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Yorodumi- PDB-7ynk: Structure of human SGLT2-MAP17 complex in the apo state in the in... -
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-Basic information
Entry | Database: PDB / ID: 7ynk | ||||||||||||
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Title | Structure of human SGLT2-MAP17 complex in the apo state in the inward-facing conformation | ||||||||||||
Components |
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Keywords | PROTEIN TRANSPORT / glucose transporter / SGLT / sodium glucose transporter / membrane protein | ||||||||||||
Function / homology | Function and homology information low-affinity glucose:sodium symporter activity / Defective SLC5A2 causes renal glucosuria (GLYS1) / alpha-glucoside transport / glucose:sodium symporter activity / alpha-glucoside transmembrane transporter activity / hexose transmembrane transport / D-glucose transmembrane transporter activity / Cellular hexose transport / renal glucose absorption / glucose import across plasma membrane ...low-affinity glucose:sodium symporter activity / Defective SLC5A2 causes renal glucosuria (GLYS1) / alpha-glucoside transport / glucose:sodium symporter activity / alpha-glucoside transmembrane transporter activity / hexose transmembrane transport / D-glucose transmembrane transporter activity / Cellular hexose transport / renal glucose absorption / glucose import across plasma membrane / sodium ion import across plasma membrane / sodium ion transport / carbohydrate metabolic process / apical plasma membrane / extracellular exosome / membrane / plasma membrane Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.48 Å | ||||||||||||
Authors | Chen, L. / Niu, Y. | ||||||||||||
Funding support | China, 3items
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Citation | Journal: Nat Commun / Year: 2023 Title: Structures of human SGLT in the occluded state reveal conformational changes during sugar transport. Authors: Wenhao Cui / Yange Niu / Zejian Sun / Rui Liu / Lei Chen / Abstract: Sodium-Glucose Cotransporters (SGLT) mediate the uphill uptake of extracellular sugars and play fundamental roles in sugar metabolism. Although their structures in inward-open and outward-open ...Sodium-Glucose Cotransporters (SGLT) mediate the uphill uptake of extracellular sugars and play fundamental roles in sugar metabolism. Although their structures in inward-open and outward-open conformations are emerging from structural studies, the trajectory of how SGLTs transit from the outward-facing to the inward-facing conformation remains unknown. Here, we present the cryo-EM structures of human SGLT1 and SGLT2 in the substrate-bound state. Both structures show an occluded conformation, with not only the extracellular gate but also the intracellular gate tightly sealed. The sugar substrate are caged inside a cavity surrounded by TM1, TM2, TM3, TM6, TM7, and TM10. Further structural analysis reveals the conformational changes associated with the binding and release of substrates. These structures fill a gap in our understanding of the structural mechanisms of SGLT transporters. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7ynk.cif.gz | 107.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ynk.ent.gz | 78.6 KB | Display | PDB format |
PDBx/mmJSON format | 7ynk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yn/7ynk ftp://data.pdbj.org/pub/pdb/validation_reports/yn/7ynk | HTTPS FTP |
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-Related structure data
Related structure data | 33964MC 7yniC 7ynjC 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: 72949.414 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SLC5A2, SGLT2 / Production host: Homo sapiens (human) / References: UniProt: P31639 |
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#2: Protein | Mass: 12235.000 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PDZK1IP1, MAP17 / Production host: Homo sapiens (human) / References: UniProt: Q13113 |
-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: human SGLT2-MAP17 complex / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Source (natural) | Organism: Homo sapiens (human) |
Source (recombinant) | Organism: Homo sapiens (human) |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
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: SPOT SCAN |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 1800 nm / Nominal defocus min: 1500 nm |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.19.2_4158: / Classification: refinement | ||||||||||||||||||||||||
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EM software | Name: cryoSPARC / Version: v4.0.3 / Category: 3D reconstruction | ||||||||||||||||||||||||
CTF correction | Type: NONE | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.48 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 39476 / Symmetry type: POINT | ||||||||||||||||||||||||
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