+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-14716 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Structure of human OCT3 in lipid nanodisc | |||||||||
Map data | ||||||||||
Sample |
| |||||||||
Function / homology | Function and homology information histamine transport / epinephrine uptake / histamine metabolic process / monocarboxylic acid transport / serotonin transport / spermidine transmembrane transporter activity / quaternary ammonium group transmembrane transporter activity / organic cation transport / quaternary ammonium group transport / epinephrine transport ...histamine transport / epinephrine uptake / histamine metabolic process / monocarboxylic acid transport / serotonin transport / spermidine transmembrane transporter activity / quaternary ammonium group transmembrane transporter activity / organic cation transport / quaternary ammonium group transport / epinephrine transport / purine-containing compound transmembrane transport / spermidine transport / Organic cation transport / organic cation transmembrane transporter activity / histamine uptake / regulation of appetite / dopamine uptake / norepinephrine uptake / toxin transmembrane transporter activity / Abacavir transmembrane transport / norepinephrine transport / serotonin uptake / organic anion transport / neurotransmitter transmembrane transporter activity / dopamine transport / organic anion transmembrane transporter activity / monoamine transmembrane transporter activity / monoamine transport / xenobiotic transport / nuclear outer membrane / cellular detoxification / neurotransmitter transport / transport across blood-brain barrier / endomembrane system / monoatomic ion transport / mitochondrial membrane / presynapse / basolateral plasma membrane / apical plasma membrane / neuronal cell body / membrane / plasma membrane Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.2 Å | |||||||||
Authors | Khanppnavar B / Korkhov V / Qi C | |||||||||
Funding support | Switzerland, 1 items
| |||||||||
Citation | Journal: Nat Commun / Year: 2022 Title: Structural basis of organic cation transporter-3 inhibition. Authors: Basavraj Khanppnavar / Julian Maier / Freja Herborg / Ralph Gradisch / Erika Lazzarin / Dino Luethi / Jae-Won Yang / Chao Qi / Marion Holy / Kathrin Jäntsch / Oliver Kudlacek / Klaus ...Authors: Basavraj Khanppnavar / Julian Maier / Freja Herborg / Ralph Gradisch / Erika Lazzarin / Dino Luethi / Jae-Won Yang / Chao Qi / Marion Holy / Kathrin Jäntsch / Oliver Kudlacek / Klaus Schicker / Thomas Werge / Ulrik Gether / Thomas Stockner / Volodymyr M Korkhov / Harald H Sitte / Abstract: Organic cation transporters (OCTs) facilitate the translocation of catecholamines, drugs and xenobiotics across the plasma membrane in various tissues throughout the human body. OCT3 plays a key role ...Organic cation transporters (OCTs) facilitate the translocation of catecholamines, drugs and xenobiotics across the plasma membrane in various tissues throughout the human body. OCT3 plays a key role in low-affinity, high-capacity uptake of monoamines in most tissues including heart, brain and liver. Its deregulation plays a role in diseases. Despite its importance, the structural basis of OCT3 function and its inhibition has remained enigmatic. Here we describe the cryo-EM structure of human OCT3 at 3.2 Å resolution. Structures of OCT3 bound to two inhibitors, corticosterone and decynium-22, define the ligand binding pocket and reveal common features of major facilitator transporter inhibitors. In addition, we relate the functional characteristics of an extensive collection of previously uncharacterized human genetic variants to structural features, thereby providing a basis for understanding the impact of OCT3 polymorphisms. | |||||||||
History |
|
-Structure visualization
Supplemental images |
---|
-Downloads & links
-EMDB archive
Map data | emd_14716.map.gz | 7 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-14716-v30.xml emd-14716.xml | 15 KB 15 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_14716_fsc.xml | 12.4 KB | Display | FSC data file |
Images | emd_14716.png | 96.3 KB | ||
Others | emd_14716_half_map_1.map.gz emd_14716_half_map_2.map.gz | 147.2 MB 147.2 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-14716 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-14716 | HTTPS FTP |
-Validation report
Summary document | emd_14716_validation.pdf.gz | 564.6 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_14716_full_validation.pdf.gz | 564.2 KB | Display | |
Data in XML | emd_14716_validation.xml.gz | 19.7 KB | Display | |
Data in CIF | emd_14716_validation.cif.gz | 25.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-14716 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-14716 | HTTPS FTP |
-Related structure data
Related structure data | 7zh0MC 7zh6C 7zhaC M: atomic model generated by this map C: citing same article (ref.) |
---|---|
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_14716.map.gz / Format: CCP4 / Size: 163.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Voxel size | X=Y=Z: 0.66 Å | ||||||||||||||||||||
Density |
| ||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
|
-Supplemental data
-Half map: half1
File | emd_14716_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | half1 | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: half2
File | emd_14716_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | half2 | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Sample components
-Entire : human OCT3 in lipid nanodisc
Entire | Name: human OCT3 in lipid nanodisc |
---|---|
Components |
|
-Supramolecule #1: human OCT3 in lipid nanodisc
Supramolecule | Name: human OCT3 in lipid nanodisc / type: cell / ID: 1 / Parent: 0 / Macromolecule list: all |
---|---|
Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: Solute carrier family 22 member 3
Macromolecule | Name: Solute carrier family 22 member 3 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 61.332836 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MPSFDEALQR VGEFGRFQRR VFLLLCLTGV TFAFLFVGVV FLGTQPDHYW CRGPSAAALA ERCGWSPEEE WNRTAPASRG PEPPERRGR CQRYLLEAAN DSASATSALS CADPLAAFPN RSAPLVPCRG GWRYAQAHST IVSEFDLVCV NAWMLDLTQA I LNLGFLTG ...String: MPSFDEALQR VGEFGRFQRR VFLLLCLTGV TFAFLFVGVV FLGTQPDHYW CRGPSAAALA ERCGWSPEEE WNRTAPASRG PEPPERRGR CQRYLLEAAN DSASATSALS CADPLAAFPN RSAPLVPCRG GWRYAQAHST IVSEFDLVCV NAWMLDLTQA I LNLGFLTG AFTLGYAADR YGRIVIYLLS CLGVGVTGVV VAFAPNFPVF VIFRFLQGVF GKGTWMTCYV IVTEIVGSKQ RR IVGIVIQ MFFTLGIIIL PGIAYFIPNW QGIQLAITLP SFLFLLYYWV VPESPRWLIT RKKGDKALQI LRRIAKCNGK YLS SNYSEI TVTDEEVSNP SFLDLVRTPQ MRKCTLILMF AWFTSAVVYQ GLVMRLGIIG GNLYIDFFIS GVVELPGALL ILLT IERLG RRLPFAASNI VAGVACLVTA FLPEGIAWLR TTVATLGRLG ITMAFEIVYL VNSELYPTTL RNFGVSLCSG LCDFG GIIA PFLLFRLAAV WLELPLIIFG ILASICGGLV MLLPETKGIA LPETVDDVEK LGSPHSCKCG RNKKTPVSRS HL |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 |
---|---|
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Image recording | #0 - Image recording ID: 1 / #0 - Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / #0 - Average electron dose: 48.0 e/Å2 / #0 - Details: Data set 1, 2 and 3 / #1 - Image recording ID: 2 / #1 - Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / #1 - Average electron dose: 49.0 e/Å2 / #1 - Details: Data set 4 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.5 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: AB INITIO MODEL / Overall B value: 80 |
---|---|
Output model | PDB-7zh0: |