+Open data
-Basic information
Entry | Database: PDB / ID: 7rt9 | ||||||
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Title | Crystal structures of human PYY and NPY | ||||||
Components |
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Keywords | HORMONE/IMMUNE SYSTEM / peptide hormone C-terminal amidation helix antibody / HORMONE / HORMONE-IMMUNE SYSTEM complex | ||||||
Function / homology | Function and homology information neuropeptide Y receptor binding / intestinal epithelial cell differentiation / neuropeptide hormone activity / feeding behavior / neuropeptide signaling pathway / Peptide ligand-binding receptors / G protein-coupled receptor binding / hormone activity / G alpha (i) signalling events / extracellular space / extracellular region Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å | ||||||
Authors | Langley, D.B. / Christ, D. | ||||||
Funding support | Australia, 1items
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Citation | Journal: Neuropeptides / Year: 2022 Title: Crystal structures of human neuropeptide Y (NPY) and peptide YY (PYY). Authors: Langley, D.B. / Schofield, P. / Jackson, J. / Herzog, H. / Christ, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7rt9.cif.gz | 196.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7rt9.ent.gz | 152.7 KB | Display | PDB format |
PDBx/mmJSON format | 7rt9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rt/7rt9 ftp://data.pdbj.org/pub/pdb/validation_reports/rt/7rt9 | HTTPS FTP |
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-Related 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: 23954.686 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) #2: Antibody | Mass: 23595.240 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) #3: Protein/peptide | Mass: 4314.795 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P10082 #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 2.55 Å3/Da / Density % sol: 51.7 % / Description: Rods |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 6.65 Details: Fab-PYY (~5.5 mg/mL with respect to Fab, 2.4:1 molar ratio of PYY:Fab, in 25 mM Tris (pH 7.5), 100 mM NaCl) was mixed with an equal volume (2 uL) of well solution comprising 200 mM citrate ...Details: Fab-PYY (~5.5 mg/mL with respect to Fab, 2.4:1 molar ratio of PYY:Fab, in 25 mM Tris (pH 7.5), 100 mM NaCl) was mixed with an equal volume (2 uL) of well solution comprising 200 mM citrate (pH 6.65) and 13% (w/v) PEG1500. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å | |||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 1, 2015 | |||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 | |||||||||||||||||||||||||||
Reflection | Resolution: 1.9→42.11 Å / Num. obs: 87134 / % possible obs: 99.6 % / Redundancy: 6.6 % / CC1/2: 0.996 / Rmerge(I) obs: 0.12 / Rpim(I) all: 0.05 / Rrim(I) all: 0.13 / Net I/σ(I): 8.8 / Num. measured all: 571023 / Scaling rejects: 92 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / % possible all: 98.3
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: generic Fab Resolution: 1.9→42.11 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.937 / WRfactor Rfree: 0.2058 / WRfactor Rwork: 0.1732 / FOM work R set: 0.8546 / SU B: 3.148 / SU ML: 0.09 / SU R Cruickshank DPI: 0.1299 / SU Rfree: 0.1232 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.13 / ESU R Free: 0.123 / Stereochemistry target values: MAXIMUM LIKELIHOOD 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 69.33 Å2 / Biso mean: 21.313 Å2 / Biso min: 8.65 Å2
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Refinement step | Cycle: final / Resolution: 1.9→42.11 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.949 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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