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- EMDB-30143: Cryo-EM structure of the human MCT2 -

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Basic information

Entry
Database: EMDB / ID: EMD-30143
TitleCryo-EM structure of the human MCT2
Map data
Sample
  • Complex: Monocarboxylate transporter 2
    • Protein or peptide: Monocarboxylate transporter 2
KeywordsMonocarboxylate transporter 2 / Major facilitator superfamily / Cooperative transport / TRANSPORT PROTEIN
Function / homology
Function and homology information


pyruvate secondary active transmembrane transporter activity / lactate transmembrane transport / plasma membrane lactate transport / pyruvate transmembrane transport / lactate transmembrane transporter activity / Proton-coupled monocarboxylate transport / pyruvate transmembrane transporter activity / symporter activity / parallel fiber to Purkinje cell synapse / transport across blood-brain barrier ...pyruvate secondary active transmembrane transporter activity / lactate transmembrane transport / plasma membrane lactate transport / pyruvate transmembrane transport / lactate transmembrane transporter activity / Proton-coupled monocarboxylate transport / pyruvate transmembrane transporter activity / symporter activity / parallel fiber to Purkinje cell synapse / transport across blood-brain barrier / hippocampal mossy fiber to CA3 synapse / postsynaptic density membrane / Schaffer collateral - CA1 synapse / basolateral plasma membrane / glutamatergic synapse / nucleoplasm / identical protein binding / plasma membrane / cytosol
Similarity search - Function
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsZhang B / Jin Q
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, 2020-
Header (metadata) releaseJun 3, 2020-
Map releaseJun 3, 2020-
UpdateMar 27, 2024-
Current statusMar 27, 2024Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.6
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.6
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7bp3
  • Surface level: 0.6
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7bp3
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_30143.png

Downloads & links

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Map

FileDownload / File: emd_30143.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 240 pix.
= 198.84 Å		0.83 Å/pix.
x 240 pix.
= 198.84 Å		0.83 Å/pix.
x 240 pix.
= 198.84 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8285 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.542 / Movie #1: 0.6
Minimum - Maximum-1.1734607 - 2.435834
Average (Standard dev.)0.021242067 (±0.10375611)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 198.84 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.82850.82850.8285
M x/y/z240240240
origin x/y/z0.0000.0000.000
length x/y/z198.840198.840198.840
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS240240240
D min/max/mean-1.1732.4360.021

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Supplemental data

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Sample components

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Entire : Monocarboxylate transporter 2

EntireName: Monocarboxylate transporter 2
Components
  • Complex: Monocarboxylate transporter 2
    • Protein or peptide: Monocarboxylate transporter 2

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Supramolecule #1: Monocarboxylate transporter 2

SupramoleculeName: Monocarboxylate transporter 2 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Monocarboxylate transporter 2

MacromoleculeName: Monocarboxylate transporter 2 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 53.919707 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MPPMPSAPPV HPPPDGGWGW IVVGAAFISI GFSYAFPKAV TVFFKEIQQI FHTTYSEIAW ISSIMLAVMY AGGPVSSVLV NKYGSRPVV IAGGLLCCLG MVLASFSSSV VQLYLTMGFI TGLGLAFNLQ PALTIIGKYF YRKRPMANGL AMAGSPVFLS S LAPFNQYL ...String:
MPPMPSAPPV HPPPDGGWGW IVVGAAFISI GFSYAFPKAV TVFFKEIQQI FHTTYSEIAW ISSIMLAVMY AGGPVSSVLV NKYGSRPVV IAGGLLCCLG MVLASFSSSV VQLYLTMGFI TGLGLAFNLQ PALTIIGKYF YRKRPMANGL AMAGSPVFLS S LAPFNQYL FNTFGWKGSF LILGSLLLNA CVAGSLMRPL GPNQTTSKSK NKTGKTEDDS SPKKIKTKKS TWEKVNKYLD FS LFKHRGF LIYLSGNVIM FLGFFAPIIF LAPYAKDQGI DEYSAAFLLS VMAFVDMFAR PSVGLIANSK YIRPRIQYFF SFA IMFNGV CHLLCPLAQD YTSLVLYAVF FGLGFGSVSS VLFETLMDLV GAPRFSSAVG LVTIVECGPV LLGPPLAGKL VDLT GEYKY MYMSCGAIVV AASVWLLIGN AINYRLLAKE RKEENARQKT RESEPLSKSK HSEDVNVKVS NAQSVTSERE TNIVE GGSS GGWSHPQFEK

UniProtKB: Monocarboxylate transporter 2

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration4 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
50.0 mMHEPES4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid4-(2-Hydroxyethyl)-1-piperazineethanesulfonic acid
150.0 mMNaClsodium chloride
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 150 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: blot for 4 seconds before plunging.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average exposure time: 0.25 sec. / Average electron dose: 82.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 302904
Startup modelType of model: NONE
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 2.0) / Number images used: 100909
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
Final 3D classificationNumber classes: 4 / Avg.num./class: 72810

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

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

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