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- PDB-7yr5: Embigin facilitates monocarboxylate transporter 1 localization to... -

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Basic information

Entry
Database: PDB / ID: 7yr5
TitleEmbigin facilitates monocarboxylate transporter 1 localization to plasma membrane and transition to a decoupling state
Components
  • Embigin
  • Monocarboxylate transporter 1
KeywordsMEMBRANE PROTEIN / MCT1 / embigin
Function / homology
Function and homology information


mevalonate transmembrane transporter activity / mevalonate transport / plasma membrane lactate transport / behavioral response to nutrient / pyruvate transmembrane transport / monocarboxylic acid transmembrane transporter activity / 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 / plasma membrane lactate transport / behavioral response to nutrient / pyruvate transmembrane transport / monocarboxylic acid transmembrane transporter activity / 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 / pyruvate catabolic process / succinate transmembrane transporter activity / dendrite self-avoidance / cell-cell adhesion mediator activity / carboxylic acid transmembrane transport / carboxylic acid transmembrane transporter activity / organic cyclic compound binding / Pyruvate metabolism / anchoring junction / centrosome cycle / Basigin interactions / response to food / Aspirin ADME / homophilic cell adhesion via plasma membrane adhesion molecules / plasma membrane => GO:0005886 / regulation of insulin secretion / transport across blood-brain barrier / cellular response to organic cyclic compound / lateral plasma membrane / basal plasma membrane / axon guidance / lipid metabolic process / glucose homeostasis / cell junction / basolateral plasma membrane / apical plasma membrane / axon / intracellular membrane-bounded organelle / centrosome / synapse / extracellular exosome / membrane / identical protein binding / plasma membrane
Similarity search - Function
Embigin / Monocarboxylate transporter / Basigin-like / Major facilitator superfamily / Major Facilitator Superfamily / Major facilitator superfamily domain / Major facilitator superfamily (MFS) profile. / MFS transporter superfamily / Immunoglobulin / Immunoglobulin domain ...Embigin / Monocarboxylate transporter / Basigin-like / Major facilitator superfamily / Major Facilitator Superfamily / Major facilitator superfamily domain / Major facilitator superfamily (MFS) profile. / MFS transporter superfamily / Immunoglobulin / Immunoglobulin domain / 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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.63 Å
AuthorsXu, B. / Ye, S.
Funding support China, 1items
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, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 28, 2022Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Embigin
A: Monocarboxylate transporter 1


Theoretical massNumber of molelcules
Total (without water)92,0202
Polymers92,0202
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area1700 Å2
ΔGint-17 kcal/mol
Surface area29720 Å2

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Components

#1: Protein Embigin


Mass: 36921.844 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EMB / Production host: Insecta environmental sample (insect) / References: UniProt: Q6PCB8
#2: Protein Monocarboxylate transporter 1 / / MCT 1 / Solute carrier family 16 member 1


Mass: 55098.012 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SLC16A1, MCT1 / Production host: Insecta environmental sample (insect) / References: UniProt: P53985

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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: MCT1-embigin / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Insecta environmental sample (insect)
Buffer solutionpH: 8
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: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 1200 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 57 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

Software
NameVersionClassificationNB
phenix.real_space_refine1.20.1_4487refinement
PHENIX1.20.1_4487refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.63 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 97000 / Symmetry type: POINT
RefinementCross valid method: NONE

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