+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-38692 | |||||||||
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Title | Pyridoxamine-bound human SLC19A3 | |||||||||
Map data | ||||||||||
Sample |
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Keywords | SLC19A3 / pyridoxamine / TRANSPORT PROTEIN | |||||||||
Function / homology | Function and homology information pyridoxine transport / thiamine-containing compound metabolic process / Vitamin B1 (thiamin) metabolism / thiamine transmembrane transport / thiamine transmembrane transporter activity / thiamine transport / thiamine diphosphate biosynthetic process / electron transport chain / transmembrane transport / periplasmic space ...pyridoxine transport / thiamine-containing compound metabolic process / Vitamin B1 (thiamin) metabolism / thiamine transmembrane transport / thiamine transmembrane transporter activity / thiamine transport / thiamine diphosphate biosynthetic process / electron transport chain / transmembrane transport / periplasmic space / electron transfer activity / iron ion binding / heme binding / membrane / plasma membrane Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.7 Å | |||||||||
Authors | Dang Y / Wang GP / Zhang Z | |||||||||
Funding support | China, 2 items
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Citation | Journal: Cell Res / Year: 2024 Title: Substrate and drug recognition mechanisms of SLC19A3. Authors: Yu Dang / Tianyi Zhang / Shabareesh Pidathala / Guopeng Wang / Yijie Wang / Nanhao Chen / Chen Song / Chia-Hsueh Lee / Zhe Zhang / | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_38692.map.gz | 54.8 MB | EMDB map data format | |
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Header (meta data) | emd-38692-v30.xml emd-38692.xml | 14.3 KB 14.3 KB | Display Display | EMDB header |
Images | emd_38692.png | 174.7 KB | ||
Filedesc metadata | emd-38692.cif.gz | 5.6 KB | ||
Others | emd_38692_half_map_1.map.gz emd_38692_half_map_2.map.gz | 59.3 MB 59.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-38692 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-38692 | HTTPS FTP |
-Validation report
Summary document | emd_38692_validation.pdf.gz | 664.9 KB | Display | EMDB validaton report |
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Full document | emd_38692_full_validation.pdf.gz | 664.5 KB | Display | |
Data in XML | emd_38692_validation.xml.gz | 11.8 KB | Display | |
Data in CIF | emd_38692_validation.cif.gz | 13.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-38692 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-38692 | HTTPS FTP |
-Related structure data
Related structure data | 8xv5MC 8xv2C 8xv9C M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_38692.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 1.04 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #1
File | emd_38692_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_38692_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : human SLC19A3 in complex with pyridoxamine
Entire | Name: human SLC19A3 in complex with pyridoxamine |
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Components |
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-Supramolecule #1: human SLC19A3 in complex with pyridoxamine
Supramolecule | Name: human SLC19A3 in complex with pyridoxamine / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 60 KDa |
-Macromolecule #1: Soluble cytochrome b562,Thiamine transporter 2
Macromolecule | Name: Soluble cytochrome b562,Thiamine transporter 2 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 67.910008 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: LEVLFQGPSR ATADLEDNWE TLNDNLKVIE KADNAAQVKD ALTKMRAAAL DAQKATPPKL EDKSPDSPEM KDFRHGFDIL VGQIDDALK LANEGKVKEA QAAAEQLKTT RNAYIQKYLS WIYPTVILCL FGFFSMMRPS EPFLIPYLSG PDKNLTSAEI T NEIFPVWT ...String: LEVLFQGPSR ATADLEDNWE TLNDNLKVIE KADNAAQVKD ALTKMRAAAL DAQKATPPKL EDKSPDSPEM KDFRHGFDIL VGQIDDALK LANEGKVKEA QAAAEQLKTT RNAYIQKYLS WIYPTVILCL FGFFSMMRPS EPFLIPYLSG PDKNLTSAEI T NEIFPVWT YSYLVLLLPV FVLTDYVRYK PVIILQGISF IITWLLLLFG QGVKTMQVVE FFYGMVTAAE VAYYAYIYSV VS PEHYQRV SGYCRSVTLA AYTAGSVLAQ LLVSLANMSY FYLNVISLAS VSVAFLFSLF LPMPKKSMFF HAKPSREIKK SSS VNPVLE ETHEGEAPGC EEQKPTSEIL STSGKLNKGQ LNSLKPSNVT VDVFVQWFQD LKECYSSKRL FYWSLWWAFA TAGF NQVLN YVQILWDYKA PSQDSSIYNG AVEAIATFGG AVAAFAVGYV KVNWDLLGEL ALVVFSVVNA GSLFLMHYTA NIWAC YAGY LIFKSSYMLL ITIAVFQIAV NLNVERYALV FGINTFIALV IQTIMTVIVV DQRGLNLPVS IQFLVYGSYF AVIAGI FLM RSMYITYSTK SQKDVQSPAP SENPDVSHPE EESNIIMSTK LSNS UniProtKB: Soluble cytochrome b562, Thiamine transporter 2 |
-Macromolecule #2: 4-(AMINOMETHYL)-5-(HYDROXYMETHYL)-2-METHYLPYRIDIN-3-OL
Macromolecule | Name: 4-(AMINOMETHYL)-5-(HYDROXYMETHYL)-2-METHYLPYRIDIN-3-OL type: ligand / ID: 2 / Number of copies: 1 / Formula: PXM |
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Molecular weight | Theoretical: 168.193 Da |
Chemical component information | ChemComp-PXM: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 4 mg/mL |
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Buffer | pH: 7.5 |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / 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 / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.7000000000000001 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: NONE |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 246167 |
Initial angle assignment | Type: ANGULAR RECONSTITUTION |
Final angle assignment | Type: ANGULAR RECONSTITUTION |