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Yorodumi- PDB-7yr5: Embigin facilitates monocarboxylate transporter 1 localization to... -
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-Basic information
Entry | Database: PDB / ID: 7yr5 | ||||||
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Title | Embigin facilitates monocarboxylate transporter 1 localization to plasma membrane and transition to a decoupling state | ||||||
Components |
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Keywords | MEMBRANE 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 / carboxylic acid transmembrane transport / carboxylic acid transmembrane transporter activity / dendrite self-avoidance / cell-cell adhesion mediator activity / organic cyclic compound binding / centrosome cycle / anchoring junction / Basigin interactions / response to food / Aspirin ADME / homophilic cell adhesion via plasma membrane adhesion molecules / plasma membrane => GO:0005886 / regulation of insulin secretion / cellular response to organic cyclic compound / transport across blood-brain barrier / lateral plasma membrane / 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 | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.63 Å | ||||||
Authors | Xu, B. / Ye, S. | ||||||
Funding support | China, 1items
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Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7yr5.cif.gz | 118.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7yr5.ent.gz | 90.6 KB | Display | PDB format |
PDBx/mmJSON format | 7yr5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7yr5_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 7yr5_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 7yr5_validation.xml.gz | 30.9 KB | Display | |
Data in CIF | 7yr5_validation.cif.gz | 42.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yr/7yr5 ftp://data.pdbj.org/pub/pdb/validation_reports/yr/7yr5 | HTTPS FTP |
-Related structure data
Related structure data | 34046MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | 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 |
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#2: Protein | 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 |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: MCT1-embigin / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Source (natural) | Organism: Homo sapiens (human) |
Source (recombinant) | Organism: Insecta environmental sample (insect) |
Buffer solution | pH: 8 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 1200 nm / Nominal defocus min: 800 nm |
Image recording | Electron dose: 57 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
Software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||
3D reconstruction | Resolution: 3.63 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 97000 / Symmetry type: POINT | ||||||||||||
Refinement | Cross valid method: NONE |