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Yorodumi- PDB-7y1q: 5.0 angstrom cryo-EM structure of transmembrane regions of mouse ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7y1q | |||||||||
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Title | 5.0 angstrom cryo-EM structure of transmembrane regions of mouse Basigin/MCT1 in complex with antibody 6E7F1 | |||||||||
Components |
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Keywords | TRANSPORT PROTEIN / Transporter / glucose metabolism / monocarboxylic acid transport / alpha helical TMs | |||||||||
Function / homology | Function and homology information lactate transmembrane transport / plasma membrane lactate transport / behavioral response to nutrient / pyruvate transmembrane transport / monocarboxylic acid transmembrane transporter activity / lactate transmembrane transporter activity / solute:proton symporter activity / monocarboxylic acid transport / lactate:proton symporter activity / succinate transmembrane transport ...lactate transmembrane transport / plasma membrane lactate transport / behavioral response to nutrient / pyruvate transmembrane transport / monocarboxylic acid transmembrane transporter activity / lactate transmembrane transporter activity / solute:proton symporter activity / monocarboxylic acid transport / lactate:proton symporter activity / succinate transmembrane transport / pyruvate catabolic process / succinate transmembrane transporter activity / positive regulation of matrix metallopeptidase secretion / acrosomal membrane / carboxylic acid transmembrane transport / carboxylic acid transmembrane transporter activity / response to mercury ion / organic cyclic compound binding / neural retina development / endothelial tube morphogenesis / photoreceptor cell maintenance / centrosome cycle / response to food / odontogenesis of dentin-containing tooth / mannose binding / regulation of insulin secretion / decidualization / cellular response to organic cyclic compound / photoreceptor outer segment / positive regulation of vascular endothelial growth factor production / lateral plasma membrane / embryo implantation / response to cAMP / photoreceptor inner segment / basal plasma membrane / neutrophil chemotaxis / positive regulation of endothelial cell migration / axon guidance / protein localization to plasma membrane / sarcolemma / lipid metabolic process / response to peptide hormone / positive regulation of interleukin-6 production / glucose homeostasis / virus receptor activity / signaling receptor activity / cell junction / spermatogenesis / basolateral plasma membrane / angiogenesis / positive regulation of viral entry into host cell / cell adhesion / endosome / membrane raft / apical plasma membrane / intracellular membrane-bounded organelle / centrosome / synapse / endoplasmic reticulum membrane / mitochondrion / identical protein binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Mus musculus (house mouse) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 5.03 Å | |||||||||
Authors | Zhang, 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
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Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7y1q.cif.gz | 71.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7y1q.ent.gz | 45 KB | Display | PDB format |
PDBx/mmJSON format | 7y1q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y1/7y1q ftp://data.pdbj.org/pub/pdb/validation_reports/y1/7y1q | HTTPS FTP |
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-Related structure data
Related structure data | 33570MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | 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 |
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#2: Protein | 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 |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: 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 | |||||||||||||||
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Molecular weight | Value: 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 solution | pH: 7.5 / Details: 20 mM HEPES pH 7.5, 150 mM NaCl | |||||||||||||||
Buffer component |
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Specimen | Conc.: 0.7 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: This sample was monodisperse | |||||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: C-flat-1.2/1.3 | |||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 283 K / Details: blot for 3.5-4.5 s before plunging |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN |
Electron lens | Mode: DIFFRACTION / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm |
Image recording | Average 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 scans | Width: 1034 / Height: 1034 / Movie frames/image: 48 / Used frames/image: 1-48 |
-Processing
EM software |
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Image processing | Details: raw image processed by patch motion. | ||||||||||||||||||||||||||||||||||||||||||||||||||
CTF correction | Details: Movies CTF amplitude correction was performed by patch CTF. Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 1610675 Details: Minimum particle diameter (A) 120 Maximum particle diameter (A) 140 Lowpass filter to apply (A) 10 Circular blob | ||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 5.03 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 129990 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | B 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 |
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