[English] 日本語
Yorodumi- EMDB-27394: Cryo-EM structure of the human reduced folate carrier, apo condition -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-27394 | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Cryo-EM structure of the human reduced folate carrier, apo condition | ||||||||||||
Map data | |||||||||||||
Sample |
| ||||||||||||
Keywords | reduced folate carrier / membrane protein / membrane transporter / methotrexate / SLC19A1 / solute carrier family 19 / TRANSPORT PROTEIN | ||||||||||||
Function / homology | Function and homology information folic acid transmembrane transporter activity / folate:monoatomic anion antiporter activity / methotrexate transport / 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 ...folic acid transmembrane transporter activity / folate:monoatomic anion antiporter activity / methotrexate transport / 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 / xenobiotic transmembrane transport / organic anion transport / 2',3'-cyclic GMP-AMP binding / organic anion transmembrane transporter activity / Metabolism of folate and pterines / antiporter activity / folic acid binding / 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 / iron ion binding / apical plasma membrane / heme binding / plasma membrane Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.6 Å | ||||||||||||
Authors | Wright NJ / Fedor JG / Lee S-Y | ||||||||||||
Funding support | United States, 3 items
| ||||||||||||
Citation | Journal: Nature / Year: 2022 Title: Methotrexate recognition by the human reduced folate carrier SLC19A1. Authors: Nicholas J Wright / Justin G Fedor / Han Zhang / Pyeonghwa Jeong / Yang Suo / Jiho Yoo / Jiyong Hong / Wonpil Im / Seok-Yong Lee / Abstract: Folates are essential nutrients with important roles as cofactors in one-carbon transfer reactions, being heavily utilized in the synthesis of nucleic acids and the metabolism of amino acids during ...Folates are essential nutrients with important roles as cofactors in one-carbon transfer reactions, being heavily utilized in the synthesis of nucleic acids and the metabolism of amino acids during cell division. Mammals lack de novo folate synthesis pathways and thus rely on folate uptake from the extracellular milieu. The human reduced folate carrier (hRFC, also known as SLC19A1) is the major importer of folates into the cell, as well as chemotherapeutic agents such as methotrexate. As an anion exchanger, RFC couples the import of folates and antifolates to anion export across the cell membrane and it is a major determinant in methotrexate (antifolate) sensitivity, as genetic variants and its depletion result in drug resistance. Despite its importance, the molecular basis of substrate specificity by hRFC remains unclear. Here we present cryo-electron microscopy structures of hRFC in the apo state and captured in complex with methotrexate. Combined with molecular dynamics simulations and functional experiments, our study uncovers key determinants of hRFC transport selectivity among folates and antifolate drugs while shedding light on important features of anion recognition by hRFC. | ||||||||||||
History |
|
-Structure visualization
Supplemental images |
---|
-Downloads & links
-EMDB archive
Map data | emd_27394.map.gz | 20.4 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-27394-v30.xml emd-27394.xml | 19.9 KB 19.9 KB | Display Display | EMDB header |
Images | emd_27394.png | 60.4 KB | ||
Filedesc metadata | emd-27394.cif.gz | 6.3 KB | ||
Others | emd_27394_half_map_1.map.gz emd_27394_half_map_2.map.gz | 28.3 MB 28.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-27394 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-27394 | HTTPS FTP |
-Validation report
Summary document | emd_27394_validation.pdf.gz | 905.1 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_27394_full_validation.pdf.gz | 904.7 KB | Display | |
Data in XML | emd_27394_validation.xml.gz | 10.6 KB | Display | |
Data in CIF | emd_27394_validation.cif.gz | 12.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-27394 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-27394 | HTTPS FTP |
-Related structure data
Related structure data | 8depMC 7tx6C 7tx7C C: citing same article (ref.) M: atomic model generated by this map |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|---|
Related items in Molecule of the Month |
-Map
File | Download / File: emd_27394.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.08 Å | ||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
|
-Supplemental data
-Half map: #2
File | emd_27394_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: #1
File | emd_27394_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Sample components
-Entire : Human reduced folate carrier
Entire | Name: Human reduced folate carrier |
---|---|
Components |
|
-Supramolecule #1: Human reduced folate carrier
Supramolecule | Name: Human reduced folate carrier / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 / Details: apo state |
---|---|
Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: Reduced folate transporter,Soluble cytochrome b562
Macromolecule | Name: Reduced folate transporter,Soluble cytochrome b562 / type: protein_or_peptide / ID: 1 Details: UNPID P41440 residues 215-241 removed and replaced with a fragment of soluble cytochrome b562,UNPID P41440 residues 215-241 removed and replaced with a fragment of soluble cytochrome ...Details: UNPID P41440 residues 215-241 removed and replaced with a fragment of soluble cytochrome b562,UNPID P41440 residues 215-241 removed and replaced with a fragment of soluble cytochrome b562,UNPID P41440 residues 215-241 removed and replaced with a fragment of soluble cytochrome b562,UNPID P41440 residues 215-241 removed and replaced with a fragment of soluble cytochrome b562,UNPID P41440 residues 215-241 removed and replaced with a fragment of soluble cytochrome b562,UNPID P41440 residues 215-241 removed and replaced with a fragment of soluble cytochrome b562,UNPID P41440 residues 215-241 removed and replaced with a fragment of soluble cytochrome b562,UNPID P41440 residues 215-241 removed and replaced with a fragment of soluble cytochrome b562,UNPID P41440 residues 215-241 removed and replaced with a fragment of soluble cytochrome b562 Number of copies: 1 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 74.797195 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: 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 SLFFNRDLED NWETLNDNLK VIEKADNAAQ VK DALTKMR AAALDAQKAT PPKLEDKSPD SPEMKDFRHG FDILVGQIDD ALKLANEGKV KEAQAAAEQL KTTRNAYIQK YLL RVACGD SVLARMLREL GDSLRRPQLR LWSLWWVFNS AGYYLVVYYV HILWNEVDPT TNSARVYNGA ADAASTLLGA ITSF AAGFV KIRWARWSKL LIAGVTATQA GLVFLLAHTR HPSSIWLCYA AFVLFRGSYQ FLVPIATFQI ASSLSKELCA LVFGV NTFF ATIVKTIITF IVSDVRGLGL PVRKQFQLYS VYFLILSIIY FLGAMLDGLR HCQRGHHPRQ PPAQGLRSAA EEKAAQ ALS VQDKGLGGLQ PAQSPPLSPE DSLGAVGPAS LEQRQSDPYL AQAPAPQAAE FLSPVTTPSP CTLCSAQASG PEAADET CP QLAVHPPGVS KLGLQCLPSD GVQNVNQANS LEVLFQ UniProtKB: Reduced folate transporter, Soluble cytochrome b562, Reduced folate transporter |
-Macromolecule #2: Digitonin
Macromolecule | Name: Digitonin / type: ligand / ID: 2 / Number of copies: 4 / Formula: AJP |
---|---|
Molecular weight | Theoretical: 1.229312 KDa |
Chemical component information | ChemComp-AJP: |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 5 mg/mL |
---|---|
Buffer | pH: 8 |
Grid | Model: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 200 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.00039000000000000005 kPa |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 85 % / Chamber temperature: 277 K / Instrument: LEICA EM GP |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Specialist optics | Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number grids imaged: 1 / Number real images: 12201 / Average exposure time: 2.3 sec. / Average electron dose: 60.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 81000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |