+Open data
-Basic information
Entry | Database: PDB / ID: 6l6p | ||||||
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Title | hASIC2a co-crystallized with Mamb-1 | ||||||
Components | Acid-sensing ion channel 2 | ||||||
Keywords | TRANSPORT PROTEIN / Ion channel / complex | ||||||
Function / homology | Function and homology information regulation of systemic arterial blood pressure by aortic arch baroreceptor feedback / sensory perception of sour taste / monoatomic ion-gated channel activity / ligand-gated sodium channel activity / detection of mechanical stimulus involved in sensory perception / protein localization to synapse / peripheral nervous system development / response to acidic pH / regulation of monoatomic ion transmembrane transport / positive regulation of synapse assembly ...regulation of systemic arterial blood pressure by aortic arch baroreceptor feedback / sensory perception of sour taste / monoatomic ion-gated channel activity / ligand-gated sodium channel activity / detection of mechanical stimulus involved in sensory perception / protein localization to synapse / peripheral nervous system development / response to acidic pH / regulation of monoatomic ion transmembrane transport / positive regulation of synapse assembly / inorganic cation transmembrane transport / plasma membrane => GO:0005886 / phototransduction / regulation of vasoconstriction / sodium ion transmembrane transport / monoatomic ion transmembrane transport / regulation of membrane potential / central nervous system development / sensory perception of sound / Stimuli-sensing channels / chemical synaptic transmission / dendritic spine / neuronal cell body / negative regulation of apoptotic process / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.08 Å | ||||||
Authors | Lei, F. / Jian, S. | ||||||
Funding support | China, 1items
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Citation | Journal: To Be Published Title: hASIC2a co-crystallized with Mamb-1 Authors: Lei, F. / Jian, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6l6p.cif.gz | 260 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6l6p.ent.gz | 217.7 KB | Display | PDB format |
PDBx/mmJSON format | 6l6p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6l6p_validation.pdf.gz | 452.6 KB | Display | wwPDB validaton report |
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Full document | 6l6p_full_validation.pdf.gz | 478.1 KB | Display | |
Data in XML | 6l6p_validation.xml.gz | 46.8 KB | Display | |
Data in CIF | 6l6p_validation.cif.gz | 63.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l6/6l6p ftp://data.pdbj.org/pub/pdb/validation_reports/l6/6l6p | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
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-Components
#1: Protein | Mass: 52254.723 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ASIC2, ACCN, ACCN1, BNAC1, MDEG / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q16515 #2: 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: 4.27 Å3/Da / Density % sol: 71.21 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 4% Tascimate pH 8.0, 12% w/v PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 1, 2019 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97853 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 3.08→49.33 Å / Num. obs: 50203 / % possible obs: 99.6 % / Redundancy: 6.6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.107 / Rpim(I) all: 0.045 / Rrim(I) all: 0.117 / Net I/σ(I): 12.6 / Num. measured all: 329259 / Scaling rejects: 38 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.08→49.23 Å / Cor.coef. Fo:Fc: 0.912 / Cor.coef. Fo:Fc free: 0.828 / SU B: 27.73 / SU ML: 0.426 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.968 / ESU R Free: 0.415 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: 230.7 Å2 / Biso mean: 100.171 Å2 / Biso min: 35.19 Å2
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Refinement step | Cycle: final / Resolution: 3.08→49.23 Å
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Refine LS restraints |
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Refine LS restraints NCS | Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05
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LS refinement shell | Resolution: 3.08→3.16 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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