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- PDB-7wsm: Cryo-EM structure of human glucose transporter GLUT4 bound to cyt... -

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Basic information

Entry
Database: PDB / ID: 7wsm
TitleCryo-EM structure of human glucose transporter GLUT4 bound to cytochalasin B in lipid nanodiscs
ComponentsSolute carrier family 2, facilitated glucose transporter member 4
KeywordsTRANSPORT PROTEIN / glucose transporter / GLUT4 / diabetes / cytochalasin B
Function / homology
Function and homology information


amylopectin biosynthetic process / D-glucose uniporter activity / regulation of synaptic vesicle budding from presynaptic endocytic zone membrane / white fat cell proliferation / positive regulation of brain-derived neurotrophic factor receptor signaling pathway / dehydroascorbic acid transport / D-glucose transmembrane transporter activity / : / glucose import in response to insulin stimulus / Cellular hexose transport ...amylopectin biosynthetic process / D-glucose uniporter activity / regulation of synaptic vesicle budding from presynaptic endocytic zone membrane / white fat cell proliferation / positive regulation of brain-derived neurotrophic factor receptor signaling pathway / dehydroascorbic acid transport / D-glucose transmembrane transporter activity / : / glucose import in response to insulin stimulus / Cellular hexose transport / insulin-responsive compartment / D-glucose transmembrane transport / short-term memory / trans-Golgi network transport vesicle / cellular response to osmotic stress / vesicle membrane / clathrin-coated vesicle / D-glucose import / transport across blood-brain barrier / endomembrane system / long-term memory / brown fat cell differentiation / clathrin-coated pit / T-tubule / multivesicular body / sarcoplasmic reticulum / Translocation of SLC2A4 (GLUT4) to the plasma membrane / trans-Golgi network / cytoplasmic vesicle membrane / sarcolemma / Transcriptional regulation of white adipocyte differentiation / cellular response to insulin stimulus / cellular response to tumor necrosis factor / glucose homeostasis / presynapse / cellular response to hypoxia / response to ethanol / carbohydrate metabolic process / learning or memory / membrane raft / external side of plasma membrane / perinuclear region of cytoplasm / extracellular exosome / membrane / plasma membrane / cytosol
Similarity search - Function
Glucose transporter, type 4 (GLUT4) / Glucose transporter GLUT / Sugar/inositol transporter / Sugar transport proteins signature 2. / Sugar transport proteins signature 1. / Major facilitator, sugar transporter-like / Sugar (and other) transporter / Sugar transporter, conserved site / Major facilitator superfamily domain / Major facilitator superfamily (MFS) profile. / MFS transporter superfamily
Similarity search - Domain/homology
Cytochalasin B / Solute carrier family 2, facilitated glucose transporter member 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.25 Å
AuthorsYuan, Y. / Kong, F. / Xu, H. / Zhu, A. / Yan, N. / Yan, C.
Funding support China, 2items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2020YFA0509301 China
Beijing Academy of Science and TechnologyZ201100006820039 China
CitationJournal: Nat Commun / Year: 2022
Title: Cryo-EM structure of human glucose transporter GLUT4.
Authors: Yafei Yuan / Fang Kong / Hanwen Xu / Angqi Zhu / Nieng Yan / Chuangye Yan /
Abstract: GLUT4 is the primary glucose transporter in adipose and skeletal muscle tissues. Its cellular trafficking is regulated by insulin signaling. Failed or reduced plasma membrane localization of GLUT4 is ...GLUT4 is the primary glucose transporter in adipose and skeletal muscle tissues. Its cellular trafficking is regulated by insulin signaling. Failed or reduced plasma membrane localization of GLUT4 is associated with diabetes. Here, we report the cryo-EM structures of human GLUT4 bound to a small molecule inhibitor cytochalasin B (CCB) at resolutions of 3.3 Å in both detergent micelles and lipid nanodiscs. CCB-bound GLUT4 exhibits an inward-open conformation. Despite the nearly identical conformation of the transmembrane domain to GLUT1, the cryo-EM structure reveals an extracellular glycosylation site and an intracellular helix that is invisible in the crystal structure of GLUT1. The structural study presented here lays the foundation for further mechanistic investigation of the modulation of GLUT4 trafficking. Our methods for cryo-EM analysis of GLUT4 will also facilitate structural determination of many other small size solute carriers.
History
DepositionJan 30, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 18, 2022Provider: repository / Type: Initial release
Revision 1.1May 25, 2022Group: Database references / Category: citation / citation_author
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 / _citation_author.identifier_ORCID
Revision 1.2Nov 20, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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: Solute carrier family 2, facilitated glucose transporter member 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,0123
Polymers56,1081
Non-polymers9042
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Solute carrier family 2, facilitated glucose transporter member 4 / Glucose transporter type 4 / insulin-responsive / GLUT-4


Mass: 56108.199 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SLC2A4, GLUT4 / Production host: Homo sapiens (human) / References: UniProt: P14672
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#3: Chemical ChemComp-5RH / Cytochalasin B


Mass: 479.608 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C29H37NO5 / Feature type: SUBJECT OF INVESTIGATION / Comment: toxin*YM
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: GLUT4 / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 56 kDa/nm / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 8
SpecimenConc.: 1.8 mg/ml / Embedding 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: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.18_3855: / Classification: refinement
EM software
IDNameCategory
10cryoSPARCinitial Euler assignment
11cryoSPARCfinal Euler assignment
13cryoSPARC3D reconstruction
CTF correctionType: NONE
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.25 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 73000 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0053660
ELECTRON MICROSCOPYf_angle_d0.7024990
ELECTRON MICROSCOPYf_dihedral_angle_d10.255544
ELECTRON MICROSCOPYf_chiral_restr0.039602
ELECTRON MICROSCOPYf_plane_restr0.006616

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