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Yorodumi- PDB-7rcp: GltPh mutant (S279E/D405N) in complex with aspartate and sodium ions -
+Open data
-Basic information
Entry | Database: PDB / ID: 7rcp | ||||||||||||
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Title | GltPh mutant (S279E/D405N) in complex with aspartate and sodium ions | ||||||||||||
Components | Glutamate transporter homolog | ||||||||||||
Keywords | TRANSPORT PROTEIN / outward-facing / substrate-bound | ||||||||||||
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: 2.2 Å | ||||||||||||
Authors | Reddy, K.D. / Boudker, O. | ||||||||||||
Funding support | United States, 3items
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Citation | Journal: J Gen Physiol / Year: 2022 Title: The archaeal glutamate transporter homologue GltPh shows heterogeneous substrate binding. Authors: Krishna D Reddy / Didar Ciftci / Amanda J Scopelliti / Olga Boudker / Abstract: Integral membrane glutamate transporters couple the concentrative substrate transport to ion gradients. There is a wealth of structural and mechanistic information about this protein family. Recent ...Integral membrane glutamate transporters couple the concentrative substrate transport to ion gradients. There is a wealth of structural and mechanistic information about this protein family. Recent studies of an archaeal homologue, GltPh, revealed transport rate heterogeneity, which is inconsistent with simple kinetic models; however, its structural and mechanistic determinants remain undefined. Here, we demonstrate that in a mutant GltPh, which exclusively populates the outward-facing state, at least two substates coexist in slow equilibrium, binding the substrate with different apparent affinities. Wild type GltPh shows similar binding properties, and modulation of the substate equilibrium correlates with transport rates. The low-affinity substate of the mutant is transient following substrate binding. Consistently, cryo-EM on samples frozen within seconds after substrate addition reveals the presence of structural classes with perturbed helical packing of the extracellular half of the transport domain in regions adjacent to the binding site. By contrast, an equilibrated structure does not show such classes. The structure at 2.2-Å resolution details a pattern of waters in the intracellular half of the domain and resolves classes with subtle differences in the substrate-binding site. We hypothesize that the rigid cytoplasmic half of the domain mediates substrate and ion recognition and coupling, whereas the extracellular labile half sets the affinity and dynamic properties. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7rcp.cif.gz | 398.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7rcp.ent.gz | 327.4 KB | Display | PDB format |
PDBx/mmJSON format | 7rcp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rc/7rcp ftp://data.pdbj.org/pub/pdb/validation_reports/rc/7rcp | HTTPS FTP |
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-Related structure data
Related structure data | 24405MC 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS oper:
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-Components
#1: Protein | Mass: 43927.055 Da / Num. of mol.: 3 / Mutation: S279E, D405N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3) (archaea) Strain: ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3 Gene: PH1295 Production host: Escherichia coli str. K-12 substr. DH10B (bacteria) References: UniProt: O59010 #2: Chemical | #3: Chemical | ChemComp-NA / #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-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 glutamate transporter homologue GltPh mutant (S279E/D405N) with sodium nitrate and aspartate Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: #1 / Source: RECOMBINANT | ||||||||||||||||||||
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Source (natural) | Organism: Pyrococcus horikoshii (archaea) | ||||||||||||||||||||
Source (recombinant) | Organism: Escherichia coli str. K-12 substr. DH10B (bacteria) | ||||||||||||||||||||
Buffer solution | pH: 7.4 | ||||||||||||||||||||
Buffer component |
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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 FIELDBright-field microscopy |
Image recording | Electron dose: 47.91 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
Software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Symmetry | Point symmetry: C3 (3 fold cyclic) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 2.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 503427 / Symmetry type: POINT | ||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.78 Å2 | ||||||||||||||||||||||||
Refine LS restraints |
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Refine LS restraints NCS |
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