+Open data
-Basic information
Entry | Database: PDB / ID: 8hpy | ||||||
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Title | Crystal structure of human LGI1-ADAM22 complex | ||||||
Components |
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Keywords | MEMBRANE PROTEIN / synaptic modulator / complex | ||||||
Function / homology | Function and homology information LGI-ADAM interactions / axon initial segment / negative regulation of cell adhesion / neurotransmitter receptor localization to postsynaptic specialization membrane / positive regulation of synaptic transmission / synaptic cleft / axon guidance / central nervous system development / postsynaptic density membrane / metalloendopeptidase activity ...LGI-ADAM interactions / axon initial segment / negative regulation of cell adhesion / neurotransmitter receptor localization to postsynaptic specialization membrane / positive regulation of synaptic transmission / synaptic cleft / axon guidance / central nervous system development / postsynaptic density membrane / metalloendopeptidase activity / neuron projection development / integrin binding / nervous system development / positive regulation of cell growth / cell adhesion / axon / signaling receptor binding / glutamatergic synapse / dendrite / Golgi apparatus / endoplasmic reticulum / proteolysis / extracellular space / extracellular region / membrane / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 5.87 Å | ||||||
Authors | Liu, H. / Xu, F. | ||||||
Funding support | China, 1items
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Citation | Journal: To Be Published Title: Crystal structure of human LGI1-ADAM22 complex Authors: Liu, H. / Xu, F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8hpy.cif.gz | 414.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8hpy.ent.gz | 331.2 KB | Display | PDB format |
PDBx/mmJSON format | 8hpy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8hpy_validation.pdf.gz | 462.8 KB | Display | wwPDB validaton report |
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Full document | 8hpy_full_validation.pdf.gz | 492.1 KB | Display | |
Data in XML | 8hpy_validation.xml.gz | 42.8 KB | Display | |
Data in CIF | 8hpy_validation.cif.gz | 62.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hp/8hpy ftp://data.pdbj.org/pub/pdb/validation_reports/hp/8hpy | HTTPS FTP |
-Related structure data
Related structure data | 5zxr 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 53743.102 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ADAM22, MDC2 / Production host: Homo sapiens (human) / References: UniProt: Q9P0K1 #2: Protein | Mass: 60616.598 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: LGI1, EPT, UNQ775/PRO1569 / Production host: Homo sapiens (human) / References: UniProt: O95970 #3: Sugar | ChemComp-NAG / #4: Chemical | ChemComp-CA / 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: 4.02 Å3/Da / Density % sol: 69.42 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 2.5M sodium chloride, 0.1M HEPES pH=7.5, 2% (w/v) Benzamidine |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: May 17, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 5.87→50 Å / Num. obs: 9884 / % possible obs: 99.1 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.073 / Rsym value: 0.058 / Net I/σ(I): 25.905 |
Reflection shell | Resolution: 5.87→5.97 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.891 / Mean I/σ(I) obs: 2.514 / Num. unique obs: 502 / Rsym value: 0.625 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5ZXR 5zxr Resolution: 5.87→48.08 Å / SU ML: 1.3 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 46.57
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 5.87→48.08 Å
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Refine LS restraints |
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LS refinement shell |
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