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- EMDB-33451: Cryo-EM structure of SLC19A1 -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-33451
TitleCryo-EM structure of SLC19A1
Map data
Sample
  • Complex: human SLC19A1
    • Protein or peptide: Reduced folate transporter
KeywordsTransporter / 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 / cyclic-GMP-AMP transmembrane transporter activity / cyclic-GMP-AMP transmembrane import across plasma membrane / 2',3'-cyclic GMP-AMP binding ...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 / cyclic-GMP-AMP transmembrane transporter activity / cyclic-GMP-AMP transmembrane import across plasma membrane / 2',3'-cyclic GMP-AMP binding / organic anion transport / Metabolism of folate and pterines / xenobiotic transmembrane transport / positive regulation of cGAS/STING signaling pathway / organic anion transmembrane transporter activity / folic acid binding / antiporter activity / folic acid metabolic process / xenobiotic transmembrane transporter activity / transport across blood-brain barrier / female pregnancy / brush border membrane / response to toxic substance / basolateral plasma membrane / apical plasma membrane / response to xenobiotic stimulus / plasma membrane
Similarity search - Function
Reduced folate transporter SLC19A1 / Reduced folate carrier / Reduced folate carrier / MFS transporter superfamily
Similarity search - Domain/homology
Reduced folate transporter
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.89 Å
AuthorsZhang MF / Shan YY / Pei DQ
Funding support China, 1 items
OrganizationGrant numberCountry
National Basic Research Program of China (973 Program)2017YFA0504100 China
CitationJournal: To Be Published
Title: Structure of human SLC19A1.
Authors: Zhang MF / Shan YY / Pei DQ
History
DepositionMay 17, 2022-
Header (metadata) releaseJun 21, 2023-
Map releaseJun 21, 2023-
UpdateJul 3, 2024-
Current statusJul 3, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_33451.png

Downloads & links

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Map

FileDownload / File: emd_33451.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 320 pix.
= 271.68 Å		0.85 Å/pix.
x 320 pix.
= 271.68 Å		0.85 Å/pix.
x 320 pix.
= 271.68 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.849 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.3
Minimum - Maximum-3.0400224 - 4.0029936
Average (Standard dev.)-0.0007321518 (±0.06242137)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 271.68 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_33451_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_33451_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 SLC19A1

EntireName: human SLC19A1
Components
  • Complex: human SLC19A1
    • Protein or peptide: Reduced folate transporter

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Supramolecule #1: human SLC19A1

SupramoleculeName: human SLC19A1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 60 KDa

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Macromolecule #1: Reduced folate transporter

MacromoleculeName: Reduced folate transporter / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 64.926984 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MVPSSPAVEK QVPVEPGPDP ELRSWRHLVC YLCFYGFMAQ IRPGESFITP YLLGPDKNFT REQVTNEITP VLSYSYLAVL VPVFLLTDY LRYTPVLLLQ GLSFVSVWLL LLLGHSVAHM QLMELFYSVT MAARIAYSSY IFSLVRPARY QRVAGYSRAA V LLGVFTSS ...String:
MVPSSPAVEK QVPVEPGPDP ELRSWRHLVC YLCFYGFMAQ IRPGESFITP YLLGPDKNFT REQVTNEITP VLSYSYLAVL VPVFLLTDY LRYTPVLLLQ GLSFVSVWLL LLLGHSVAHM QLMELFYSVT MAARIAYSSY IFSLVRPARY QRVAGYSRAA V LLGVFTSS VLGQLLVTVG RVSFSTLNYI SLAFLTFSVV LALFLKRPKR SLFFNRDDRG RCETSASELE RMNPGPGGKL GH ALRVACG DSVLARMLRE LGDSLRRPQL RLWSLWWVFN SAGYYLVVYY VHILWNEVDP TTNSARVYNG AADAASTLLG AIT SFAAGF VKIRWARWSK LLIAGVTATQ AGLVFLLAHT RHPSSIWLCY AAFVLFRGSY QFLVPIATFQ IASSLSKELC ALVF GVNTF FATIVKTIIT FIVSDVRGLG LPVRKQFQLY SVYFLILSII YFLGAMLDGL RHCQRGHHPR QPPAQGLRSA AEEKA AQAL SVQDKGLGGL QPAQSPPLSP EDSLGAVGPA SLEQRQSDPY LAQAPAPQAA EFLSPVTTPS PCTLCSAQAS GPEAAD ETC PQLAVHPPGV SKLGLQCLPS DGVQNVNQ

UniProtKB: 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: 7.4 / Component - Concentration: 150.0 mM / Component - Formula: NaCl / Component - Name: sodium chloride
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
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: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.5 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: 2.89 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 282410
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementProtocol: AB INITIO MODEL
Output model

PDB-7xtk:
Cryo-EM structure of SLC19A1

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