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- EMDB-37596: Human AGT1-rBAT complex in the apo-state -

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Basic information

Entry
Database: EMDB / ID: EMD-37596
TitleHuman AGT1-rBAT complex in the apo-state
Map data
Sample
  • Complex: Human AGT1-rBAT complex in the apo-state
    • Protein or peptide: Amino acid transporter heavy chain SLC3A1
    • Protein or peptide: Solute carrier family 7 member 13
  • Ligand: CALCIUM ION
Keywordscomplex / transport amino acid / leu-T fold / MEMBRANE PROTEIN
Function / homology
Function and homology information


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-amino acid transmembrane transporter activity / L-glutamate transmembrane transport ...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-amino acid transmembrane transporter activity / L-glutamate transmembrane transport / Amino acid transport across the plasma membrane / amino acid transmembrane transporter activity / vacuolar membrane / antiporter activity / amino acid transport / brush border membrane / 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
Amino acid transporter heavy chain SLC3A1 / Solute carrier family 7 member 13
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.64 Å
AuthorsYan RH / Shi TH / Dong J
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Human AGT1-rBAT complex in the apo-state
Authors: Yan RH / Shi TH / Dong J
History
DepositionSep 27, 2023-
Header (metadata) releaseApr 2, 2025-
Map releaseApr 2, 2025-
UpdateApr 2, 2025-
Current statusApr 2, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_37596.png

Downloads & links

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Map

FileDownload / File: emd_37596.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 256 pix.
= 280.32 Å		1.1 Å/pix.
x 256 pix.
= 280.32 Å		1.1 Å/pix.
x 256 pix.
= 280.32 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.095 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.24
Minimum - Maximum-0.46438318 - 1.3904227
Average (Standard dev.)0.0035150023 (±0.05426196)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 280.32 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_37596_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_37596_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Human AGT1-rBAT complex in the apo-state

EntireName: Human AGT1-rBAT complex in the apo-state
Components
  • Complex: Human AGT1-rBAT complex in the apo-state
    • Protein or peptide: Amino acid transporter heavy chain SLC3A1
    • Protein or peptide: Solute carrier family 7 member 13
  • Ligand: CALCIUM ION

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Supramolecule #1: Human AGT1-rBAT complex in the apo-state

SupramoleculeName: Human AGT1-rBAT complex in the apo-state / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Amino acid transporter heavy chain SLC3A1

MacromoleculeName: Amino acid transporter heavy chain SLC3A1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 83.856781 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: SGGTMASGHS AWSHPQFEKG GGSGGGSGGS AWSHPQFEKV GSEEVDAGSS GRAEDKSKRD SIEMSMKGCQ TNNGFVHNED ILEQTPDPG SSTDNLKHST RGILGSQEPD FKGVQPYAGM PKEVLFQFSG QARYRIPREI LFWLTVASVL VLIAATIAII A LSPKCLDW ...String:
SGGTMASGHS AWSHPQFEKG GGSGGGSGGS AWSHPQFEKV GSEEVDAGSS GRAEDKSKRD SIEMSMKGCQ TNNGFVHNED ILEQTPDPG SSTDNLKHST RGILGSQEPD FKGVQPYAGM PKEVLFQFSG QARYRIPREI LFWLTVASVL VLIAATIAII A LSPKCLDW WQEGPMYQIY PRSFKDSNKD GNGDLKGIQD KLDYITALNI KTVWITSFYK SSLKDFRYGV EDFREVDPIF GT MEDFENL VAAIHDKGLK LIIDFIPNHT SDKHIWFQLS RTRTGKYTDY YIWHDCTHEN GKTIPPNNWL SVYGNSSWHF DEV RNQCYF HQFMKEQPDL NFRNPDVQEE IKEILRFWLT KGVDGFSLDA VKFLLEAKHL RDEIQVNKTQ IPDTVTQYSE LYHD FTTTQ VGMHDIVRSF RQTMDQYSTE PGRYRFMGTE AYAESIDRTV MYYGLPFIQE ADFPFNNYLS MLDTVSGNSV YEVIT SWME NMPEGKWPNW MIGGPDSSRL TSRLGNQYVN VMNMLLFTLP GTPITYYGEE IGMGNIVAAN LNESYDINTL RSKSPM QWD NSSNAGFSEA SNTWLPTNSD YHTVNVDVQK TQPRSALKLY QDLSLLHANE LLLNRGWFCH LRNDSHYVVY TRELDGI DR IFIVVLNFGE STLLNLHNMI SGLPAKMRIR LSTNSADKGS KVDTSGIFLD KGEGLIFEHN TKNLLHRQTA FRDRCFVS N RACYSSVLNI LYTSC

UniProtKB: Amino acid transporter heavy chain SLC3A1

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Macromolecule #2: Solute carrier family 7 member 13

MacromoleculeName: Solute carrier family 7 member 13 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 55.159797 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DYRSGGTMAD YKDDDDKSGP DEVDASGRMD RGEKIQLKRV FGYWWGTSFL LINIIGAGIF VSPKGVLAYS CMNVGVSLCV WAGCAILAM TSTLCSAEIS ISFPCSGAQY YFLKRYFGST VAFLNLWTSL FLGSGVVAGQ ALLLAEYSIQ PFFPSCSVPK L PKKCLALA ...String:
DYRSGGTMAD YKDDDDKSGP DEVDASGRMD RGEKIQLKRV FGYWWGTSFL LINIIGAGIF VSPKGVLAYS CMNVGVSLCV WAGCAILAM TSTLCSAEIS ISFPCSGAQY YFLKRYFGST VAFLNLWTSL FLGSGVVAGQ ALLLAEYSIQ PFFPSCSVPK L PKKCLALA MLWIVGILTS RGVKEVTWLQ IASSVLKVSI LSFISLTGVV FLIRGKKENV ERFQNAFDAE LPDISHLIQA IF QGYFAYS GGACFTLIAG ELKKPRTTIP KCIFTALPLV TVVYLLVNIS YLTVLTPREI LSSDAVAITW ADRAFPSLAW IMP FAISTS LFSNLLISIF KSSRPIYLAS QEGQLPLLFN TLNSHSSPFT AVLLLVTLGS LAIILTSLID LINYIFFTGS LWSI LLMIG ILRRRYQEPN LSIPYKVFLS FPLATIVIDV GLVVIPLVKS PNVHYVYVLL LVLSGLLFYI PLIHFKIRLA WFEKM TCYL QLLFNICLPD VSEE

UniProtKB: Solute carrier family 7 member 13

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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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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 5.0 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.64 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 462604
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER

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