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- PDB-9jri: outward-open hSLC19A1 + 5-MTHF -

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Basic information

Entry
Database: PDB / ID: 9jri
Titleoutward-open hSLC19A1 + 5-MTHF
ComponentsSoluble cytochrome b562,Reduced folate transporter,fusion protein
KeywordsMEMBRANE PROTEIN / outward-open hSLC19A1
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 / xenobiotic transmembrane transport / positive regulation of cGAS/STING signaling pathway / Metabolism of folate and pterines / 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 / electron transport chain / brush border membrane / basolateral plasma membrane / electron transfer activity / periplasmic space / 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
5-METHYL-5,6,7,8-TETRAHYDROFOLIC ACID / Soluble cytochrome b562 / Reduced folate transporter
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.43 Å
AuthorsZhang, Q.X. / Liu, K.X. / Gao, P.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Molecular basis of SLC19A1-mediated folate and cyclic dinucleotide transport
Authors: Zhang, Q.X. / Zhang, X.Y. / Liu, K.X. / Gao, P.
History
DepositionSep 29, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Feb 26, 2025Provider: repository / Type: Initial release
Revision 1.0Feb 26, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Feb 26, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Feb 26, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Feb 26, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Feb 26, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Feb 26, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Soluble cytochrome b562,Reduced folate transporter,fusion protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,9792
Polymers77,5201
Non-polymers4591
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Antibody Soluble cytochrome b562,Reduced folate transporter,fusion protein / Cytochrome b-562 / FOLT / Cyclic dinucleotide:anion antiporter SLC19A1 / Folate:anion antiporter ...Cytochrome b-562 / FOLT / Cyclic dinucleotide:anion antiporter SLC19A1 / Folate:anion antiporter SLC19A1 / 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: 77519.953 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli), (gene. exp.) Homo sapiens (human)
Gene: cybC, SLC19A1, FLOT1, RFC1 / Production host: Homo sapiens (human) / References: UniProt: P0ABE7, UniProt: P41440
#2: Chemical ChemComp-C2F / 5-METHYL-5,6,7,8-TETRAHYDROFOLIC ACID


Mass: 459.456 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H25N7O6 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

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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: outward-open hSLC19A1 + 5-MTHF / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1000 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K2 QUANTUM (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.43 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 220166 / Symmetry type: POINT

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