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- PDB-7y1b: 3.2 angstrom cryo-EM structure of extracellular region of mouse B... -

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Basic information

Entry
Database: PDB / ID: 7y1b
Title3.2 angstrom cryo-EM structure of extracellular region of mouse Basigin-2 in complex with the Fab fragment of antibody 6E7F1
Components
  • Heavy chain of 6E7F1
  • Isoform 2 of Basigin
  • Light chain of 6E7F1
KeywordsTRANSPORT PROTEIN / Transporter / glucose metabolism / monocarboxylic acid transport / alpha helical TMs
Function / homology
Function and homology information


Proton-coupled monocarboxylate transport / Aspirin ADME / Basigin interactions / acrosomal membrane / Degradation of the extracellular matrix / Integrin cell surface interactions / endothelial tube morphogenesis / response to mercury ion / neural retina development / photoreceptor cell maintenance ...Proton-coupled monocarboxylate transport / Aspirin ADME / Basigin interactions / acrosomal membrane / Degradation of the extracellular matrix / Integrin cell surface interactions / endothelial tube morphogenesis / response to mercury ion / neural retina development / photoreceptor cell maintenance / D-mannose binding / odontogenesis of dentin-containing tooth / decidualization / positive regulation of vascular endothelial growth factor production / response to cAMP / photoreceptor outer segment / neutrophil chemotaxis / photoreceptor inner segment / embryo implantation / positive regulation of endothelial cell migration / protein localization to plasma membrane / response to peptide hormone / sarcolemma / signaling receptor activity / angiogenesis / spermatogenesis / basolateral plasma membrane / cell differentiation / endoplasmic reticulum membrane / plasma membrane
Similarity search - Function
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
Biological speciesMus musculus (house mouse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.23 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
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 1.1Oct 16, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Isoform 2 of Basigin
H: Heavy chain of 6E7F1
L: Light chain of 6E7F1


Theoretical massNumber of molelcules
Total (without water)80,9083
Polymers80,9083
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, The combination of electron microscopy and biochemical assay indicate that the Basigin has extensive interactions with its antibody 6E7F1
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: 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
#2: Antibody Heavy chain of 6E7F1


Mass: 25275.400 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Mus musculus (house mouse)
#3: Antibody Light chain of 6E7F1


Mass: 25924.785 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Mus musculus (house mouse)
Has protein modificationY

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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: 3.2 angstrom cryo-EM structure of extracellular region of mouse MCT1/Basigin-2 in complex with its monoclonal antibody 6E7F1
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.1 MDa / Experimental value: YES
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 pH7.5, 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 is monodisperse
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: 283 K / Details: blot for 3.5-4.5 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: SPOT SCAN
Electron lensMode: DIFFRACTION / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN
Image recordingAverage exposure time: 2.5 sec. / Electron dose: 75 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of real images: 2842
Image scansSampling size: 1.9 µm / Width: 1034 / Height: 1034 / Movie frames/image: 48

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Processing

EM software
IDNameVersionCategory
1cryoSPARC2.15particle selection
4cryoSPARC2.15CTF correction
7cryoSPARC2.15model fitting
9PHENIX1.19.2model refinement
10cryoSPARC2.15initial Euler assignment
11cryoSPARC2.15final Euler assignment
12cryoSPARC2.15classification
13cryoSPARC2.153D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 712923
3D reconstructionResolution: 3.23 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 106160 / Symmetry type: POINT
Atomic model buildingB value: 39.46 / Protocol: AB INITIO MODEL / Space: REAL / Target criteria: Correlation coefficient

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