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Yorodumi- PDB-7p0i: Crystal structure of a CGRP receptor ectodomain heterodimer bound... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7p0i | ||||||
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Title | Crystal structure of a CGRP receptor ectodomain heterodimer bound to macrocyclic inhibitor Compound 13 | ||||||
Components | Maltose/maltodextrin-binding periplasmic protein,Receptor activity-modifying protein 1,Calcitonin gene-related peptide type 1 receptor | ||||||
Keywords | MEMBRANE PROTEIN / GPCR / CGRP / ectodomain / inhibitor / macrocycle | ||||||
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 / detection of maltose stimulus / maltose transport complex / carbohydrate transport / G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / coreceptor activity / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / cellular response to hormone stimulus / positive regulation of vascular associated smooth muscle cell proliferation / ATP-binding cassette (ABC) transporter complex / cell chemotaxis / 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 / outer membrane-bounded periplasmic space / G alpha (s) signalling events / angiogenesis / periplasmic space / cell surface receptor signaling pathway / lysosome / receptor complex / endosome / G protein-coupled receptor signaling pathway / DNA damage response / cell surface / endoplasmic reticulum / membrane / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Southall, S.M. | ||||||
Citation | Journal: Acs Chem Neurosci / Year: 2022 Title: Novel Macrocyclic Antagonists of the Calcitonin Gene-Related Peptide Receptor: Design, Realization, and Structural Characterization of Protein-Ligand Complexes. Authors: Cansfield, A.D. / Ator, M.A. / Banerjee, J. / Bestwick, M. / Bortolato, A. / Brown, G.A. / Brown, J. / Butkovic, K. / Cansfield, J.E. / Christopher, J.A. / Congreve, M. / Cseke, G. / ...Authors: Cansfield, A.D. / Ator, M.A. / Banerjee, J. / Bestwick, M. / Bortolato, A. / Brown, G.A. / Brown, J. / Butkovic, K. / Cansfield, J.E. / Christopher, J.A. / Congreve, M. / Cseke, G. / Deflorian, F. / Dugan, B. / Hunjadi, M.P. / Hutinec, A. / Inturi, T.K. / Landek, G. / Mason, J. / O'Brien, A. / Ott, G.R. / Rupcic, R. / Saxty, G. / Southall, S.M. / Zadravec, R. / Watson, S.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7p0i.cif.gz | 256.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7p0i.ent.gz | 202.6 KB | Display | PDB format |
PDBx/mmJSON format | 7p0i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7p0i_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 7p0i_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 7p0i_validation.xml.gz | 24.2 KB | Display | |
Data in CIF | 7p0i_validation.cif.gz | 34.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p0/7p0i ftp://data.pdbj.org/pub/pdb/validation_reports/p0/7p0i | HTTPS FTP |
-Related structure data
Related structure data | 7p0fC 4rwfS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 66360.555 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (strain K12) (bacteria), (gene. exp.) Homo sapiens (human) Strain: K12 / Gene: malE, b4034, JW3994, RAMP1, CALCRL, CGRPR / Production host: Homo sapiens (human) References: UniProt: P0AEX9, UniProt: O60894, UniProt: Q16602 | ||||||
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#2: Polysaccharide | alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose | ||||||
#3: Chemical | #4: Chemical | ChemComp-7IU / ( | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.04 Å3/Da / Density % sol: 39.71 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop Details: 0.1 M BIS-TRIS pH 5.5, 0.1 M ammonium acetate, 15 % PEG 10,000 |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.96862 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 17, 2017 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.96862 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2.3→41.43 Å / Num. obs: 24809 / % possible obs: 100 % / Redundancy: 7.3 % / Biso Wilson estimate: 34.03 Å2 / CC1/2: 0.987 / Rmerge(I) obs: 0.332 / Rpim(I) all: 0.132 / Rrim(I) all: 0.357 / Net I/σ(I): 6.2 / Num. measured all: 180617 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4RWF Resolution: 2.3→29.69 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 27.23 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 159.31 Å2 / Biso mean: 40.9462 Å2 / Biso min: 18.56 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.3→29.69 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9 / % reflection obs: 100 %
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Refinement TLS params. | Method: refined / Origin x: 12.6709 Å / Origin y: -2.27 Å / Origin z: -12.8279 Å
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Refinement TLS group |
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