[English] 日本語
Yorodumi- EMDB-22963: CryoEM structure of the CGRP receptor with bound CGRP peptide in ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-22963 | |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | CryoEM structure of the CGRP receptor with bound CGRP peptide in a detergent micelle | |||||||||||||||
Map data | Main map refined using non-uniform refinement in cryoSPARC | |||||||||||||||
Sample |
| |||||||||||||||
Keywords | GPCR / CGRP receptor / MEMBRANE PROTEIN / SIGNALING PROTEIN | |||||||||||||||
Function / homology | Function and homology information nervous system process involved in regulation of systemic arterial blood pressure / 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 ...nervous system process involved in regulation of systemic arterial blood pressure / 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 / positive regulation of interleukin-1 alpha production / amylin receptor signaling pathway / Calcitonin-like ligand receptors / negative regulation of calcium ion transport into cytosol / positive regulation of macrophage differentiation / regulation of G protein-coupled receptor signaling pathway / G protein-coupled receptor internalization / vasculature development / negative regulation of bone resorption / endothelial cell proliferation / leukocyte cell-cell adhesion / activation of adenylate cyclase activity / negative regulation of osteoclast differentiation / G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger / endothelial cell migration / coreceptor activity / cellular response to hormone stimulus / positive regulation of vascular associated smooth muscle cell proliferation / regulation of cytosolic calcium ion concentration / negative regulation of blood pressure / positive regulation of interleukin-8 production / protein localization to plasma membrane / G protein-coupled receptor activity / intracellular protein transport / adenylate cyclase-activating G protein-coupled receptor signaling pathway / hormone activity / receptor internalization / regulation of blood pressure / vasodilation / calcium ion transport / protein transport / cell-cell signaling / heart development / phospholipase C-activating G protein-coupled receptor signaling pathway / G alpha (s) signalling events / angiogenesis / lysosome / receptor complex / cell surface receptor signaling pathway / endosome / G protein-coupled receptor signaling pathway / protein phosphorylation / signaling receptor binding / protein-containing complex binding / cell surface / endoplasmic reticulum / extracellular space / extracellular region / plasma membrane / cytoplasm Similarity search - Function | |||||||||||||||
Biological species | Homo sapiens (human) | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.49 Å | |||||||||||||||
Authors | Belousoff MJ / Danev R | |||||||||||||||
Funding support | Australia, 4 items
| |||||||||||||||
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 |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_22963.map.gz | 26.2 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-22963-v30.xml emd-22963.xml | 19.9 KB 19.9 KB | Display Display | EMDB header |
Images | emd_22963.png | 49.7 KB | ||
Masks | emd_22963_msk_1.map | 52.7 MB | Mask map | |
Filedesc metadata | emd-22963.cif.gz | 5.9 KB | ||
Others | emd_22963_additional_1.map.gz emd_22963_half_map_1.map.gz emd_22963_half_map_2.map.gz | 4.8 MB 49 MB 49 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-22963 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-22963 | HTTPS FTP |
-Validation report
Summary document | emd_22963_validation.pdf.gz | 1 MB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_22963_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | emd_22963_validation.xml.gz | 11.7 KB | Display | |
Data in CIF | emd_22963_validation.cif.gz | 13.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-22963 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-22963 | HTTPS FTP |
-Related structure data
Related structure data | 7knuMC 7kntC M: atomic model generated by this map C: citing same article (ref.) |
---|---|
Similar structure data | |
EM raw data | EMPIAR-10671 (Title: CryoEM structure of the CGRP receptor with bound CGRP peptide in a detergent micelle Data size: 1.6 TB Data #1: Non-gain-normalized LZW-TIFF compressed movies of CGRPR-CGRP in a detergent micelle [micrographs - multiframe]) |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|---|
Related items in Molecule of the Month |
-Map
File | Download / File: emd_22963.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Main map refined using non-uniform refinement in cryoSPARC | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.83 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Mask #1
File | emd_22963_msk_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Additional map: Map refined using SIDESplitter reconstruction in combination with...
File | emd_22963_additional_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Map refined using SIDESplitter reconstruction in combination with RELION maximum likelihood. | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: Half map 1
File | emd_22963_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Half map 1 | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: Half map 2
File | emd_22963_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Half map 2 | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Sample components
-Entire : CGRP receptor bound to CGRP and RAMP1
Entire | Name: CGRP receptor bound to CGRP and RAMP1 |
---|---|
Components |
|
-Supramolecule #1: CGRP receptor bound to CGRP and RAMP1
Supramolecule | Name: CGRP receptor bound to CGRP and RAMP1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
---|
-Supramolecule #2: CGRP receptor with RAMP1
Supramolecule | Name: CGRP receptor with RAMP1 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1, #3 |
---|---|
Source (natural) | Organism: Homo sapiens (human) |
-Supramolecule #3: Calcitonin gene-related peptide 1
Supramolecule | Name: Calcitonin gene-related peptide 1 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2 |
---|---|
Source (natural) | Organism: Homo sapiens (human) / Synthetically produced: Yes |
-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 |
---|---|
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 UniProtKB: Receptor activity-modifying protein 1 |
-Macromolecule #2: Calcitonin gene-related peptide 1
Macromolecule | Name: Calcitonin gene-related peptide 1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 3.797347 KDa |
Sequence | String: ACDTATCVTH RLAGLLSRSG GVVKNNFVPT NVGSKAF UniProtKB: Calcitonin gene-related peptide 1 |
-Macromolecule #3: Calcitonin gene-related peptide type 1 receptor
Macromolecule | Name: Calcitonin gene-related peptide type 1 receptor / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
---|---|
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 UniProtKB: Calcitonin gene-related peptide type 1 receptor |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
---|---|
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | TFS KRIOS |
---|---|
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
Startup model | Type of model: INSILICO MODEL |
---|---|
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.49 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 284400 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |