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Yorodumi- EMDB-25143: Structure of positive allosteric modulator-bound active human cal... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-25143 | |||||||||||||||||||||
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Title | Structure of positive allosteric modulator-bound active human calcium-sensing receptor | |||||||||||||||||||||
Map data | ||||||||||||||||||||||
Sample |
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Function / homology | Isoform 1 of Extracellular calcium-sensing receptor Function and homology information | |||||||||||||||||||||
Biological species | Homo sapiens (human) | |||||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.7 Å | |||||||||||||||||||||
Authors | Park J / Zuo H / Frangaj A / Fu Z / Yen LY / Zhang Z / Mosyak L / Slavkovich VN / Liu J / Ray KM ...Park J / Zuo H / Frangaj A / Fu Z / Yen LY / Zhang Z / Mosyak L / Slavkovich VN / Liu J / Ray KM / Cao B / Vallese F / Geng Y / Chen S / Grassucci R / Dandey VP / Tan YZ / Eng E / Lee Y / Kloss B / Liu Z / Hendrickson WA / Potter CS / Carragher B / Graziano J / Conigrave AD / Frank J / Clarke OB / Fan QR | |||||||||||||||||||||
Funding support | United States, 6 items
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Citation | Journal: Proc Natl Acad Sci U S A / Year: 2021 Title: Symmetric activation and modulation of the human calcium-sensing receptor. Authors: Jinseo Park / Hao Zuo / Aurel Frangaj / Ziao Fu / Laura Y Yen / Zhening Zhang / Lidia Mosyak / Vesna N Slavkovich / Jonathan Liu / Kimberly M Ray / Baohua Cao / Francesca Vallese / Yong Geng ...Authors: Jinseo Park / Hao Zuo / Aurel Frangaj / Ziao Fu / Laura Y Yen / Zhening Zhang / Lidia Mosyak / Vesna N Slavkovich / Jonathan Liu / Kimberly M Ray / Baohua Cao / Francesca Vallese / Yong Geng / Shaoxia Chen / Robert Grassucci / Venkata P Dandey / Yong Zi Tan / Edward Eng / Yeji Lee / Brian Kloss / Zheng Liu / Wayne A Hendrickson / Clinton S Potter / Bridget Carragher / Joseph Graziano / Arthur D Conigrave / Joachim Frank / Oliver B Clarke / Qing R Fan / Abstract: The human extracellular calcium-sensing (CaS) receptor controls plasma Ca levels and contributes to nutrient-dependent maintenance and metabolism of diverse organs. Allosteric modulation of the CaS ...The human extracellular calcium-sensing (CaS) receptor controls plasma Ca levels and contributes to nutrient-dependent maintenance and metabolism of diverse organs. Allosteric modulation of the CaS receptor corrects disorders of calcium homeostasis. Here, we report the cryogenic-electron microscopy reconstructions of a near-full-length CaS receptor in the absence and presence of allosteric modulators. Activation of the homodimeric CaS receptor requires a break in the transmembrane 6 (TM6) helix of each subunit, which facilitates the formation of a TM6-mediated homodimer interface and expansion of homodimer interactions. This transformation in TM6 occurs without a positive allosteric modulator. Two modulators with opposite functional roles bind to overlapping sites within the transmembrane domain through common interactions, acting to stabilize distinct rotamer conformations of key residues on the TM6 helix. The positive modulator reinforces TM6 distortion and maximizes subunit contact to enhance receptor activity, while the negative modulator strengthens an intact TM6 to dampen receptor function. In both active and inactive states, the receptor displays symmetrical transmembrane conformations that are consistent with its homodimeric assembly. | |||||||||||||||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_25143.map.gz | 8.2 MB | EMDB map data format | |
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Header (meta data) | emd-25143-v30.xml emd-25143.xml | 23 KB 23 KB | Display Display | EMDB header |
Images | emd_25143.png | 117.1 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-25143 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-25143 | HTTPS FTP |
-Validation report
Summary document | emd_25143_validation.pdf.gz | 349.5 KB | Display | EMDB validaton report |
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Full document | emd_25143_full_validation.pdf.gz | 349.1 KB | Display | |
Data in XML | emd_25143_validation.xml.gz | 4.2 KB | Display | |
Data in CIF | emd_25143_validation.cif.gz | 4.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-25143 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-25143 | HTTPS FTP |
-Related structure data
Related structure data | 7silMC 7simC 7sinC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | |
EM raw data | EMPIAR-10834 (Title: Structures of positive allosteric modulator-bound and unbound active human calcium-sensing receptor Data size: 3.8 TB Data #1: Unaligned multi-frame micrographs of calcium-sensing receptor in both PAM-bound and unbound active states [micrographs - multiframe]) |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_25143.map.gz / Format: CCP4 / Size: 16 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 0.83 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Homodimer human calcium sensing receptor
Entire | Name: Homodimer human calcium sensing receptor |
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Components |
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-Supramolecule #1: Homodimer human calcium sensing receptor
Supramolecule | Name: Homodimer human calcium sensing receptor / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Homo sapiens (human) / Recombinant cell: HEK 293 GnTl- / Recombinant plasmid: modified bacMam |
Molecular weight | Theoretical: 192 KDa |
-Macromolecule #1: Isoform 1 of Extracellular calcium-sensing receptor
Macromolecule | Name: Isoform 1 of Extracellular calcium-sensing receptor / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 99.299461 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MAFYSCCWVL LALTWHTSAY GPDQRAQKKG DIILGGLFPI HFGVAAKDQD LKSRPESVEC IRYNFRGFRW LQAMIFAIEE INSSPALLP NLTLGYRIFD TCNTVSKALE ATLSFVAQNK IDSLNLDEFC NCSEHIPSTI AVVGATGSGV STAVANLLGL F YIPQVSYA ...String: MAFYSCCWVL LALTWHTSAY GPDQRAQKKG DIILGGLFPI HFGVAAKDQD LKSRPESVEC IRYNFRGFRW LQAMIFAIEE INSSPALLP NLTLGYRIFD TCNTVSKALE ATLSFVAQNK IDSLNLDEFC NCSEHIPSTI AVVGATGSGV STAVANLLGL F YIPQVSYA SSSRLLSNKN QFKSFLRTIP NDEHQATAMA DIIEYFRWNW VGTIAADDDY GRPGIEKFRE EAEERDICID FS ELISQYS DEEEIQHVVE VIQNSTAKVI VVFSSGPDLE PLIKEIVRRN ITGKIWLASE AWASSSLIAM PQYFHVVGGT IGF ALKAGQ IPGFREFLKK VHPRKSVHNG FAKEFWEETF NCHLQEGAKG PLPVDTFLRG HEESGDRFSN SSTAFRPLCT GDEN ISSVE TPYIDYTHLR ISYNVYLAVY SIAHALQDIY TCLPGRGLFT NGSCADIKKV EAWQVLKHLR HLNFTNNMGE QVTFD ECGD LVGNYSIINW HLSPEDGSIV FKEVGYYNVY AKKGERLFIN EEKILWSGFS REVPFSNCSR DCLAGTRKGI IEGEPT CCF ECVECPDGEY SDETDASACN KCPDDFWSNE NHTSCIAKEI EFLSWTEPFG IALTLFAVLG IFLTAFVLGV FIKFRNT PI VKATNRELSY LLLFSLLCCF SSSLFFIGEP QDWTCRLRQP AFGISFVLCI SCILVKTNRV LLVFEAKIPT SFHRKWWG L NLQFLLVFLC TFMQIVICVI WLYTAPPSSY RNQELEDEII FITCHEGSLM ALGFLIGYTC LLAAICFFFA FKSRKLPEN FNEAKFITFS MLIFFIVWIS FIPAYASTYG KFVSAVEVIA ILAASFGLLA CIFFNKIYII LFKPSRNTIE DYKDDDDK |
-Macromolecule #3: 2-acetamido-2-deoxy-beta-D-glucopyranose
Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 3 / Number of copies: 6 / Formula: NAG |
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Molecular weight | Theoretical: 221.208 Da |
Chemical component information | ChemComp-NAG: |
-Macromolecule #4: CYCLOMETHYLTRYPTOPHAN
Macromolecule | Name: CYCLOMETHYLTRYPTOPHAN / type: ligand / ID: 4 / Number of copies: 2 / Formula: TCR |
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Molecular weight | Theoretical: 216.236 Da |
Chemical component information | ChemComp-TCR: |
-Macromolecule #5: PHOSPHATE ION
Macromolecule | Name: PHOSPHATE ION / type: ligand / ID: 5 / Number of copies: 2 / Formula: PO4 |
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Molecular weight | Theoretical: 94.971 Da |
Chemical component information | ChemComp-PO4: |
-Macromolecule #6: CALCIUM ION
Macromolecule | Name: CALCIUM ION / type: ligand / ID: 6 / Number of copies: 8 / Formula: CA |
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Molecular weight | Theoretical: 40.078 Da |
-Macromolecule #7: 3-(2-chlorophenyl)-N-[(1R)-1-(3-methoxyphenyl)ethyl]propan-1-amine
Macromolecule | Name: 3-(2-chlorophenyl)-N-[(1R)-1-(3-methoxyphenyl)ethyl]propan-1-amine type: ligand / ID: 7 / Number of copies: 2 / Formula: 9IG |
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Molecular weight | Theoretical: 303.826 Da |
Chemical component information | ChemComp-9IG: |
-Macromolecule #8: CHOLESTEROL
Macromolecule | Name: CHOLESTEROL / type: ligand / ID: 8 / Number of copies: 8 / Formula: CLR |
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Molecular weight | Theoretical: 386.654 Da |
Chemical component information | ChemComp-CLR: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 2.6 mg/mL | ||||||||||||||||||||||||
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Buffer | pH: 7.5 Component:
Details: Solution were made fresh from concentrated, and filtered to avoid microbial contamination. | ||||||||||||||||||||||||
Grid | Model: Quantifoil R0.6/1 / Material: GOLD / Mesh: 300 / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Atmosphere: OTHER | ||||||||||||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: blot for 4 seconds before plunging. | ||||||||||||||||||||||||
Details | This sample was monodisperse |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Temperature | Max: 100.0 K |
Specialist optics | Energy filter - Name: GIF Quantum ER / Energy filter - Slit width: 20 eV |
Details | Preliminary grid screening was performed manually. |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 13246 / Average electron dose: 70.35 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 105000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |