptide: b0,+AT

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Supramolecule #1: b0,+AT-rBAT complex bound with Arginine, focused refined on TM domain

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

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Macromolecule #1: rBAT

MacromoleculeName: rBAT / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: 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

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Macromolecule #2: b0,+AT

MacromoleculeName: b0,+AT / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: 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

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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
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm 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 assignmentType: OTHER
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3) / Number images used: 1331654

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