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Yorodumi- EMDB-36081: Structure of beta-arrestin2 in complex with D6Rpp (Local Refine) -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-36081 | |||||||||||||||
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Title | Structure of beta-arrestin2 in complex with D6Rpp (Local Refine) | |||||||||||||||
Map data | ||||||||||||||||
Sample |
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Keywords | GPCR / Arrestin / SIGNALING PROTEIN / SIGNALING PROTEIN-IMMUNE SYSTEM complex | |||||||||||||||
Function / homology | Function and homology information angiotensin receptor binding / chemokine receptor activity / desensitization of G protein-coupled receptor signaling pathway / C-C chemokine receptor activity / inositol hexakisphosphate binding / C-C chemokine binding / scavenger receptor activity / G protein-coupled receptor internalization / Chemokine receptors bind chemokines / phosphatidylinositol-3,4,5-trisphosphate binding ...angiotensin receptor binding / chemokine receptor activity / desensitization of G protein-coupled receptor signaling pathway / C-C chemokine receptor activity / inositol hexakisphosphate binding / C-C chemokine binding / scavenger receptor activity / G protein-coupled receptor internalization / Chemokine receptors bind chemokines / phosphatidylinositol-3,4,5-trisphosphate binding / positive regulation of receptor internalization / endocytic vesicle / clathrin-coated pit / phosphatidylinositol binding / cell chemotaxis / actin filament / calcium-mediated signaling / receptor internalization / recycling endosome / protein transport / positive regulation of cytosolic calcium ion concentration / nuclear membrane / positive regulation of ERK1 and ERK2 cascade / molecular adaptor activity / early endosome / intracellular signal transduction / immune response / inflammatory response / external side of plasma membrane / intracellular membrane-bounded organelle / signal transduction / nucleoplasm / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | |||||||||||||||
Biological species | Bos taurus (cattle) / Mus musculus (house mouse) / Homo sapiens (human) | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.22 Å | |||||||||||||||
Authors | Maharana J / Sarma P / Yadav MK / Chami M / Banerjee R / Shukla AK | |||||||||||||||
Funding support | India, 4 items
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Citation | Journal: Science / Year: 2024 Title: Molecular insights into atypical modes of β-arrestin interaction with seven transmembrane receptors. Authors: Jagannath Maharana / Fumiya K Sano / Parishmita Sarma / Manish K Yadav / Longhan Duan / Tomasz M Stepniewski / Madhu Chaturvedi / Ashutosh Ranjan / Vinay Singh / Sayantan Saha / Gargi ...Authors: Jagannath Maharana / Fumiya K Sano / Parishmita Sarma / Manish K Yadav / Longhan Duan / Tomasz M Stepniewski / Madhu Chaturvedi / Ashutosh Ranjan / Vinay Singh / Sayantan Saha / Gargi Mahajan / Mohamed Chami / Wataru Shihoya / Jana Selent / Ka Young Chung / Ramanuj Banerjee / Osamu Nureki / Arun K Shukla / Abstract: β-arrestins (βarrs) are multifunctional proteins involved in signaling and regulation of seven transmembrane receptors (7TMRs), and their interaction is driven primarily by agonist-induced receptor ...β-arrestins (βarrs) are multifunctional proteins involved in signaling and regulation of seven transmembrane receptors (7TMRs), and their interaction is driven primarily by agonist-induced receptor activation and phosphorylation. Here, we present seven cryo-electron microscopy structures of βarrs either in the basal state, activated by the muscarinic receptor subtype 2 (M2R) through its third intracellular loop, or activated by the βarr-biased decoy D6 receptor (D6R). Combined with biochemical, cellular, and biophysical experiments, these structural snapshots allow the visualization of atypical engagement of βarrs with 7TMRs and also reveal a structural transition in the carboxyl terminus of βarr2 from a β strand to an α helix upon activation by D6R. Our study provides previously unanticipated molecular insights into the structural and functional diversity encoded in 7TMR-βarr complexes with direct implications for exploring novel therapeutic avenues. | |||||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_36081.map.gz | 168.1 MB | EMDB map data format | |
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Header (meta data) | emd-36081-v30.xml emd-36081.xml | 22.8 KB 22.8 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_36081_fsc.xml | 11.9 KB | Display | FSC data file |
Images | emd_36081.png | 72.5 KB | ||
Filedesc metadata | emd-36081.cif.gz | 7 KB | ||
Others | emd_36081_half_map_1.map.gz emd_36081_half_map_2.map.gz | 164.7 MB 164.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-36081 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-36081 | HTTPS FTP |
-Related structure data
Related structure data | 8j8vMC 8go9C 8j8rC 8j8zC 8j97C 8j9kC 8ja3C 8jafC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_36081.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 1.0933 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #1
File | emd_36081_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_36081_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : beta-arrestin2 in complex with D6Rpp
Entire | Name: beta-arrestin2 in complex with D6Rpp |
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Components |
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-Supramolecule #1: beta-arrestin2 in complex with D6Rpp
Supramolecule | Name: beta-arrestin2 in complex with D6Rpp / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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-Supramolecule #2: beta-arrestin2
Supramolecule | Name: beta-arrestin2 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1 |
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Source (natural) | Organism: Bos taurus (cattle) |
-Supramolecule #3: Fab30
Supramolecule | Name: Fab30 / type: complex / ID: 3 / Parent: 2 / Macromolecule list: #2-#3 |
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Source (natural) | Organism: Mus musculus (house mouse) |
-Supramolecule #4: Atypical chemokine receptor 2
Supramolecule | Name: Atypical chemokine receptor 2 / type: complex / ID: 4 / Parent: 3 / Macromolecule list: #4 |
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Source (natural) | Organism: Homo sapiens (human) / Synthetically produced: Yes |
-Macromolecule #1: Beta-arrestin-2
Macromolecule | Name: Beta-arrestin-2 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Bos taurus (cattle) |
Molecular weight | Theoretical: 47.217676 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MGEKPGTRVF KKSSPNGKLT VYLGKRDFVD HLDKVDPVDG VVLVDPDYLK DRKVFVTLTV AFRYGREDCD VLGLSFRKDL FIANYQAFP PTPNPPRPPT RLQERLLRKL GQHAHPFFFT IPQNLPSSVT LQPGPEDTGK ALGVDFEIRA FVAKSLEEKS H KRNSVRLV ...String: MGEKPGTRVF KKSSPNGKLT VYLGKRDFVD HLDKVDPVDG VVLVDPDYLK DRKVFVTLTV AFRYGREDCD VLGLSFRKDL FIANYQAFP PTPNPPRPPT RLQERLLRKL GQHAHPFFFT IPQNLPSSVT LQPGPEDTGK ALGVDFEIRA FVAKSLEEKS H KRNSVRLV IRKVQFAPEK PGPQPSAETT RHFLMSDRSL HLEASLDKEL YYHGEPLNVN VHVTNNSTKT VKKIKVSVRQ YA DIVLFST AQYKVPVAQV EQDDQVSPSS TFSKVYTITP FLANNREKRG LALDGKLKHE DTNLASSTIV KEGANKEVLG ILV SYRVKV KLVVSRGGDV SVELPFVLMH PKPHDHIALP RPQSAATHPP TLLPSAVPET DAPVDTNLIE FETNYATDDD IVFE DFARL RLKGLKDEDY DDQFC UniProtKB: Beta-arrestin-2 |
-Macromolecule #2: Fab30 Heavy Chain
Macromolecule | Name: Fab30 Heavy Chain / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Mus musculus (house mouse) |
Molecular weight | Theoretical: 25.512354 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: EISEVQLVES GGGLVQPGGS LRLSCAASGF NVYSSSIHWV RQAPGKGLEW VASISSYYGY TYYADSVKGR FTISADTSKN TAYLQMNSL RAEDTAVYYC ARSRQFWYSG LDYWGQGTLV TVSSASTKGP SVFPLAPSSK STSGGTAALG CLVKDYFPEP V TVSWNSGA ...String: EISEVQLVES GGGLVQPGGS LRLSCAASGF NVYSSSIHWV RQAPGKGLEW VASISSYYGY TYYADSVKGR FTISADTSKN TAYLQMNSL RAEDTAVYYC ARSRQFWYSG LDYWGQGTLV TVSSASTKGP SVFPLAPSSK STSGGTAALG CLVKDYFPEP V TVSWNSGA LTSGVHTFPA VLQSSGLYSL SSVVTVPSSS LGTQTYICNV NHKPSNTKVD KKVEPKSCDK THHHHHHHH |
-Macromolecule #3: Fab30 Light Chain
Macromolecule | Name: Fab30 Light Chain / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Mus musculus (house mouse) |
Molecular weight | Theoretical: 23.435064 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: SDIQMTQSPS SLSASVGDRV TITCRASQSV SSAVAWYQQK PGKAPKLLIY SASSLYSGVP SRFSGSRSGT DFTLTISSLQ PEDFATYYC QQYKYVPVTF GQGTKVEIKR TVAAPSVFIF PPSDSQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGN S QESVTEQD ...String: SDIQMTQSPS SLSASVGDRV TITCRASQSV SSAVAWYQQK PGKAPKLLIY SASSLYSGVP SRFSGSRSGT DFTLTISSLQ PEDFATYYC QQYKYVPVTF GQGTKVEIKR TVAAPSVFIF PPSDSQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGN S QESVTEQD SKDSTYSLSS TLTLSKADYE KHKVYACEVT HQGLSSPVTK SFNRGEC |
-Macromolecule #4: Atypical chemokine receptor 2
Macromolecule | Name: Atypical chemokine receptor 2 / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 2.352668 KDa |
Sequence | String: G(TPO)AQA(SEP)L(SEP)(SEP)C (SEP)E(SEP)(SEP)IL(TPO)A UniProtKB: Atypical chemokine receptor 2 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 Component:
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Vitrification | Cryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 283.15 K / Instrument: LEICA EM GP / Details: Blotted for 3 seconds before plunging.. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 165000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number real images: 10028 / Average electron dose: 56.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |