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Yorodumi- EMDB-20922: GltPh in complex with L-aspartate and sodium ions in outward-faci... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-20922 | |||||||||
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Title | GltPh in complex with L-aspartate and sodium ions in outward-facing state | |||||||||
Map data | GltPh in complex with L-aspartate and sodium ions map | |||||||||
Sample |
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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 | single particle reconstruction / cryo EM / Resolution: 3.08 Å | |||||||||
Authors | Wang X / Boudker O | |||||||||
Funding support | United States, 2 items
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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 | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_20922.map.gz | 3.4 MB | EMDB map data format | |
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Header (meta data) | emd-20922-v30.xml emd-20922.xml | 10.9 KB 10.9 KB | Display Display | EMDB header |
Images | emd_20922.png | 27.8 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-20922 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-20922 | HTTPS FTP |
-Validation report
Summary document | emd_20922_validation.pdf.gz | 304.8 KB | Display | EMDB validaton report |
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Full document | emd_20922_full_validation.pdf.gz | 304.4 KB | Display | |
Data in XML | emd_20922_validation.xml.gz | 6 KB | Display | |
Data in CIF | emd_20922_validation.cif.gz | 6.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-20922 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-20922 | HTTPS FTP |
-Related structure data
Related structure data | 6uwfMC 6uwlC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_20922.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | GltPh in complex with L-aspartate and sodium ions map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.06 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Complex of GltPh with L-aspartate and sodium ions in MSP1E3 nanodisc
Entire | Name: Complex of GltPh with L-aspartate and sodium ions in MSP1E3 nanodisc |
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Components |
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-Supramolecule #1: Complex of GltPh with L-aspartate and sodium ions in MSP1E3 nanodisc
Supramolecule | Name: Complex of GltPh with L-aspartate and sodium ions in MSP1E3 nanodisc type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Pyrococcus horikoshii (archaea) |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Molecular weight | Theoretical: 134 KDa |
-Macromolecule #1: Glutamate transporter homolog
Macromolecule | Name: Glutamate transporter homolog / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Pyrococcus horikoshii (archaea) |
Molecular weight | Theoretical: 44.669957 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: (FME)GLYRKYIEY PVLQKILIGL ILGAIVGLIL GHYGYAHAVH TYVKPFGDLF VRLLKMLVMP IVFASLVVGA ASISPA RLG RVGVKIVVYY LLTSAFAVTL GIIMARLFNP GAGIHLAVGG QQFQPHQAPP LVHILLDIVP TNPFGALANG QVLPTIF FA IILGIAITYL ...String: (FME)GLYRKYIEY PVLQKILIGL ILGAIVGLIL GHYGYAHAVH TYVKPFGDLF VRLLKMLVMP IVFASLVVGA ASISPA RLG RVGVKIVVYY LLTSAFAVTL GIIMARLFNP GAGIHLAVGG QQFQPHQAPP LVHILLDIVP TNPFGALANG QVLPTIF FA IILGIAITYL MNSENEKVRK SAETLLDAIN GLAEAMYKIV NGVMQYAPIG VFALIAYVMA EQGVHVVGEL AKVTAAVY V GLTLQILLVY FVLLKIYGID PISFIKHAKD AMLTAFVTRS SSGTLPVTMR VAKEMGISEG IYSFTLPLGA TINMDGTAL YQGVCTFFIA NALGSHLTVG QQLTIVLTAV LASIGTAGVP GAGAIMLAMV LHSVGLPLTD PNVAAAYAMI LGIDAILDMG RTMVNVTGD LTGTAIVAKT EGTLVPR |
-Macromolecule #2: ASPARTIC ACID
Macromolecule | Name: ASPARTIC ACID / type: ligand / ID: 2 / Number of copies: 1 / Formula: ASP |
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Molecular weight | Theoretical: 133.103 Da |
Chemical component information | ChemComp-ASP: |
-Macromolecule #3: [(2~{R})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyl...
Macromolecule | Name: [(2~{R})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy-propan-2-yl] (~{Z})-octadec-9-enoate type: ligand / ID: 3 / Number of copies: 2 / Formula: 6OU |
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Molecular weight | Theoretical: 717.996 Da |
Chemical component information | ChemComp-6OU: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
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Sugar embedding | Material: ice |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.1615 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.08 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 94731 |
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Initial angle assignment | Type: ANGULAR RECONSTITUTION |
Final angle assignment | Type: ANGULAR RECONSTITUTION |