+Open data
-Basic information
Entry | Database: PDB / ID: 2yx8 | ||||||
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Title | Crystal structure of the extracellular domain of human RAMP1 | ||||||
Components | Receptor activity-modifying protein 1 | ||||||
Keywords | PROTEIN TRANSPORT / TRANSMEMBRANE / DISEASE / MIGRAINE / TRAFFICKING / FOLDING / GPCR / CLR / CRLR / CGRP / ENDOPLASMIC RETICULUM / BIBN4096BS / GLYCOSYLATION / ADRENOMEDULIN / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information calcitonin gene-related peptide binding / CGRP receptor complex / calcitonin gene-related peptide receptor signaling pathway / positive regulation of protein glycosylation / amylin receptor activity / calcitonin gene-related peptide receptor activity / amylin receptor signaling pathway / Calcitonin-like ligand receptors / regulation of G protein-coupled receptor signaling pathway / coreceptor activity ...calcitonin gene-related peptide binding / CGRP receptor complex / calcitonin gene-related peptide receptor signaling pathway / positive regulation of protein glycosylation / amylin receptor activity / calcitonin gene-related peptide receptor activity / amylin receptor signaling pathway / Calcitonin-like ligand receptors / regulation of G protein-coupled receptor signaling pathway / coreceptor activity / cellular response to hormone stimulus / protein localization to plasma membrane / intracellular protein transport / adenylate cyclase-activating G protein-coupled receptor signaling pathway / receptor internalization / calcium ion transport / protein transport / G alpha (s) signalling events / angiogenesis / receptor complex / G protein-coupled receptor signaling pathway / cell surface / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.4 Å | ||||||
Authors | Kusano, S. / Kukimoto-Niino, M. / Shirouzu, M. / Shindo, T. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: Protein Sci. / Year: 2008 Title: Crystal structure of the human receptor activity-modifying protein 1 extracellular domain. Authors: Kusano, S. / Kukimoto-Niino, M. / Akasaka, R. / Toyama, M. / Terada, T. / Shirouzu, M. / Shindo, T. / Yokoyama, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2yx8.cif.gz | 25.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2yx8.ent.gz | 19 KB | Display | PDB format |
PDBx/mmJSON format | 2yx8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yx/2yx8 ftp://data.pdbj.org/pub/pdb/validation_reports/yx/2yx8 | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
-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: Protein | Mass: 10781.900 Da / Num. of mol.: 1 / Fragment: Extracellular Domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RAMP1 / Plasmid: PE060926-03 / Production host: Escherichia coli (E. coli) / References: UniProt: O60894 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.88 Å3/Da / Density % sol: 31.159447 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.4 Details: 0.1M tri-Sodium Citrate Dihydrate, 0.15M di-Ammonium Citrate, 25% PEG3350, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 0.9789, 0.9793, 0.9640 | ||||||||||||
Detector | Type: RIGAKU JUPITER 210 / Detector: CCD / Date: Mar 26, 2007 | ||||||||||||
Radiation | Monochromator: Si double crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.4→50 Å / Num. obs: 3371 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Redundancy: 15.15 % / Biso Wilson estimate: 30 Å2 / Rsym value: 0.095 / Net I/σ(I): 21.26 | ||||||||||||
Reflection shell | Resolution: 2.4→2.49 Å / Mean I/σ(I) obs: 2.59 / Rsym value: 0.33 / % possible all: 93.2 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.4→24.56 Å / Rfactor Rfree error: 0.016 / Data cutoff high absF: 1048459.05 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 54.2507 Å2 / ksol: 0.461846 e/Å3 | ||||||||||||||||||||
Displacement parameters | Biso mean: 36.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.4→24.56 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.55 Å / Rfactor Rfree error: 0.049 / Total num. of bins used: 6
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Xplor file |
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