[English] 日本語
![](img/lk-miru.gif)
- EMDB-41265: Cryo-EM structure of the Tripartite ATP-independent Periplasmic (... -
+
Open data
-
Basic information
Entry | ![]() | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Cryo-EM structure of the Tripartite ATP-independent Periplasmic (TRAP) transporter SiaQM from Haemophilus influenzae (parallel dimer) | |||||||||
![]() | ||||||||||
![]() |
| |||||||||
![]() | Sugar transport / sialic acid / TRAP transporter / secondary active transport / ion transporter superfamily / TRANSPORT PROTEIN | |||||||||
Function / homology | TRAP transporter large membrane protein DctM / TRAP transporter, small membrane protein DctQ / TRAP C4-dicarboxylate transport system permease DctM subunit / Tripartite ATP-independent periplasmic transporters, DctQ component / Tripartite ATP-independent periplasmic transporter, DctM component / : / transmembrane transporter activity / plasma membrane / Sialic acid TRAP transporter permease protein SiaT![]() | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.36 Å | |||||||||
![]() | Davies JS / Currie MC / Dobson RCJ / North RA | |||||||||
Funding support | ![]()
| |||||||||
![]() | ![]() Title: Structural and biophysical analysis of a tripartite ATP-independent periplasmic (TRAP) transporter. Authors: Michael J Currie / James S Davies / Mariafrancesca Scalise / Ashutosh Gulati / Joshua D Wright / Michael C Newton-Vesty / Gayan S Abeysekera / Ramaswamy Subramanian / Weixiao Y Wahlgren / ...Authors: Michael J Currie / James S Davies / Mariafrancesca Scalise / Ashutosh Gulati / Joshua D Wright / Michael C Newton-Vesty / Gayan S Abeysekera / Ramaswamy Subramanian / Weixiao Y Wahlgren / Rosmarie Friemann / Jane R Allison / Peter D Mace / Michael D W Griffin / Borries Demeler / Soichi Wakatsuki / David Drew / Cesare Indiveri / Renwick C J Dobson / Rachel A North / ![]() ![]() ![]() ![]() ![]() ![]() Abstract: Tripartite ATP-independent periplasmic (TRAP) transporters are secondary-active transporters that receive their substrates via a soluble-binding protein to move bioorganic acids across bacterial or ...Tripartite ATP-independent periplasmic (TRAP) transporters are secondary-active transporters that receive their substrates via a soluble-binding protein to move bioorganic acids across bacterial or archaeal cell membranes. Recent cryo-electron microscopy (cryo-EM) structures of TRAP transporters provide a broad framework to understand how they work, but the mechanistic details of transport are not yet defined. Here we report the cryo-EM structure of the -acetylneuraminate TRAP transporter (SiaQM) at 2.99 Å resolution (extending to 2.2 Å at the core), revealing new features. The improved resolution (the previous SiaQM structure is 4.7 Å resolution) permits accurate assignment of two Na sites and the architecture of the substrate-binding site, consistent with mutagenic and functional data. Moreover, rather than a monomer, the SiaQM structure is a homodimer. We observe lipids at the dimer interface, as well as a lipid trapped within the fusion that links the SiaQ and SiaM subunits. We show that the affinity () for the complex between the soluble SiaP protein and SiaQM is in the micromolar range and that a related SiaP can bind SiaQM. This work provides key data that enhances our understanding of the 'elevator-with-an-operator' mechanism of TRAP transporters. #1: ![]() Title: Structural and biophysical analysis of a Haemophilus influenzae tripartite ATP-independent periplasmic (TRAP) transporter Authors: Currie MJ / Davies JS / Scalise M / Gulati A / Wright JD / Newton-Vesty MC / Abeysekera GS / Subramanian R / Wahlgren WY / Friemann R / Allison JR / Mace PD / Griffin MDW / Demeler B / ...Authors: Currie MJ / Davies JS / Scalise M / Gulati A / Wright JD / Newton-Vesty MC / Abeysekera GS / Subramanian R / Wahlgren WY / Friemann R / Allison JR / Mace PD / Griffin MDW / Demeler B / Wakatsuki S / Drew D / Indiveri C / Dobson RCJ / North RA | |||||||||
History |
|
-
Structure visualization
Supplemental images |
---|
-
Downloads & links
-EMDB archive
Map data | ![]() | 209 MB | ![]() | |
---|---|---|---|---|
Header (meta data) | ![]() ![]() | 23.9 KB 23.9 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 16 KB | Display | ![]() |
Images | ![]() | 116.7 KB | ||
Filedesc metadata | ![]() | 6.5 KB | ||
Others | ![]() ![]() ![]() ![]() ![]() | 205.2 MB 209.1 MB 209.4 MB 390.9 MB 390.9 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8thiMC ![]() 8thjC C: citing same article ( M: atomic model generated by this map |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
EMDB pages | ![]() ![]() |
---|
-
Map
File | ![]() | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Voxel size | X=Y=Z: 0.664 Å | ||||||||||||||||||||
Density |
| ||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
|
-Supplemental data
-Additional map: Consensus map of dimer made from auxiliary maps...
File | emd_41265_additional_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Consensus map of dimer made from auxiliary maps #1 and #2 using "vop max" command in ChimeraX. Improved resolution at dimer interface compared to primary map. | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Additional map: Monomer A focus-refined.
File | emd_41265_additional_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Monomer A focus-refined. | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Additional map: Monomer B focus-refined.
File | emd_41265_additional_3.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Monomer B focus-refined. | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: #2
File | emd_41265_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: #1
File | emd_41265_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-
Sample components
-Entire : HiSiaQM transporter protein solubilised in amphipol A8-35
Entire | Name: HiSiaQM transporter protein solubilised in amphipol A8-35 |
---|---|
Components |
|
-Supramolecule #1: HiSiaQM transporter protein solubilised in amphipol A8-35
Supramolecule | Name: HiSiaQM transporter protein solubilised in amphipol A8-35 type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
---|---|
Source (natural) | Organism: ![]() |
-Macromolecule #1: Sialic acid TRAP transporter permease protein SiaT
Macromolecule | Name: Sialic acid TRAP transporter permease protein SiaT / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 72.046812 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MGGSHHHHHH GMASMTGGQQ MGRDLYDDDD KDRWGSELEM KYINKLEEWL GGALFIAIFG ILIAQILSRQ VFHSPLIWSE ELAKLLFVY VGMLGISVAV RKQEHVFIDF LTNLMPEKIR KFTNTFVQLL VFICIFLFIH FGIRTFNGAS FPIDALGGIS E KWIFAALP ...String: MGGSHHHHHH GMASMTGGQQ MGRDLYDDDD KDRWGSELEM KYINKLEEWL GGALFIAIFG ILIAQILSRQ VFHSPLIWSE ELAKLLFVY VGMLGISVAV RKQEHVFIDF LTNLMPEKIR KFTNTFVQLL VFICIFLFIH FGIRTFNGAS FPIDALGGIS E KWIFAALP VVAILMMFRF IQAQTLNFKT GKSYLPATFF IISAVILFAI LFFAPDWFKV LRISNYIKLG SSSVYVALLV WL IIMFIGV PVGWSLFIAT LLYFSMTRWN VVNAATEKLV YSLDSFPLLA VPFYILTGIL MNTGGITERI FNFAKALLGH YTG GMGHVN IGASLLFSGM SGSALADAGG LGQLEIKAMR DAGYDDDICG GITAASCIIG PLVPPSIAMI IYGVIANESI AKLF IAGFI PGVLITLALM AMNYRIAKKR GYPRTPKATR EQLCSSFKQS FWAILTPLLI IGGIFSGLFS PTESAIVAAA YSVII GKFV YKELTLKSLF NSCIEAMAIT GVVALMIMTV TFFGDMIARE QVAMRVADVF VAVADSPLTV LIMINALLLF LGMFID ALA LQFLVLPMLI PIAMQFNIDL IFFGVMTTLN MMVGILTPPM GMALFVVARV GNMSVSTVTK GVLPFLIPVF VTLVLIT IF PQIITFVPNL LIP UniProtKB: Sialic acid TRAP transporter permease protein SiaT |
-Macromolecule #2: (1S)-2-{[{[(2R)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-...
Macromolecule | Name: (1S)-2-{[{[(2R)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE type: ligand / ID: 2 / Number of copies: 2 / Formula: PGT |
---|---|
Molecular weight | Theoretical: 751.023 Da |
Chemical component information | ![]() ChemComp-PGT: |
-Macromolecule #3: SODIUM ION
Macromolecule | Name: SODIUM ION / type: ligand / ID: 3 / Number of copies: 2 |
---|---|
Molecular weight | Theoretical: 22.99 Da |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
![]() | single particle reconstruction |
Aggregation state | particle |
-
Sample preparation
Concentration | 4.1 mg/mL |
---|---|
Buffer | pH: 8 |
Vitrification | Cryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV |
-
Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 73.1 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
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 |