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- EMDB-32761: Cryo-EM structure of human glucose transporter GLUT4 bound to cyt... -

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Basic information

Entry
Database: EMDB / ID: EMD-32761
TitleCryo-EM structure of human glucose transporter GLUT4 bound to cytochalasin B in detergent micelles
Map dataCryo-EM structure of human glucose transporter GLUT4
Sample
  • Complex: GLUT4
    • Protein or peptide: Solute carrier family 2, facilitated glucose transporter member 4
  • Ligand: 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 / cellular response to insulin stimulus / Transcriptional regulation of white adipocyte differentiation / 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
Solute carrier family 2, facilitated glucose transporter member 4
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.31 Å
AuthorsYuan Y / Kong F / Xu H / Zhu A / Yan N / Yan C
Funding support China, 2 items
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, 2022-
Header (metadata) releaseMay 18, 2022-
Map releaseMay 18, 2022-
UpdateMay 25, 2022-
Current statusMay 25, 2022Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_32761.png

Downloads & links

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Map

FileDownload / File: emd_32761.map.gz / Format: CCP4 / Size: 27 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM structure of human glucose transporter GLUT4
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 192 pix.
= 207.84 Å		1.08 Å/pix.
x 192 pix.
= 207.84 Å		1.08 Å/pix.
x 192 pix.
= 207.84 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0825 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.9
Minimum - Maximum-3.1629503 - 5.1323256
Average (Standard dev.)0.0016784676 (±0.11634488)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions192192192
Spacing192192192
CellA=B=C: 207.84 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : GLUT4

EntireName: GLUT4
Components
  • Complex: GLUT4
    • Protein or peptide: Solute carrier family 2, facilitated glucose transporter member 4
  • Ligand: Cytochalasin B

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Supramolecule #1: GLUT4

SupramoleculeName: GLUT4 / type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)
Molecular weightTheoretical: 56 kDa/nm

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Macromolecule #1: Solute carrier family 2, facilitated glucose transporter member 4

MacromoleculeName: Solute carrier family 2, facilitated glucose transporter member 4
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 56.108199 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MDYKDDDDKG TMPSGFQQIG SEDGEPPQQR VTGTLVLAVF SAVLGSLQFG YNIGVINAPQ KVIEQSYNET WLGRQGPEGP SSIPPGTLT TLWALSVAIF SVGGMISSFL IGIISQWLGR KRAMLVNNVL AVLGGSLMGL ANAAASYEML ILGRFLIGAY S GLTSGLVP ...String:
MDYKDDDDKG TMPSGFQQIG SEDGEPPQQR VTGTLVLAVF SAVLGSLQFG YNIGVINAPQ KVIEQSYNET WLGRQGPEGP SSIPPGTLT TLWALSVAIF SVGGMISSFL IGIISQWLGR KRAMLVNNVL AVLGGSLMGL ANAAASYEML ILGRFLIGAY S GLTSGLVP MYVGEIAPTH LRGALGTLNQ LAIVIGILIA QVLGLESLLG TASLWPLLLG LTVLPALLQL VLLPFCPESP RY LYIIQNL EGPARKSLKR LTGWADVSGV LAELKDEKRK LERERPLSLL QLLGSRTHRQ PLIIAVVLQL SQQLSGINAV FYY STSIFE TAGVGQPAYA TIGAGVVNTV FTLVSVLLVE RAGRRTLHLL GLAGMCGCAI LMTVALLLLE RVPAMSYVSI VAIF GFVAF FEIGPGPIPW FIVAELFSQG PRPAAMAVAG FSNWTSNFII GMGFQYVAEA MGPYVFLLFA VLLLGFFIFT FLRVP ETRG RTFDQISAAF HRTPSLLEQE VKPSTELEYL GPDEND

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Macromolecule #3: Cytochalasin B

MacromoleculeName: Cytochalasin B / type: ligand / ID: 3 / Number of copies: 1 / Formula: 5RH
Molecular weightTheoretical: 479.608 Da
Chemical component information

ChemComp-5RH:
Cytochalasin B / toxin*YM

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration1.8 mg/mL
BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.31 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 260000
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC

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