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- PDB-7y1q: 5.0 angstrom cryo-EM structure of transmembrane regions of mouse ... -

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Basic information

Entry
Database: PDB / ID: 7y1q
Title5.0 angstrom cryo-EM structure of transmembrane regions of mouse Basigin/MCT1 in complex with antibody 6E7F1
Components
  • Isoform 2 of Basigin
  • Monocarboxylate transporter 1
KeywordsTRANSPORT PROTEIN / Transporter / glucose metabolism / monocarboxylic acid transport / alpha helical TMs
Function / homology
Function and homology information


Proton-coupled monocarboxylate transport / Aspirin ADME / behavioral response to nutrient / plasma membrane lactate transport / pyruvate transmembrane transport / lactate transmembrane transporter activity / lactate:proton symporter activity / Basigin interactions / solute:proton symporter activity / pyruvate catabolic process ...Proton-coupled monocarboxylate transport / Aspirin ADME / behavioral response to nutrient / plasma membrane lactate transport / pyruvate transmembrane transport / lactate transmembrane transporter activity / lactate:proton symporter activity / Basigin interactions / solute:proton symporter activity / pyruvate catabolic process / succinate transmembrane transporter activity / acrosomal membrane / Degradation of the extracellular matrix / Integrin cell surface interactions / response to mercury ion / endothelial tube morphogenesis / : / neural retina development / photoreceptor cell maintenance / centrosome cycle / response to food / D-mannose binding / odontogenesis of dentin-containing tooth / : / decidualization / positive regulation of vascular endothelial growth factor production / photoreceptor outer segment / lateral plasma membrane / response to cAMP / photoreceptor inner segment / neutrophil chemotaxis / positive regulation of endothelial cell migration / embryo implantation / regulation of insulin secretion / protein localization to plasma membrane / sarcolemma / lipid metabolic process / response to peptide hormone / glucose homeostasis / signaling receptor activity / basolateral plasma membrane / angiogenesis / spermatogenesis / cell differentiation / apical plasma membrane / synapse / centrosome / endoplasmic reticulum membrane / mitochondrion / identical protein binding / plasma membrane
Similarity search - Function
Monocarboxylate transporter / : / Major facilitator superfamily / Major Facilitator Superfamily / Major facilitator superfamily domain / Major facilitator superfamily (MFS) profile. / Immunoglobulin domain / MFS transporter superfamily / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type ...Monocarboxylate transporter / : / Major facilitator superfamily / Major Facilitator Superfamily / Major facilitator superfamily domain / Major facilitator superfamily (MFS) profile. / Immunoglobulin domain / MFS transporter superfamily / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Basigin / Monocarboxylate transporter 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 5.03 Å
AuthorsZhang, H. / Yang, X. / Xue, Y. / Huang, Y. / Mo, X. / Zhang, H. / Li, N. / Gao, N. / Li, X. / Wang, S. ...Zhang, H. / Yang, X. / Xue, Y. / Huang, Y. / Mo, X. / Zhang, H. / Li, N. / Gao, N. / Li, X. / Wang, S. / Gao, Y. / Liao, J.
Funding support China, 2items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2017YFA0504800 China
Ministry of Science and Technology (MoST, China)2018ZX09711003-003-003 China
CitationJournal: To Be Published
Title: Allosteric modulation of monocarboxylate transporters 1 and 4 by targeting their chaperon Basigin-2
Authors: Zhang, H. / Yang, X. / Xue, Y. / Huang, Y. / Mo, Y. / Zhang, H. / Li, N. / Gao, N. / Li, X. / Wang, S. / Gao, Y. / Liao, J.
History
DepositionJun 8, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 14, 2023Provider: repository / Type: Initial release
Revision 1.1Jul 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_3d_fitting_list / em_admin
Item: _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id ..._em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Monocarboxylate transporter 1
B: Isoform 2 of Basigin


Theoretical massNumber of molelcules
Total (without water)83,0162
Polymers83,0162
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, The combination of cryo-EM study and biochemical assays indicate that the transmembrane portion of Basigin tightly binds monocarboxylate transporter 1
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Monocarboxylate transporter 1 / MCT 1 / Solute carrier family 16 member 1


Mass: 53308.883 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Slc16a1, Mct1 / Production host: Homo sapiens (human) / References: UniProt: P53986
#2: Protein Isoform 2 of Basigin / Basic immunoglobulin superfamily / HT7 antigen / Membrane glycoprotein gp42


Mass: 29707.447 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Bsg / Production host: Homo sapiens (human) / References: UniProt: P18572

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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: Ternary complex of transmembrane regions of Basigin with monocarboxylate transporter 1
Type: COMPLEX
Details: Ternary complex of transmembrane regions of Basigin with monocarboxylate transporter 1, extracellular region of Basigin is missed due to high flexibility
Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.1 MDa / Experimental value: NO
Source (natural)Organism: Mus musculus (house mouse)
Source (recombinant)Organism: Homo sapiens (human) / Cell: HEK293S / Plasmid: pEG BacMam
Buffer solutionpH: 7.5 / Details: 20 mM HEPES pH 7.5, 150 mM NaCl
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMHEPES pH 7.5HEPES1
2150 mMNaClNaCl1
SpecimenConc.: 0.7 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: This sample was monodisperse
Specimen supportGrid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: C-flat-1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 283 K / Details: blot for 3.5-4.5 s before plunging

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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: SPOT SCAN
Electron lensMode: DIFFRACTION / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm
Image recordingAverage exposure time: 2.5215 sec. / Electron dose: 1.56 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 5895
Image scansWidth: 1034 / Height: 1034 / Movie frames/image: 48 / Used frames/image: 1-48

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Processing

EM software
IDNameVersionCategoryDetails
1cryoSPARCv3.3.2particle selectionBlob picker
2SerialEMSerialEM Version 3.8.0 betaimage acquisition
4cryoSPARCv3.3.2CTF correctionPatch CTF estimation (multi)
7cryoSPARC2.15model fittingThe beta carbons of both model were generated and fitted to maps
9PHENIX1.19.2model refinementreal space refinement on TM regions
10cryoSPARCv3.3.2initial Euler assignment2D classification
11cryoSPARCv3.3.2final Euler assignment2D classification
12cryoSPARCv3.3.2classification
13cryoSPARCv3.3.23D reconstruction
Image processingDetails: raw image processed by patch motion.
CTF correctionDetails: Movies CTF amplitude correction was performed by patch CTF.
Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 1610675
Details: Minimum particle diameter (A) 120 Maximum particle diameter (A) 140 Lowpass filter to apply (A) 10 Circular blob
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 5.03 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 129990 / Symmetry type: POINT
Atomic model buildingB value: 53.6 / Protocol: BACKBONE TRACE / Space: REAL / Target criteria: Correlation coefficient
Details: The transmembrane regions of human MCT1 and Basigin-2 were first generated, with side chain of each residue truncated into beta carbon atom. The the model was initial fitted using chimera ...Details: The transmembrane regions of human MCT1 and Basigin-2 were first generated, with side chain of each residue truncated into beta carbon atom. The the model was initial fitted using chimera and then phenix was used for flexible fitting.
Atomic model building

3D fitting-ID: 1 / Accession code: 6LZ0 / Initial refinement model-ID: 1 / PDB-ID: 6LZ0

6lz0

/ Source name: PDB / Type: experimental model

IDPdb chain-IDPdb chain residue range
1A16-442
2B206-242

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