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- EMDB-34046: Embigin facilitates monocarboxylate transporter 1 localization to... -

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Basic information

Entry
Database: EMDB / ID: EMD-34046
TitleEmbigin facilitates monocarboxylate transporter 1 localization to plasma membrane and transition to a decoupling state
Map data
Sample
  • Complex: MCT1-embigin
    • Protein or peptide: Embigin
    • Protein or peptide: Monocarboxylate transporter 1
KeywordsMCT1 / embigin / MEMBRANE PROTEIN
Function / homology
Function and homology information


mevalonate transmembrane transporter activity / mevalonate transport / behavioral response to nutrient / monocarboxylic acid transmembrane transporter activity / plasma membrane lactate transport / pyruvate transmembrane transport / lactate transmembrane transporter activity / monocarboxylic acid transport / lactate:proton symporter activity / Defective SLC16A1 causes symptomatic deficiency in lactate transport (SDLT) ...mevalonate transmembrane transporter activity / mevalonate transport / behavioral response to nutrient / monocarboxylic acid transmembrane transporter activity / plasma membrane lactate transport / pyruvate transmembrane transport / lactate transmembrane transporter activity / monocarboxylic acid transport / lactate:proton symporter activity / Defective SLC16A1 causes symptomatic deficiency in lactate transport (SDLT) / succinate transmembrane transport / Proton-coupled monocarboxylate transport / succinate transmembrane transporter activity / pyruvate catabolic process / carboxylic acid transmembrane transport / carboxylic acid transmembrane transporter activity / dendrite self-avoidance / cell-cell adhesion mediator activity / organic cyclic compound binding / centrosome cycle / Basigin interactions / response to food / Aspirin ADME / homophilic cell adhesion via plasma membrane adhesion molecules / cellular response to organic cyclic compound / transport across blood-brain barrier / lateral plasma membrane / regulation of insulin secretion / basal plasma membrane / axon guidance / lipid metabolic process / cell junction / glucose homeostasis / basolateral plasma membrane / apical plasma membrane / axon / intracellular membrane-bounded organelle / centrosome / synapse / extracellular exosome / identical protein binding / membrane / plasma membrane
Similarity search - Function
Monocarboxylate transporter / : / Major facilitator superfamily / Major Facilitator Superfamily / Major facilitator superfamily domain / Major facilitator superfamily (MFS) profile. / MFS transporter superfamily / Immunoglobulin I-set / Immunoglobulin I-set domain / Immunoglobulin subtype ...Monocarboxylate transporter / : / Major facilitator superfamily / Major Facilitator Superfamily / Major facilitator superfamily domain / Major facilitator superfamily (MFS) profile. / MFS transporter superfamily / Immunoglobulin I-set / Immunoglobulin I-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Monocarboxylate transporter 1 / Embigin
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.63 Å
AuthorsXu B / Ye S
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31971127 to S.Y., 31870742 and 32071216 to H.Y., 31600606 and 32161133022 to X.Z., 91857108 and 81470839 to L.C. China
CitationJournal: Cell Rep / Year: 2022
Title: Embigin facilitates monocarboxylate transporter 1 localization to the plasma membrane and transition to a decoupling state.
Authors: Binghong Xu / Mingfeng Zhang / Bo Zhang / Wenna Chi / Xiaomin Ma / Wei Zhang / Minmin Dong / Linlin Sheng / Yi Zhang / Wenhao Jiao / Yuanyue Shan / Wenjing Chang / Peiyi Wang / Shiheng Wen / ...Authors: Binghong Xu / Mingfeng Zhang / Bo Zhang / Wenna Chi / Xiaomin Ma / Wei Zhang / Minmin Dong / Linlin Sheng / Yi Zhang / Wenhao Jiao / Yuanyue Shan / Wenjing Chang / Peiyi Wang / Shiheng Wen / Duanqing Pei / Ligong Chen / Xiaokang Zhang / Hanchi Yan / Sheng Ye /
Abstract: Cell-surface ancillary glycoproteins basigin or embigin form heterodimeric complexes with proton-coupled monocarboxylate transporters (MCTs), facilitating the membrane trafficking of MCTs and ...Cell-surface ancillary glycoproteins basigin or embigin form heterodimeric complexes with proton-coupled monocarboxylate transporters (MCTs), facilitating the membrane trafficking of MCTs and regulating their transport activities. Here, we determine the cryoelectron microscopy (cryo-EM) structure of the human MCT1-embigin complex and observe that embigin forms extensive interactions with MCT1 to facilitate its localization to the plasma membrane. In addition, the formation of the heterodimer effectively blocks MCT1 from forming a homodimer through a steric hindrance effect, releasing the coupling between two signature motifs and driving a significant conformation change in transmembrane helix 5 (TM5) of MCTs. Consequently, the substrate-binding pocket alternates between states of homodimeric coupling and heterodimeric decoupling states and exhibits differences in substrate-binding affinity, supporting the hypothesis that the substrate-induced motion originating in one subunit of the MCT dimer could be transmitted to the adjacent subunit to alter its substrate-binding affinity.
History
DepositionAug 8, 2022-
Header (metadata) releaseSep 28, 2022-
Map releaseSep 28, 2022-
UpdateOct 16, 2024-
Current statusOct 16, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_34046.png

Downloads & links

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Map

FileDownload / File: emd_34046.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 320 pix.
= 268.8 Å		0.84 Å/pix.
x 320 pix.
= 268.8 Å		0.84 Å/pix.
x 320 pix.
= 268.8 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.84 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.18
Minimum - Maximum-0.4835635 - 0.75238097
Average (Standard dev.)-0.00023755009 (±0.015033375)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 268.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_34046_half_map_1.map
Projections & Slices
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Half map: #2

Fileemd_34046_half_map_2.map
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Sample components

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Entire : MCT1-embigin

EntireName: MCT1-embigin
Components
  • Complex: MCT1-embigin
    • Protein or peptide: Embigin
    • Protein or peptide: Monocarboxylate transporter 1

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Supramolecule #1: MCT1-embigin

SupramoleculeName: MCT1-embigin / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Embigin

MacromoleculeName: Embigin / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 36.921844 KDa
Recombinant expressionOrganism: Insecta environmental sample (insect)
SequenceString: MRALPGLLEA RARTPRLLLL QCLLAAARPS SADGSAPDSP FTSPPLREEI MANNFSLESH NISLTEHSSM PVEKNITLER PSNVNLTCQ FTTSGDLNAV NVTWKKDGEQ LENNYLVSAT GSTLYTQYRF TIINSKQMGS YSCFFREEKE QRGTFNFKVP E LHGKNKPL ...String:
MRALPGLLEA RARTPRLLLL QCLLAAARPS SADGSAPDSP FTSPPLREEI MANNFSLESH NISLTEHSSM PVEKNITLER PSNVNLTCQ FTTSGDLNAV NVTWKKDGEQ LENNYLVSAT GSTLYTQYRF TIINSKQMGS YSCFFREEKE QRGTFNFKVP E LHGKNKPL ISYVGDSTVL TCKCQNCFPL NWTWYSSNGS VKVPVGVQMN KYVINGTYAN ETKLKITQLL EEDGESYWCR AL FQLGESE EHIELVVLSY LVPLKPFLVI VAEVILLVAT ILLCEKYTQK KKKHSDEGKE FEQIEQLKSD DSNGIENNVP RHR KNESLG Q

UniProtKB: Embigin

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Macromolecule #2: Monocarboxylate transporter 1

MacromoleculeName: Monocarboxylate transporter 1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 55.098012 KDa
Recombinant expressionOrganism: Insecta environmental sample (insect)
SequenceString: MPPAVGGPVG YTPPDGGWGW AVVIGAFISI GFSYAFPKSI TVFFKEIEGI FHATTSEVSW ISSIMLAVMY GGGPISSILV NKYGSRIVM IVGGCLSGCG LIAASFCNTV QQLYVCIGVI GGLGLAFNLN PALTMIGKYF YKRRPLANGL AMAGSPVFLC T LAPLNQVF ...String:
MPPAVGGPVG YTPPDGGWGW AVVIGAFISI GFSYAFPKSI TVFFKEIEGI FHATTSEVSW ISSIMLAVMY GGGPISSILV NKYGSRIVM IVGGCLSGCG LIAASFCNTV QQLYVCIGVI GGLGLAFNLN PALTMIGKYF YKRRPLANGL AMAGSPVFLC T LAPLNQVF FGIFGWRGSF LILGGLLLNC CVAGALMRPI GPKPTKAGKD KSKASLEKAG KSGVKKDLHD ANTDLIGRHP KQ EKRSVFQ TINQFLDLTL FTHRGFLLYL SGNVIMFFGL FAPLVFLSSY GKSQHYSSEK SAFLLSILAF VDMVARPSMG LVA NTKPIR PRIQYFFAAS VVANGVCHML APLSTTYVGF CVYAGFFGFA FGWLSSVLFE TLMDLVGPQR FSSAVGLVTI VECC PVLLG PPLLGRLNDM YGDYKYTYWA CGVVLIISGI YLFIGMGINY RLLAKEQKAN EQKKESKEEE TSIDVAGKPN EVTKA AESP DQKDTDGGPK EEESPVHHHH HHHH

UniProtKB: Monocarboxylate transporter 1

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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

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: 57.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.2 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.63 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 97000
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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