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- PDB-7bp3: Cryo-EM structure of the human MCT2 -

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Basic information

Entry
Database: PDB / ID: 7bp3
TitleCryo-EM structure of the human MCT2
ComponentsMonocarboxylate transporter 2
KeywordsTRANSPORT PROTEIN / Monocarboxylate transporter 2 / Major facilitator superfamily / Cooperative transport
Function / homology
Function and homology information


pyruvate secondary active transmembrane transporter activity / pyruvate transmembrane transporter activity / lactate transmembrane transport / pyruvate transmembrane transport / monocarboxylic acid transmembrane transporter activity / lactate transmembrane transporter activity / monocarboxylic acid transport / Proton-coupled monocarboxylate transport / symporter activity / plasma membrane => GO:0005886 ...pyruvate secondary active transmembrane transporter activity / pyruvate transmembrane transporter activity / lactate transmembrane transport / pyruvate transmembrane transport / monocarboxylic acid transmembrane transporter activity / lactate transmembrane transporter activity / monocarboxylic acid transport / Proton-coupled monocarboxylate transport / symporter activity / plasma membrane => GO:0005886 / transport across blood-brain barrier / membrane => GO:0016020 / nucleoplasm / plasma membrane
Similarity search - Function
Monocarboxylate transporter 2 / Monocarboxylate transporter / Major facilitator superfamily / Major Facilitator Superfamily / Major facilitator superfamily domain / Major facilitator superfamily (MFS) profile. / MFS transporter superfamily
Similarity search - Domain/homology
Monocarboxylate transporter 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsZhang, B. / Jin, Q. / Zhang, X. / Guo, J. / Ye, S.
CitationJournal: Nat Commun / Year: 2020
Title: Cooperative transport mechanism of human monocarboxylate transporter 2.
Authors: Bo Zhang / Qiuheng Jin / Lizhen Xu / Ningning Li / Ying Meng / Shenghai Chang / Xiang Zheng / Jiangqin Wang / Yuan Chen / Dante Neculai / Ning Gao / Xiaokang Zhang / Fan Yang / Jiangtao Guo / Sheng Ye /
Abstract: Proton-linked monocarboxylate transporters (MCTs) must transport monocarboxylate efficiently to facilitate monocarboxylate efflux in glycolytically active cells, and transport monocarboxylate slowly ...Proton-linked monocarboxylate transporters (MCTs) must transport monocarboxylate efficiently to facilitate monocarboxylate efflux in glycolytically active cells, and transport monocarboxylate slowly or even shut down to maintain a physiological monocarboxylate concentration in glycolytically inactive cells. To discover how MCTs solve this fundamental aspect of intracellular monocarboxylate homeostasis in the context of multicellular organisms, we analyzed pyruvate transport activity of human monocarboxylate transporter 2 (MCT2). Here we show that MCT2 transport activity exhibits steep dependence on substrate concentration. This property allows MCTs to turn on almost like a switch, which is physiologically crucial to the operation of MCTs in the cellular context. We further determined the cryo-electron microscopy structure of the human MCT2, demonstrating that the concentration sensitivity of MCT2 arises from the strong inter-subunit cooperativity of the MCT2 dimer during transport. These data establish definitively a clear example of evolutionary optimization of protein function.
History
DepositionMar 21, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 3, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Assembly

Deposited unit
A: Monocarboxylate transporter 2
B: Monocarboxylate transporter 2


Theoretical massNumber of molelcules
Total (without water)107,8392
Polymers107,8392
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area5080 Å2
ΔGint-54 kcal/mol
Surface area33690 Å2

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Components

#1: Protein Monocarboxylate transporter 2 / / MCT 2 / Solute carrier family 16 member 7


Mass: 53919.707 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SLC16A7, MCT2 / Cell line (production host): HEK293F / Production host: Homo sapiens (human) / References: UniProt: O60669

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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: Monocarboxylate transporter 2 / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.5
Buffer component
IDConc.NameFormulaBuffer-ID
150 mM4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid4-(2-Hydroxyethyl)-1-piperazineethanesulfonic acidHEPES1
2150 mMsodium chlorideNaClSodium chloride1
SpecimenConc.: 4 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K / Details: blot for 4 seconds 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: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingAverage exposure time: 0.25 sec. / Electron dose: 82 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)
Image scansMovie frames/image: 32

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Processing

EM software
IDNameVersionCategory
1RELION3particle selection
4RELION3CTF correction
7Coot0.89model fitting
9PHENIX1.14model refinement
13cryoSPARC23D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 302904
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 100909 / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL / Space: REAL

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