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- EMDB-33570: 5.0 angstrom cryo-EM structure of transmembrane regions of mouse ... -

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Basic information

Entry
Database: EMDB / ID: EMD-33570
Title5.0 angstrom cryo-EM structure of transmembrane regions of mouse Basigin/MCT1 in complex with antibody 6E7F1
Map datamain map
Sample
  • Complex: Ternary complex of transmembrane regions of Basigin with monocarboxylate transporter 1
    • Protein or peptide: Monocarboxylate transporter 1
    • Protein or peptide: Isoform 2 of Basigin
KeywordsTransporter / glucose metabolism / monocarboxylic acid transport / alpha helical TMs / TRANSPORT PROTEIN
Function / homology
Function and homology information


Proton-coupled monocarboxylate transport / Aspirin ADME / lactate transmembrane transport / behavioral response to nutrient / monocarboxylic acid transmembrane transporter activity / plasma membrane lactate transport / pyruvate transmembrane transport / lactate transmembrane transporter activity / monocarboxylic acid transport / solute:proton symporter activity ...Proton-coupled monocarboxylate transport / Aspirin ADME / lactate transmembrane transport / behavioral response to nutrient / monocarboxylic acid transmembrane transporter activity / plasma membrane lactate transport / pyruvate transmembrane transport / lactate transmembrane transporter activity / monocarboxylic acid transport / solute:proton symporter activity / lactate:proton symporter activity / Basigin interactions / succinate transmembrane transporter activity / pyruvate catabolic process / carboxylic acid transmembrane transport / carboxylic acid transmembrane transporter activity / acrosomal membrane / Degradation of the extracellular matrix / Integrin cell surface interactions / organic cyclic compound binding / response to mercury ion / endothelial tube morphogenesis / neural retina development / photoreceptor cell maintenance / centrosome cycle / response to food / odontogenesis of dentin-containing tooth / D-mannose binding / cellular response to organic cyclic compound / decidualization / positive regulation of vascular endothelial growth factor production / photoreceptor outer segment / lateral plasma membrane / response to cAMP / neutrophil chemotaxis / embryo implantation / regulation of insulin secretion / photoreceptor inner segment / positive regulation of endothelial cell migration / protein localization to plasma membrane / lipid metabolic process / sarcolemma / response to peptide hormone / glucose homeostasis / signaling receptor activity / spermatogenesis / basolateral plasma membrane / angiogenesis / cell differentiation / apical plasma membrane / centrosome / synapse / 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. / MFS transporter superfamily / Immunoglobulin domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type ...Monocarboxylate transporter / : / Major facilitator superfamily / Major Facilitator Superfamily / Major facilitator superfamily domain / Major facilitator superfamily (MFS) profile. / MFS transporter superfamily / Immunoglobulin domain / 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)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.03 Å
AuthorsZhang H / Yang X / Xue Y / Huang Y / Mo X / Li N / Gao N / Li X / Wang S / Gao Y / Liao J
Funding support China, 2 items
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, 2022-
Header (metadata) releaseJun 14, 2023-
Map releaseJun 14, 2023-
UpdateJul 3, 2024-
Current statusJul 3, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_33570.png

Downloads & links

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Map

FileDownload / File: emd_33570.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationmain map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 240 pix.
= 196.8 Å		0.82 Å/pix.
x 240 pix.
= 196.8 Å		0.82 Å/pix.
x 240 pix.
= 196.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.82 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.08
Minimum - Maximum-0.12014297 - 0.40785548
Average (Standard dev.)0.0005005894 (±0.013233275)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 196.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_33570_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 1

Fileemd_33570_half_map_1.map
Annotationhalf map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 2

Fileemd_33570_half_map_2.map
Annotationhalf map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Ternary complex of transmembrane regions of Basigin with monocarb...

EntireName: Ternary complex of transmembrane regions of Basigin with monocarboxylate transporter 1
Components
  • Complex: Ternary complex of transmembrane regions of Basigin with monocarboxylate transporter 1
    • Protein or peptide: Monocarboxylate transporter 1
    • Protein or peptide: Isoform 2 of Basigin

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Supramolecule #1: Ternary complex of transmembrane regions of Basigin with monocarb...

SupramoleculeName: Ternary complex of transmembrane regions of Basigin with monocarboxylate transporter 1
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: Ternary complex of transmembrane regions of Basigin with monocarboxylate transporter 1, extracellular region of Basigin is missed due to high flexibility
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 100 KDa

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Macromolecule #1: Monocarboxylate transporter 1

MacromoleculeName: Monocarboxylate transporter 1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 53.308883 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MPPAIGGPVG YTPPDGGWGW AVLVGAFISI GFSYAFPKSI TVFFKEIEVI FSATTSEVSW ISSIMLAVMY AGGPISSILV NKYGSRPVM IAGGCLSGCG LIAASFCNTV QELYLCIGVI GGLGLAFNLN PALTMIGKYF YKKRPLANGL AMAGSPVFLS T LAPLNQAF ...String:
MPPAIGGPVG YTPPDGGWGW AVLVGAFISI GFSYAFPKSI TVFFKEIEVI FSATTSEVSW ISSIMLAVMY AGGPISSILV NKYGSRPVM IAGGCLSGCG LIAASFCNTV QELYLCIGVI GGLGLAFNLN PALTMIGKYF YKKRPLANGL AMAGSPVFLS T LAPLNQAF FDIFDWRGSF LILGGLLLNC CVAGSLMRPI GPEQVKLEKL KSKESLQEAG KSDANTDLIG GSPKGEKLSV FQ TINKFLD LSLFTHRGFL LYLSGNVVMF FGLFTPLVFL SSYGKSKDFS SEKSAFLLSI LAFVDMVARP SMGLAANTKW IRP RIQYFF AASVVANGVC HLLAPLSTTY VGFCVYAGVF GFAFGWLSSV LFETLMDLIG PQRFSSAVGL VTIVECCPVL LGPP LLGRL NDMYGDYKYT YWACGVILII AGIYLFIGMG INYRLLAKEQ KAEEKQKREG KEDEASTDVD EKPKETMKAA QSPQQ HSSG DPTEEESPV

UniProtKB: Monocarboxylate transporter 1

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Macromolecule #2: Isoform 2 of Basigin

MacromoleculeName: Isoform 2 of Basigin / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 29.707447 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MAAALLLALA FTLLSGQGAC AAAGTIQTSV QEVNSKTQLT CSLNSSGVDI VGHRWMRGGK VLQEDTLPDL HTKYIVDADD RSGEYSCIF LPEPVGRSEI NVEGPPRIKV GKKSEHSSEG ELAKLVCKSD ASYPPITDWF WFKTSDTGEE EAITNSTEAN G KYVVVSTP ...String:
MAAALLLALA FTLLSGQGAC AAAGTIQTSV QEVNSKTQLT CSLNSSGVDI VGHRWMRGGK VLQEDTLPDL HTKYIVDADD RSGEYSCIF LPEPVGRSEI NVEGPPRIKV GKKSEHSSEG ELAKLVCKSD ASYPPITDWF WFKTSDTGEE EAITNSTEAN G KYVVVSTP EKSQLTISNL DVNVDPGTYV CNATNAQGTT RETISLRVRS RMAALWPFLG IVAEVLVLVT IIFIYEKRRK PD QTLDEDD PGAAPLKGSG THMNDKDKNV RQRNAT

UniProtKB: Basigin

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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

Concentration0.7 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
20.0 mMHEPESHEPES pH 7.5
150.0 mMNaClNaCl

Details: 20 mM HEPES pH 7.5, 150 mM NaCl
GridModel: C-flat-1.2/1.3 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 1 / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: OTHER / Pretreatment - Pressure: 101.325 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 283 K / Instrument: FEI VITROBOT MARK IV / Details: blot for 3.5-4.5 s before plunging.
DetailsThis sample was monodisperse

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Dimensions - Width: 1034 pixel / Digitization - Dimensions - Height: 1034 pixel / Digitization - Frames/image: 1-48 / Number grids imaged: 1 / Number real images: 5895 / Average exposure time: 2.5215 sec. / Average electron dose: 1.56 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: DIFFRACTION / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Detailsraw image processed by patch motion.
Particle selectionNumber selected: 1610675
Details: Minimum particle diameter (A) 120 Maximum particle diameter (A) 140 Lowpass filter to apply (A) 10 Circular blob
Startup modelType of model: NONE / Details: No other models introduced.
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 5.03 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. v3.3.2) / Number images used: 129990
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. v3.3.2) / Software - details: 2D classification / Details: Maximum resolution 6A Number of 2D classes 200
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. v3.3.2) / Software - details: 2D classification
Final 3D classificationNumber classes: 200 / Software - Name: cryoSPARC (ver. v3.3.2)

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Atomic model buiding 1

Initial model
PDB IDChain

6lz0

chain_id: A, residue_range: 16-442, source_name: PDB, initial_model_type: experimental model

6lz0

chain_id: B, residue_range: 206-242, source_name: PDB, initial_model_type: experimental model
DetailsThe 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.
RefinementSpace: REAL / Protocol: BACKBONE TRACE / Overall B value: 53.6 / Target criteria: Correlation coefficient
Output model

PDB-7y1q:
5.0 angstrom cryo-EM structure of transmembrane regions of mouse Basigin/MCT1 in complex with antibody 6E7F1

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