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Yorodumi- PDB-6uwl: GltPh in complex with L-aspartate and sodium ions in intermediate... -
+Open data
-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 | |||||||||
Components | Glutamate transporter homolog | |||||||||
Keywords | TRANSPORT PROTEIN / aspartate transporter | |||||||||
Function / homology | Function and homology information 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 / metal ion binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Pyrococcus horikoshii (archaea) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.62 Å | |||||||||
Authors | Wang, X. / Boudker, O. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Nat Chem Biol / Year: 2020 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
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6uwl.cif.gz | 91.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6uwl.ent.gz | 70.3 KB | Display | PDB format |
PDBx/mmJSON format | 6uwl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6uwl_validation.pdf.gz | 715.5 KB | Display | wwPDB validaton report |
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Full document | 6uwl_full_validation.pdf.gz | 720.1 KB | Display | |
Data in XML | 6uwl_validation.xml.gz | 19.4 KB | Display | |
Data in CIF | 6uwl_validation.cif.gz | 27.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uw/6uwl ftp://data.pdbj.org/pub/pdb/validation_reports/uw/6uwl | HTTPS FTP |
-Related structure data
Related structure data | 20923MC 6uwfC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-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.) Pyrococcus horikoshii (archaea) / Production host: Escherichia coli (E. coli) / References: UniProt: O59010*PLUS |
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#2: Chemical | ChemComp-ASP / |
#3: Chemical | ChemComp-6OU / [( |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-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: Pyrococcus horikoshii (archaea) |
Source (recombinant) | Organism: Escherichia coli (E. coli) |
Buffer solution | pH: 7.4 |
Specimen | Embedding applied: YES / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
EM embedding | Material: ice |
Vitrification | Cryogen name: ETHANE |
-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: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM | ||||||||||||
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 |