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- PDB-6uwl: GltPh in complex with L-aspartate and sodium ions in intermediate... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6uwl | |||||||||
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Title | GltPh in complex with L-aspartate and sodium ions in intermediate outward-facing state | |||||||||
![]() | Glutamate transporter homolog | |||||||||
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Function / homology | ![]() amino acid:sodium symporter activity / L-aspartate transmembrane transport / L-aspartate transmembrane transporter activity / L-aspartate import across plasma membrane / chloride transmembrane transporter activity / protein homotrimerization / chloride transmembrane transport / identical protein binding / ![]() ![]() Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Wang, X. / Boudker, O. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Use of paramagnetic F NMR to monitor domain movement in a glutamate transporter homolog. Authors: Yun Huang / Xiaoyu Wang / Guohua Lv / Asghar M Razavi / Gerard H M Huysmans / Harel Weinstein / Clay Bracken / David Eliezer / Olga Boudker / ![]() ![]() Abstract: In proteins where conformational changes are functionally important, the number of accessible states and their dynamics are often difficult to establish. Here we describe a novel F-NMR spectroscopy ...In proteins where conformational changes are functionally important, the number of accessible states and their dynamics are often difficult to establish. Here we describe a novel F-NMR spectroscopy approach to probe dynamics of large membrane proteins. We labeled a glutamate transporter homolog with a F probe via cysteine chemistry and with a Ni ion via chelation by a di-histidine motif. We used distance-dependent enhancement of the longitudinal relaxation of F nuclei by the paramagnetic metal to assign the observed resonances. We identified one inward- and two outward-facing states of the transporter, in which the substrate-binding site is near the extracellular and intracellular solutions, respectively. We then resolved the structure of the unanticipated second outward-facing state by cryo-EM. Finally, we showed that the rates of the conformational exchange are accessible from measurements of the metal-enhanced longitudinal relaxation of F nuclei. | |||||||||
History |
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Structure visualization
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 91.1 KB | Display | ![]() |
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PDB format | ![]() | 70.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 20923MC ![]() 6uwfC M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Components
#1: Protein | Mass: 44669.957 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() |
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#2: Chemical | ChemComp-ASP / ![]() |
#3: Chemical | ChemComp-6OU / [( |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: ![]() |
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Sample preparation
Component | Name: Complex of GltPh with L-aspartate and sodium ions in MSP1E3 nanodisc Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT |
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Molecular weight | Value: 0.134 MDa / Experimental value: NO |
Source (natural) | Organism: ![]() ![]() ![]() |
Source (recombinant) | Organism: ![]() ![]() ![]() |
Buffer solution | pH: 7.4 |
Specimen | Embedding applied: YES / Shadowing applied: NO / Staining applied![]() ![]() |
EM embedding | Material: ice |
Vitrification![]() | Cryogen name: ETHANE |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company | ||||||||||||
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Microscopy | Model: FEI TITAN KRIOS | ||||||||||||
Electron gun | Electron source![]() ![]() | ||||||||||||
Electron lens | Mode: BRIGHT FIELD![]() | ||||||||||||
Image recording |
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Processing
Software | Name: PHENIX / Version: (1.14_3260: phenix.real_space_refine) / Classification: refinement |
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CTF correction![]() | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
3D reconstruction![]() | Resolution: 3.62 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 120280 / Symmetry type: POINT |