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- PDB-7yni: Structure of human SGLT1-MAP17 complex bound with substrate 4D4FD... -

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Basic information

Entry
Database: PDB / ID: 7yni
TitleStructure of human SGLT1-MAP17 complex bound with substrate 4D4FDG in the occluded conformation
Components
  • PDZK1-interacting protein 1
  • Sodium/glucose cotransporter 1
KeywordsPROTEIN TRANSPORT / glucose transporter / SGLT / sodium glucose transporter / membrane protein
Function / homology
Function and homology information


myo-inositol:sodium symporter activity / pentose transmembrane transporter activity / fucose transmembrane transporter activity / galactose:sodium symporter activity / pentose transmembrane transport / myo-inositol transport / intestinal hexose absorption / Defective SLC5A1 causes congenital glucose/galactose malabsorption (GGM) / Intestinal hexose absorption / fucose transmembrane transport ...myo-inositol:sodium symporter activity / pentose transmembrane transporter activity / fucose transmembrane transporter activity / galactose:sodium symporter activity / pentose transmembrane transport / myo-inositol transport / intestinal hexose absorption / Defective SLC5A1 causes congenital glucose/galactose malabsorption (GGM) / Intestinal hexose absorption / fucose transmembrane transport / intestinal D-glucose absorption / galactose transmembrane transporter activity / alpha-glucoside transport / alpha-glucoside transmembrane transporter activity / D-glucose:sodium symporter activity / galactose transmembrane transport / intracellular organelle / water transmembrane transporter activity / D-glucose transmembrane transporter activity / renal D-glucose absorption / : / Cellular hexose transport / D-glucose import across plasma membrane / D-glucose transmembrane transport / transepithelial water transport / sodium ion import across plasma membrane / sodium ion transport / intracellular vesicle / transport across blood-brain barrier / brush border membrane / early endosome / apical plasma membrane / perinuclear region of cytoplasm / extracellular exosome / membrane / plasma membrane
Similarity search - Function
Sodium/glucose cotransporter / Sodium/glucose cotransporter / PDZK1-interacting protein 1/SMIM24 / Membrane-associated protein 117 kDa, PDZK1-interacting protein 1 / Sodium:solute symporter family signature 2. / Sodium:solute symporter family signature 1. / Sodium/solute symporter, conserved site / Sodium/solute symporter / Sodium/glucose symporter superfamily / Sodium:solute symporter family ...Sodium/glucose cotransporter / Sodium/glucose cotransporter / PDZK1-interacting protein 1/SMIM24 / Membrane-associated protein 117 kDa, PDZK1-interacting protein 1 / Sodium:solute symporter family signature 2. / Sodium:solute symporter family signature 1. / Sodium/solute symporter, conserved site / Sodium/solute symporter / Sodium/glucose symporter superfamily / Sodium:solute symporter family / Sodium:solute symporter family profile. / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-KQC / Sodium/glucose cotransporter 1 / PDZK1-interacting protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.26 Å
AuthorsChen, L. / Niu, Y. / Cui, W.
Funding support China, 3items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)91957201 China
National Natural Science Foundation of China (NSFC)31821091 China
National Natural Science Foundation of China (NSFC)31870833 China
CitationJournal: 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
DepositionJul 31, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 31, 2023Provider: repository / Type: Initial release
Revision 1.1Dec 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author / refine
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _refine.ls_d_res_high / _refine.ls_d_res_low
Revision 1.2Nov 13, 2024Group: Data collection / Structure summary
Category: em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sodium/glucose cotransporter 1
B: PDZK1-interacting protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,9753
Polymers85,7932
Non-polymers1821
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Sodium/glucose cotransporter 1 / Na(+)/glucose cotransporter 1 / High affinity sodium-glucose cotransporter / Solute carrier family 5 member 1


Mass: 73557.703 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SLC5A1, NAGT, SGLT1 / Production host: Homo sapiens (human) / References: UniProt: P13866
#2: Protein PDZK1-interacting protein 1 / 17 kDa membrane-associated protein / Protein DD96


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
#3: Sugar ChemComp-KQC / (2R,3R,4R,5S,6R)-5-fluoranyl-6-(hydroxymethyl)oxane-2,3,4-triol


Type: D-saccharide, beta linking / Mass: 182.147 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H11FO5 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: human SGLT1-MAP17 complex / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1800 nm / Nominal defocus min: 1500 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: (1.19.2_4158: ???) / Classification: refinement
EM softwareName: cryoSPARC / Version: v3.1.0 / Category: 3D reconstruction
CTF correctionType: NONE
3D reconstructionResolution: 3.26 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 444691 / Symmetry type: POINT
RefinementResolution: 3.26→3.26 Å / SU ML: 0.62 / σ(F): 2.32 / Phase error: 49.57 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.4431 1583 0.4 %
Rwork0.4451 --
obs0.4451 391424 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0054639
ELECTRON MICROSCOPYf_angle_d0.8086338
ELECTRON MICROSCOPYf_dihedral_angle_d11.4491549
ELECTRON MICROSCOPYf_chiral_restr0.044779
ELECTRON MICROSCOPYf_plane_restr0.006758
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5-3.610.59091560.562635611ELECTRON MICROSCOPY100
3.61-3.740.50171320.528235458ELECTRON MICROSCOPY100
3.74-3.890.46541680.500835499ELECTRON MICROSCOPY100
3.89-4.070.48531320.492335362ELECTRON MICROSCOPY100
4.07-4.280.42461440.444435418ELECTRON MICROSCOPY100
4.28-4.550.3927950.403135517ELECTRON MICROSCOPY100
4.55-4.90.35221440.38235435ELECTRON MICROSCOPY100
4.91-5.40.40021440.391835454ELECTRON MICROSCOPY100
5.4-6.180.44981920.440135234ELECTRON MICROSCOPY100
6.18-7.780.44771320.437935509ELECTRON MICROSCOPY100
7.79-200.160.46231440.432635344ELECTRON MICROSCOPY100

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