[English] 日本語
Yorodumi- EMDB-15775: Cryo-EM structure of the Tripartite ATP-independent Periplasmic (... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-15775 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Cryo-EM structure of the Tripartite ATP-independent Periplasmic (TRAP) transporter SiaQM from Photobacterium profundum in a nanodisc | |||||||||
Map data | ||||||||||
Sample |
| |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Photobacterium profundum (bacteria) / Helicobacter pylori (bacteria) / Photobacterium profundum SS9 (bacteria) / synthetic construct (others) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.03 Å | |||||||||
Authors | Davies JS / North RA / Dobson RCJ | |||||||||
Funding support | New Zealand, 2 items
| |||||||||
Citation | Journal: Nat Commun / Year: 2023 Title: Structure and mechanism of a tripartite ATP-independent periplasmic TRAP transporter. Authors: James S Davies / Michael J Currie / Rachel A North / Mariafrancesca Scalise / Joshua D Wright / Jack M Copping / Daniela M Remus / Ashutosh Gulati / Dustin R Morado / Sam A Jamieson / ...Authors: James S Davies / Michael J Currie / Rachel A North / Mariafrancesca Scalise / Joshua D Wright / Jack M Copping / Daniela M Remus / Ashutosh Gulati / Dustin R Morado / Sam A Jamieson / Michael C Newton-Vesty / Gayan S Abeysekera / Subramanian Ramaswamy / Rosmarie Friemann / Soichi Wakatsuki / Jane R Allison / Cesare Indiveri / David Drew / Peter D Mace / Renwick C J Dobson / Abstract: In bacteria and archaea, tripartite ATP-independent periplasmic (TRAP) transporters uptake essential nutrients. TRAP transporters receive their substrates via a secreted soluble substrate-binding ...In bacteria and archaea, tripartite ATP-independent periplasmic (TRAP) transporters uptake essential nutrients. TRAP transporters receive their substrates via a secreted soluble substrate-binding protein. How a sodium ion-driven secondary active transporter is strictly coupled to a substrate-binding protein is poorly understood. Here we report the cryo-EM structure of the sialic acid TRAP transporter SiaQM from Photobacterium profundum at 2.97 Å resolution. SiaM comprises a "transport" domain and a "scaffold" domain, with the transport domain consisting of helical hairpins as seen in the sodium ion-coupled elevator transporter VcINDY. The SiaQ protein forms intimate contacts with SiaM to extend the size of the scaffold domain, suggesting that TRAP transporters may operate as monomers, rather than the typically observed oligomers for elevator-type transporters. We identify the Na and sialic acid binding sites in SiaM and demonstrate a strict dependence on the substrate-binding protein SiaP for uptake. We report the SiaP crystal structure that, together with docking studies, suggest the molecular basis for how sialic acid is delivered to the SiaQM transporter complex. We thus propose a model for substrate transport by TRAP proteins, which we describe herein as an 'elevator-with-an-operator' mechanism. | |||||||||
History |
|
-Structure visualization
Supplemental images |
---|
-Downloads & links
-EMDB archive
Map data | emd_15775.map.gz | 51.4 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-15775-v30.xml emd-15775.xml | 21.5 KB 21.5 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_15775_fsc.xml | 9.9 KB | Display | FSC data file |
Images | emd_15775.png | 92.9 KB | ||
Others | emd_15775_half_map_1.map.gz emd_15775_half_map_2.map.gz | 95.7 MB 95.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-15775 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-15775 | HTTPS FTP |
-Validation report
Summary document | emd_15775_validation.pdf.gz | 781.5 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_15775_full_validation.pdf.gz | 781.1 KB | Display | |
Data in XML | emd_15775_validation.xml.gz | 18.2 KB | Display | |
Data in CIF | emd_15775_validation.cif.gz | 23.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-15775 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-15775 | HTTPS FTP |
-Related structure data
Related structure data | 8b01MC 7qhaC 7t3eC 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 |
---|
-Map
File | Download / File: emd_15775.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.886 Å | ||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
|
-Supplemental data
-Half map: #2
File | emd_15775_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: #1
File | emd_15775_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Sample components
+Entire : SiaQM with megabody
+Supramolecule #1: SiaQM with megabody
+Supramolecule #2: SiaQM
+Supramolecule #3: MegaBody
+Macromolecule #1: Putative TRAP-type C4-dicarboxylate transport system, small perme...
+Macromolecule #2: Putative TRAP-type C4-dicarboxylate transport system, large perme...
+Macromolecule #3: Megabody c7HopQ
+Macromolecule #4: N-OCTANE
+Macromolecule #5: PHOSPHATIDYLETHANOLAMINE
+Macromolecule #6: DOCOSANE
+Macromolecule #7: DECANE
+Macromolecule #8: SODIUM ION
+Macromolecule #9: TRIDECANE
+Macromolecule #10: HEXANE
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1 mg/mL |
---|---|
Buffer | pH: 8 |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 8127 / Average exposure time: 2.0 sec. / Average electron dose: 70.9 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: 2.0 µm / Nominal defocus min: 0.4 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |