+Open data
-Basic information
Entry | Database: PDB / ID: 7ugx | |||||||||
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Title | Asp-bound GltPh RSMR mutant in IFS-B1 state | |||||||||
Components | Glutamate transporter homolog | |||||||||
Keywords | TRANSPORT PROTEIN / GltPh / glutamate transporter / substrate | |||||||||
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: 2.96 Å | |||||||||
Authors | Huang, Y. / Boudker, O. | |||||||||
Funding support | United States, 2items
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Citation | Journal: J Am Chem Soc / Year: 2023 Title: Environmentally Ultrasensitive Fluorine Probe to Resolve Protein Conformational Ensembles by F NMR and Cryo-EM. Authors: Yun Huang / Krishna D Reddy / Clay Bracken / Biao Qiu / Wenhu Zhan / David Eliezer / Olga Boudker / Abstract: Limited chemical shift dispersion represents a significant barrier to studying multistate equilibria of large membrane proteins by F NMR. We describe a novel monofluoroethyl F probe that dramatically ...Limited chemical shift dispersion represents a significant barrier to studying multistate equilibria of large membrane proteins by F NMR. We describe a novel monofluoroethyl F probe that dramatically increases the chemical shift dispersion. The improved conformational sensitivity and line shape enable the detection of previously unresolved states in one-dimensional (1D) F NMR spectra of a 134 kDa membrane transporter. Changes in the populations of these states in response to ligand binding, mutations, and temperature correlate with population changes of distinct conformations in structural ensembles determined by single-particle cryo-electron microscopy (cryo-EM). Thus, F NMR can guide sample preparation to discover and visualize novel conformational states and facilitate image analysis and three-dimensional (3D) classification. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7ugx.cif.gz | 102 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ugx.ent.gz | 75.7 KB | Display | PDB format |
PDBx/mmJSON format | 7ugx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7ugx_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 7ugx_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 7ugx_validation.xml.gz | 31.7 KB | Display | |
Data in CIF | 7ugx_validation.cif.gz | 42.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ug/7ugx ftp://data.pdbj.org/pub/pdb/validation_reports/ug/7ugx | HTTPS FTP |
-Related structure data
Related structure data | 26498MC 7ugvC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 44133.230 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus horikoshii (archaea) Strain: ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3 Gene: PH1295 / Production host: Escherichia coli (E. coli) / References: UniProt: O59010 | ||
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#2: Chemical | ChemComp-ASP / | ||
#3: Chemical | Has ligand of interest | Y | |
-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: GltPh RSMR mutant bound with Na and Asp / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT |
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Source (natural) | Organism: Pyrococcus horikoshii (archaea) |
Source (recombinant) | Organism: Escherichia coli (E. coli) |
Buffer solution | pH: 7.4 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 303 K |
-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 / Nominal defocus max: 1500 nm / Nominal defocus min: 1300 nm |
Image recording | Electron dose: 50.94 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.19.2_4158: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: NONE | ||||||||||||||||||||||||
3D reconstruction | Resolution: 2.96 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 326008 / Symmetry type: POINT | ||||||||||||||||||||||||
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