[English] 日本語
Yorodumi
- EMDB-34046: Embigin facilitates monocarboxylate transporter 1 localization to... -

+
Open data


ID or keywords:

Loading...

-
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
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)
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-
UpdateSep 28, 2022-
Current statusSep 28, 2022Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_34046.png

Downloads & links

-
Map

FileDownload / File: emd_34046.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.84 Å
Density
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 °

-
Supplemental data

-
Half map: #1

Fileemd_34046_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_34046_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : MCT1-embigin

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

-
Supramolecule #1: MCT1-embigin

SupramoleculeName: MCT1-embigin / type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Insecta environmental sample (insect)

-
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

-
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

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 1.2 µm / Nominal defocus min: 0.8 µm
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 57.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.63 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 97000

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more