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Yorodumi- PDB-6umg: Crystal structure of erenumab Fab bound to the extracellular doma... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6umg | ||||||
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Title | Crystal structure of erenumab Fab bound to the extracellular domain of CGRP receptor | ||||||
Components |
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Keywords | MEMBRANE PROTEIN/IMMUNE SYSTEM / Class B GPCR / Complex / Fragment antigen binding / MEMBRANE PROTEIN-IMMUNE SYSTEM complex | ||||||
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 / G protein-coupled receptor activity / protein localization to plasma membrane / 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 / lysosome / cell surface receptor signaling pathway / receptor complex / endosome / G protein-coupled receptor signaling pathway / cell surface / endoplasmic reticulum / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | Mohr, C. | ||||||
Citation | Journal: Cell Rep / Year: 2020 Title: Molecular Insight into Recognition of the CGRPR Complex by Migraine Prevention Therapy Aimovig (Erenumab). Authors: Garces, F. / Mohr, C. / Zhang, L. / Huang, C.S. / Chen, Q. / King, C. / Xu, C. / Wang, Z. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6umg.cif.gz | 251.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6umg.ent.gz | 199.3 KB | Display | PDB format |
PDBx/mmJSON format | 6umg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/um/6umg ftp://data.pdbj.org/pub/pdb/validation_reports/um/6umg | HTTPS FTP |
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-Related structure data
Related structure data | 6umhC 6umiC 6umjC 3n7pS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Antibody | Mass: 25483.525 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pTT5 / Cell line (production host): HEK 293-6E / Production host: Homo sapiens (human) #2: Antibody | Mass: 22827.324 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pTT5 / Cell line (production host): HEK 293-6E / Production host: Homo sapiens (human) #3: Protein | Mass: 16269.885 Da / Num. of mol.: 2 / Fragment: extracellular domain (UNP residues 23-133) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CALCRL, CGRPR / Plasmid: pDEST 17 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q16602 #4: Protein | Mass: 13840.678 Da / Num. of mol.: 2 / Fragment: extracellular domain (UNP residues 26-117) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RAMP1 / Plasmid: pDEST 17 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O60894 #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.95 Å3/Da / Density % sol: 36.98 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.12 M ethylene glycols, 0.1 M HEPES:MOPS, pH 7.5, 37.5% MPD + PEG1000 + PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5418 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU SATURN 92 / Detector: CCD / Date: May 26, 2015 / Details: VariMax HF | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.7→30 Å / Num. obs: 33135 / % possible obs: 99.9 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.14 / Rpim(I) all: 0.088 / Rrim(I) all: 0.165 / Χ2: 1 / Net I/σ(I): 5.6 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Χ2: 1 / Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3N7P Resolution: 2.7→30 Å / Cor.coef. Fo:Fc: 0.895 / Cor.coef. Fo:Fc free: 0.864 / SU B: 18.626 / SU ML: 0.365 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.433 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 76.64 Å2 / Biso mean: 36.707 Å2 / Biso min: 13.79 Å2
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Refinement step | Cycle: final / Resolution: 2.7→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.7→2.77 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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