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- PDB-7xtk: Cryo-EM structure of SLC19A1 -

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Basic information

Entry
Database: PDB / ID: 7xtk
TitleCryo-EM structure of SLC19A1
ComponentsReduced folate transporter
KeywordsMEMBRANE PROTEIN / Transporter
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 / Metabolism of folate and pterines / positive regulation of cGAS/STING signaling pathway / xenobiotic transmembrane transport / organic anion transport / : / folic acid binding / antiporter activity / folic acid metabolic process / xenobiotic transmembrane transporter activity / transport across blood-brain barrier / brush border membrane / female pregnancy / response to toxic substance / basolateral plasma membrane / apical plasma membrane / response to xenobiotic stimulus / plasma membrane
Similarity search - Function
Multidrug resistance protein D / Multidrug resistance protein D / Reduced folate transporter SLC19A1 / Reduced folate carrier / Reduced folate carrier / MFS transporter superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Reduced folate transporter
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.89 Å
AuthorsZhang, M.F. / Shan, Y.Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Basic Research Program of China (973 Program)2017YFA0504100 China
CitationJournal: To Be Published
Title: Structure of human SLC19A1.
Authors: Zhang, M.F. / Shan, Y.Y. / Pei, D.Q.
History
DepositionMay 17, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 21, 2023Provider: repository / Type: Initial release
Revision 1.1Jul 3, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond / em_admin / Item: _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Reduced folate transporter


Theoretical massNumber of molelcules
Total (without water)64,9271
Polymers64,9271
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Reduced folate transporter / FOLT / Intestinal folate carrier 1 / IFC-1 / Placental folate transporter / Reduced folate carrier ...FOLT / Intestinal folate carrier 1 / IFC-1 / Placental folate transporter / Reduced folate carrier protein / RFC / hRFC / Reduced folate transporter 1 / RFT-1 / Solute carrier family 19 member 1 / hSLC19A1


Mass: 64926.984 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SLC19A1 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: P41440

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: human SLC19A1 / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.06 MDa / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human) / Cell: HEK293
Buffer solutionpH: 7.4
Buffer componentConc.: 150 mM / Name: sodium chloride / Formula: NaCl
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1500 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.89 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 282410 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL

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