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Yorodumi- EMDB-22962: CryoEM structure of the apo-CGRP receptor in a detergent micelle -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-22962 | |||||||||||||||
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Title | CryoEM structure of the apo-CGRP receptor in a detergent micelle | |||||||||||||||
Map data | Main map output from cryoSPARC, non-uniform refinement | |||||||||||||||
Sample |
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Function / homology | Function and homology information calcitonin gene-related peptide binding / CGRP receptor complex / calcitonin gene-related peptide receptor signaling pathway / adrenomedullin binding / positive regulation of protein glycosylation / cellular response to sucrose stimulus / adrenomedullin receptor activity / adrenomedullin receptor complex / adrenomedullin receptor signaling pathway / amylin receptor activity ...calcitonin gene-related peptide binding / CGRP receptor complex / calcitonin gene-related peptide receptor signaling pathway / adrenomedullin binding / positive regulation of protein glycosylation / cellular response to sucrose stimulus / adrenomedullin receptor activity / adrenomedullin receptor complex / adrenomedullin receptor signaling pathway / amylin receptor activity / calcitonin receptor activity / vascular associated smooth muscle cell proliferation / calcitonin gene-related peptide receptor activity / amylin receptor signaling pathway / Calcitonin-like ligand receptors / regulation of G protein-coupled receptor signaling pathway / G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger / coreceptor activity / cellular response to hormone stimulus / positive regulation of vascular associated smooth muscle cell proliferation / protein localization to plasma membrane / G protein-coupled receptor activity / intracellular protein transport / adenylate cyclase-activating G protein-coupled receptor signaling pathway / receptor internalization / calcium ion transport / protein transport / heart development / G alpha (s) signalling events / angiogenesis / receptor complex / endosome / cell surface receptor signaling pathway / lysosome / G protein-coupled receptor signaling pathway / cell surface / endoplasmic reticulum / plasma membrane / cytoplasm Similarity search - Function | |||||||||||||||
Biological species | Homo sapiens (human) | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.15 Å | |||||||||||||||
Authors | Belousoff MJ / Danev R | |||||||||||||||
Funding support | Australia, 4 items
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Citation | Journal: Science / Year: 2021 Title: Structure and dynamics of the CGRP receptor in apo and peptide-bound forms. Authors: Tracy M Josephs / Matthew J Belousoff / Yi-Lynn Liang / Sarah J Piper / Jianjun Cao / Daniel J Garama / Katie Leach / Karen J Gregory / Arthur Christopoulos / Debbie L Hay / Radostin Danev / ...Authors: Tracy M Josephs / Matthew J Belousoff / Yi-Lynn Liang / Sarah J Piper / Jianjun Cao / Daniel J Garama / Katie Leach / Karen J Gregory / Arthur Christopoulos / Debbie L Hay / Radostin Danev / Denise Wootten / Patrick M Sexton / Abstract: G protein-coupled receptors (GPCRs) are key regulators of information transmission between cells and organs. Despite this, we have only a limited understanding of the behavior of GPCRs in the apo ...G protein-coupled receptors (GPCRs) are key regulators of information transmission between cells and organs. Despite this, we have only a limited understanding of the behavior of GPCRs in the apo state and the conformational changes upon agonist binding that lead to G protein recruitment and activation. We expressed and purified unmodified apo and peptide-bound calcitonin gene-related peptide (CGRP) receptors from insect cells to determine their cryo-electron microscopy (cryo-EM) structures, and we complemented these with analysis of protein conformational dynamics using hydrogen-deuterium exchange mass spectrometry and three-dimensional variance analysis of the cryo-EM data. Together with our previously published structure of the active, Gs-bound CGRP receptor complex, our work provides insight into the mechanisms of class B1 GPCR activation. | |||||||||||||||
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_22962.map.gz | 26.2 MB | EMDB map data format | |
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Header (meta data) | emd-22962-v30.xml emd-22962.xml | 18.1 KB 18.1 KB | Display Display | EMDB header |
Images | emd_22962.png | 40.3 KB | ||
Masks | emd_22962_msk_1.map | 52.7 MB | Mask map | |
Others | emd_22962_additional_1.map.gz emd_22962_half_map_1.map.gz emd_22962_half_map_2.map.gz | 1.5 MB 49 MB 49 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-22962 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-22962 | HTTPS FTP |
-Validation report
Summary document | emd_22962_validation.pdf.gz | 820.4 KB | Display | EMDB validaton report |
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Full document | emd_22962_full_validation.pdf.gz | 820 KB | Display | |
Data in XML | emd_22962_validation.xml.gz | 11.8 KB | Display | |
Data in CIF | emd_22962_validation.cif.gz | 13.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-22962 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-22962 | HTTPS FTP |
-Related structure data
Related structure data | 7kntMC 7knuC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | |
EM raw data | EMPIAR-10668 (Title: CryoEM structure of the apo-CGRP receptor in a detergent micelle Data size: 1.7 TB Data #1: Non-gain-normalized LZW-TIFF compressed movies of CGRPR in a detergent micelle [micrographs - single frame]) |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_22962.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Main map output from cryoSPARC, non-uniform refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
-Mask #1
File | emd_22962_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: Map refined using the SIDESPLITTER reconstruction in combination...
File | emd_22962_additional_1.map | ||||||||||||
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Annotation | Map refined using the SIDESPLITTER reconstruction in combination with RELION 3.1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map1
File | emd_22962_half_map_1.map | ||||||||||||
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Annotation | Half map1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map2
File | emd_22962_half_map_2.map | ||||||||||||
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Annotation | Half map2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : apo CGRP receptor
Entire | Name: apo CGRP receptor |
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Components |
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-Supramolecule #1: apo CGRP receptor
Supramolecule | Name: apo CGRP receptor / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Trichoplusia ni (cabbage looper) |
-Macromolecule #1: Receptor activity-modifying protein 1
Macromolecule | Name: Receptor activity-modifying protein 1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 17.066701 KDa |
Recombinant expression | Organism: Trichoplusia ni (cabbage looper) |
Sequence | String: MKTIIALSYI FCLVFADYKD DDDKHGSCQE ANYGALLREL CLTQFQVDME AVGETLWCDW GRTIRSYREL ADCTWHMAEK LGCFWPNAE VDRFFLAVHG RYFRSCPISG RAVRDPPGSI LYPFIVVPIT VTLLVTALVV WQSKRTEGIV |
-Macromolecule #2: Calcitonin gene-related peptide type 1 receptor
Macromolecule | Name: Calcitonin gene-related peptide type 1 receptor / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 56.27452 KDa |
Recombinant expression | Organism: Trichoplusia ni (cabbage looper) |
Sequence | String: MKTIIALSYI FCLVFADYKD DDDLEVLFQG PAELEESPED SIQLGVTRNK IMTAQYECYQ KIMQDPIQQA EGVYCNRTWD GWLCWNDVA AGTESMQLCP DYFQDFDPSE KVTKICDQDG NWFRHPASNR TWTNYTQCNV NTHEKVKTAL NLFYLTIIGH G LSIASLLI ...String: MKTIIALSYI FCLVFADYKD DDDLEVLFQG PAELEESPED SIQLGVTRNK IMTAQYECYQ KIMQDPIQQA EGVYCNRTWD GWLCWNDVA AGTESMQLCP DYFQDFDPSE KVTKICDQDG NWFRHPASNR TWTNYTQCNV NTHEKVKTAL NLFYLTIIGH G LSIASLLI SLGIFFYFKS LSCQRITLHK NLFFSFVCNS VVTIIHLTAV ANNQALVATN PVSCKVSQFI HLYLMGCNYF WM LCEGIYL HTLIVVAVFA EKQHLMWYYF LGWGFPLIPA CIHAIARSLY YNDNCWISSD THLLYIIHGP ICAALLVNLF FLL NIVRVL ITKLKVTHQA ESNLYMKAVR ATLILVPLLG IEFVLIPWRP EGKIAEEVYD YIMHILMHFQ GLLVSTIFCF FNGE VQAIL RRNWNQYKIQ FGNSFSNSEA LRSASYTVST ISDGPGYSHD CPSEHLNGKS IHDIENVLLK PENLYNPAGL EVLFQ GPHH HHHHHH |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | TFS KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 57.3 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.15 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 542650 |
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Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |