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- EMDB-61690: outward-open hSLC19A1 -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-61690
Titleoutward-open hSLC19A1
Map data
Sample
  • Complex: outward-open hSLC19A1
    • Protein or peptide: Soluble cytochrome b562,Reduced folate transporter,fusion protein
Keywordsoutward-open hSLC19A1 / MEMBRANE PROTEIN
Function / homology
Function and homology information


folate:monoatomic anion antiporter activity / methotrexate transport / folic acid transmembrane transporter activity / methotrexate transmembrane transporter activity / folic acid transport / folate transmembrane transport / folate import across plasma membrane / positive regulation of cGAS/STING signaling pathway / cyclic-GMP-AMP transmembrane transporter activity / cyclic-GMP-AMP transmembrane import across plasma membrane ...folate:monoatomic anion antiporter activity / methotrexate transport / folic acid transmembrane transporter activity / methotrexate transmembrane transporter activity / folic acid transport / folate transmembrane transport / folate import across plasma membrane / positive regulation of cGAS/STING signaling pathway / cyclic-GMP-AMP transmembrane transporter activity / cyclic-GMP-AMP transmembrane import across plasma membrane / 2',3'-cyclic GMP-AMP binding / organic anion transport / xenobiotic transmembrane transport / organic anion transmembrane transporter activity / Metabolism of folate and pterines / folic acid binding / antiporter activity / xenobiotic transmembrane transporter activity / folic acid metabolic process / transport across blood-brain barrier / female pregnancy / brush border membrane / electron transport chain / basolateral plasma membrane / periplasmic space / electron transfer activity / apical plasma membrane / iron ion binding / heme binding / plasma membrane
Similarity search - Function
Reduced folate transporter SLC19A1 / Reduced folate carrier / Reduced folate carrier / Cytochrome b562 / Cytochrome b562 / MFS transporter superfamily / Cytochrome c/b562
Similarity search - Domain/homology
Soluble cytochrome b562 / Reduced folate transporter
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.94 Å
AuthorsZhang QX / Liu KX / Gao P
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Molecular basis of SLC19A1-mediaed folate and cyclic dinucleotide transport
Authors: Zhang QX / Zhang XY / Liu KX / Gao P
History
DepositionSep 25, 2024-
Header (metadata) releaseFeb 26, 2025-
Map releaseFeb 26, 2025-
UpdateFeb 26, 2025-
Current statusFeb 26, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_61690.png

Downloads & links

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Map

FileDownload / File: emd_61690.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 Å/pix.
x 256 pix.
= 256. Å		1 Å/pix.
x 256 pix.
= 256. Å		1 Å/pix.
x 256 pix.
= 256. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.85
Minimum - Maximum-6.044876 - 7.9793015
Average (Standard dev.)-0.00069503876 (±0.11762297)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 256.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_61690_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_61690_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 : outward-open hSLC19A1

EntireName: outward-open hSLC19A1
Components
  • Complex: outward-open hSLC19A1
    • Protein or peptide: Soluble cytochrome b562,Reduced folate transporter,fusion protein

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Supramolecule #1: outward-open hSLC19A1

SupramoleculeName: outward-open hSLC19A1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Soluble cytochrome b562,Reduced folate transporter,fusion protein

MacromoleculeName: Soluble cytochrome b562,Reduced folate transporter,fusion protein
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 77.480914 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MADLEDNWET LNDNLKVIEK ADNAAQVKDA LTKMRAAALD AQKATPPKLE DKSPDSPEMK DFRHGFDILV GQIDDALKLA NEGKVKEAQ AAAEQLKTTR NAYIQKYLSW RHLVCYLCFY GFMAQIRPGE SFITPYLLGP DKQFTREQVT NEITPVLSYS Y LAVLVPVF ...String:
MADLEDNWET LNDNLKVIEK ADNAAQVKDA LTKMRAAALD AQKATPPKLE DKSPDSPEMK DFRHGFDILV GQIDDALKLA NEGKVKEAQ AAAEQLKTTR NAYIQKYLSW RHLVCYLCFY GFMAQIRPGE SFITPYLLGP DKQFTREQVT NEITPVLSYS Y LAVLVPVF LLTDYLRYTP VLLLQGLSFV SVWLLLLLGH SVAHMQLMEL FYSVTMAARI AYSSYIFSLV RPARYQRVAG YS RAAVLLG VFTSSVLGQL LVTVGRVSFS TLNYISLAFL TFSVVLALFL KRPKRSLFFN RDDRGRCETS ASELERMNPG PGG KLGHAL RVACGDSVLA RMLRELGDSL RRPQLRLWSL WWVFNSAGYY LVVYYVHILW NEVDPTTNSA RVYNFAADAA STLL GAITS FAAGFVKIRW ARWSKLLIAG VTATQAGLVF LLAHTRHPSS IWLCYAAFVL FRGSYQFLVP IATFQIASSL SKELC ALVF GVNTFFATIV KTIITFIVSD VRGLGLPVRK QFQLYSVYFL ILSIIYFLGA MLDGLRHAEE EKRKAEEEKR KGSGSQ VQL QESGGGLVQP GGSLRLSCAA SGRTISRYAM SWFRQAPGKE REFVAVARRS GDGAFYADSV QGRFTVSRDD AKNTVYL QM NSLKPEDTAV YYCAIDSDTF YSGSYDYWGQ GTQVTVSSHH HHHHHHHH

UniProtKB: Soluble cytochrome b562, Reduced folate transporter

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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 TALOS ARCTICA
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.0 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.94 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 345903
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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