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- EMDB-33559: 3.2 angstrom cryo-EM structure of extracellular region of mouse B... -

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Basic information

Entry
Database: EMDB / ID: EMD-33559
Title3.2 angstrom cryo-EM structure of extracellular region of mouse Basigin-2 in complex with the Fab fragment of antibody 6E7F1
Map datamain map
Sample
  • Complex: 3.2 angstrom cryo-EM structure of extracellular region of mouse MCT1/Basigin-2 in complex with its monoclonal antibody 6E7F1
    • Protein or peptide: Isoform 2 of Basigin
    • Protein or peptide: Heavy chain of 6E7F1
    • Protein or peptide: Light chain of 6E7F1
KeywordsTransporter / glucose metabolism / monocarboxylic acid transport / alpha helical TMs / TRANSPORT PROTEIN
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 / response to mercury ion / endothelial tube morphogenesis / 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 / response to mercury ion / endothelial tube morphogenesis / neural retina development / photoreceptor cell maintenance / odontogenesis of dentin-containing tooth / D-mannose binding / decidualization / positive regulation of vascular endothelial growth factor production / photoreceptor outer segment / response to cAMP / neutrophil chemotaxis / embryo implantation / photoreceptor inner segment / positive regulation of endothelial cell migration / protein localization to plasma membrane / sarcolemma / response to peptide hormone / signaling receptor activity / spermatogenesis / basolateral plasma membrane / angiogenesis / 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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.23 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
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-
UpdateOct 16, 2024-
Current statusOct 16, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_33559.png

Downloads & links

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Map

FileDownload / File: emd_33559.map.gz / Format: CCP4 / Size: 125 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.)
0.84 Å/pix.
x 320 pix.
= 268.8 Å		0.84 Å/pix.
x 320 pix.
= 268.8 Å		0.84 Å/pix.
x 320 pix.
= 268.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.84 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.18
Minimum - Maximum-0.81496453 - 1.2838789
Average (Standard dev.)-0.00029742208 (±0.027122159)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 268.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_33559_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_33559_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_33559_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 : 3.2 angstrom cryo-EM structure of extracellular region of mouse M...

EntireName: 3.2 angstrom cryo-EM structure of extracellular region of mouse MCT1/Basigin-2 in complex with its monoclonal antibody 6E7F1
Components
  • Complex: 3.2 angstrom cryo-EM structure of extracellular region of mouse MCT1/Basigin-2 in complex with its monoclonal antibody 6E7F1
    • Protein or peptide: Isoform 2 of Basigin
    • Protein or peptide: Heavy chain of 6E7F1
    • Protein or peptide: Light chain of 6E7F1

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Supramolecule #1: 3.2 angstrom cryo-EM structure of extracellular region of mouse M...

SupramoleculeName: 3.2 angstrom cryo-EM structure of extracellular region of mouse MCT1/Basigin-2 in complex with its monoclonal antibody 6E7F1
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 100 KDa

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Macromolecule #1: Isoform 2 of Basigin

MacromoleculeName: Isoform 2 of Basigin / type: protein_or_peptide / ID: 1 / 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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Macromolecule #2: Heavy chain of 6E7F1

MacromoleculeName: Heavy chain of 6E7F1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 25.2754 KDa
Recombinant expressionOrganism: Mus musculus (house mouse)
SequenceString: MGWSYIILFL VTTATGVHSQ VQLQQPGAEL VKPGASVNLS CKASGYTFTN YWIHWVKQRP GQGLEWIGMI HPNSGTINYN EKFKTKATL TVDKSSSTAY MQLSSLTSED SAVYYCARVG TGSLDYWGQG TSVTVSSAKT TAPSVYPLAP VCGDTTGSSV T LGCLVKGY ...String:
MGWSYIILFL VTTATGVHSQ VQLQQPGAEL VKPGASVNLS CKASGYTFTN YWIHWVKQRP GQGLEWIGMI HPNSGTINYN EKFKTKATL TVDKSSSTAY MQLSSLTSED SAVYYCARVG TGSLDYWGQG TSVTVSSAKT TAPSVYPLAP VCGDTTGSSV T LGCLVKGY FPEPVTLTWN SGSLSSGVHT FPAVLQSDLY TLSSSVTVTS STWPSQSITC NVAHPASSTK VDKKIEPR

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Macromolecule #3: Light chain of 6E7F1

MacromoleculeName: Light chain of 6E7F1 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 25.924785 KDa
Recombinant expressionOrganism: Mus musculus (house mouse)
SequenceString: MVSTSQLLGL LLFWTSASRC DIVMTQSPAT LSVTPGDRVS LSCRASQSIS DYLHWYQQKS HESPRLLIKY VSQSISGIPS RFSGSGSGS YFTLSIDSVE PEDVGVYYCQ NGHRFPYTFG GGTKLEIKRA DAAPTVSIFP PSSEQLTSGG ASVVCFLNNF Y PKDINVKW ...String:
MVSTSQLLGL LLFWTSASRC DIVMTQSPAT LSVTPGDRVS LSCRASQSIS DYLHWYQQKS HESPRLLIKY VSQSISGIPS RFSGSGSGS YFTLSIDSVE PEDVGVYYCQ NGHRFPYTFG GGTKLEIKRA DAAPTVSIFP PSSEQLTSGG ASVVCFLNNF Y PKDINVKW KIDGSERQNG VLNSWTDQDS KDSTYSMSST LTLTKDEYER HNSYTCEATH KTSTSPIVKS FNRNEC

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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 pH7.5, 150 mM NaCl
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 10
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 283 K / Instrument: FEI VITROBOT MARK IV / Details: blot for 3.5-4.5 seconds before plunging.
DetailsThis sample is 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 / Number real images: 2842 / Average exposure time: 2.5 sec. / Average electron dose: 75.0 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: 2.0 µm / Nominal defocus min: 1.0 µm
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 712923
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.23 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 2.15) / Number images used: 106160
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 2.15)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 2.15)
Final 3D classificationNumber classes: 200 / Software - Name: cryoSPARC (ver. 2.15)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL / Overall B value: 39.46 / Target criteria: Correlation coefficient
Output model

PDB-7y1b:
3.2 angstrom cryo-EM structure of extracellular region of mouse Basigin-2 in complex with the Fab fragment of antibody 6E7F1

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