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Open data
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Basic information
Entry | Database: PDB / ID: 6m3r | ||||||
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Title | Crystal structure of AnkG/beta4-spectrin complex | ||||||
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![]() | STRUCTURAL PROTEIN / PROTEIN BINDING | ||||||
Function / homology | ![]() Interaction between L1 and Ankyrins / positive regulation of sodium ion import across plasma membrane / positive regulation of cell communication by electrical coupling / positive regulation of membrane depolarization during cardiac muscle cell action potential / regulation of protein targeting / maintenance of protein location in plasma membrane / membrane assembly / NCAM signaling for neurite out-growth / reproductive process / protein localization to axon ...Interaction between L1 and Ankyrins / positive regulation of sodium ion import across plasma membrane / positive regulation of cell communication by electrical coupling / positive regulation of membrane depolarization during cardiac muscle cell action potential / regulation of protein targeting / maintenance of protein location in plasma membrane / membrane assembly / NCAM signaling for neurite out-growth / reproductive process / protein localization to axon / spectrin / clustering of voltage-gated sodium channels / positive regulation of sodium ion transmembrane transporter activity / establishment or maintenance of microtubule cytoskeleton polarity / regulation of peptidyl-serine phosphorylation / regulation of potassium ion transport / spectrin-associated cytoskeleton / COPI-mediated anterograde transport / magnesium ion homeostasis / positive regulation of membrane potential / RAF/MAP kinase cascade / phosphorylation-dependent protein binding / plasma membrane organization / central nervous system projection neuron axonogenesis / negative regulation of delayed rectifier potassium channel activity / cell body fiber / positive regulation of homotypic cell-cell adhesion / positive regulation of cation channel activity / maintenance of protein location in cell / axon initial segment / cardiac conduction / paranode region of axon / positive regulation of sodium ion transport / Golgi to plasma membrane protein transport / axon hillock / negative regulation of endocytosis / actin filament capping / node of Ranvier / costamere / positive regulation of multicellular organism growth / cellular response to magnesium ion / anterograde axonal transport / fertilization / adult walking behavior / ankyrin binding / negative regulation of heart rate / neuromuscular junction development / adult behavior / cortical actin cytoskeleton / spectrin binding / axon development / transmission of nerve impulse / intercalated disc / response to immobilization stress / mitotic cytokinesis / lateral plasma membrane / positive regulation of protein targeting to membrane / neuronal action potential / phosphatase binding / regulation of sodium ion transport / axon cytoplasm / T-tubule / cytoskeletal protein binding / axonogenesis / basal plasma membrane / sarcoplasmic reticulum / cell projection / protein localization to plasma membrane / sensory perception of sound / synapse organization / axon guidance / establishment of protein localization / neuromuscular junction / protein localization / structural constituent of cytoskeleton / phospholipid binding / sarcolemma / PML body / nuclear matrix / Z disc / positive regulation of non-canonical NF-kappaB signal transduction / actin filament binding / cell junction / protein-macromolecule adaptor activity / actin binding / actin cytoskeleton organization / basolateral plasma membrane / postsynaptic membrane / RNA polymerase II-specific DNA-binding transcription factor binding / transmembrane transporter binding / lysosome / cytoskeleton / cadherin binding / neuron projection / axon / neuronal cell body / synapse / dendrite / positive regulation of gene expression / regulation of transcription by RNA polymerase II Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Li, J. / Chen, K. / Zhu, R. / Zhang, M. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structural Basis Underlying Strong Interactions between Ankyrins and Spectrins. Authors: Li, J. / Chen, K. / Zhu, R. / Zhang, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 148.8 KB | Display | ![]() |
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PDB format | ![]() | 108.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 441.5 KB | Display | ![]() |
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Full document | ![]() | 452.7 KB | Display | |
Data in XML | ![]() | 26.6 KB | Display | |
Data in CIF | ![]() | 35.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6m3pC ![]() 6m3qC ![]() 3kbtS ![]() 4d8oS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
#1: Protein | Mass: 54560.531 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Protein | Mass: 36877.199 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 6.5 Å3/Da / Density % sol: 81.08 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion / pH: 8.5 Details: 0.8 M potassium sodium tartrate tetrahydrate, 0.1 M Tris, pH 8.5 and 0.5% w/v polyethylene glycol monomethyl ether 5,000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 20, 2016 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97853 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 4.3→50 Å / Num. obs: 16538 / % possible obs: 99.9 % / Redundancy: 15.7 % / Biso Wilson estimate: 77.93 Å2 / Rmerge(I) obs: 0.159 / Rpim(I) all: 0.059 / Rrim(I) all: 0.142 / Χ2: 0.961 / Net I/σ(I): 2.2 / Num. measured all: 259971 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4D8O, 3KBT Resolution: 4.313→39.896 Å / SU ML: 0.74 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 31.9
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 349.62 Å2 / Biso mean: 87.6322 Å2 / Biso min: 3.08 Å2 | ||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 4.313→39.896 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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