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- PDB-6qk8: Crystal structure of yeast 14-3-3 protein (Bmh1) from Saccharomyc... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6qk8 | ||||||
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Title | Crystal structure of yeast 14-3-3 protein (Bmh1) from Saccharomyces cerevisiae with the Nha1p (yeast Na+/H+ antiporter) 14-3-3 binding motif Ser481 | ||||||
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![]() | SIGNALING PROTEIN / 14-3-3 protein / Bmh / Na+/H+ antiporter / Nha1p | ||||||
Function / homology | ![]() : / : / signal transduction involved in filamentous growth / mitotic spindle orientation checkpoint signaling / : / pseudohyphal growth / ascospore formation / potassium ion transmembrane transporter activity / potassium ion export across plasma membrane / regulation of glycogen metabolic process ...: / : / signal transduction involved in filamentous growth / mitotic spindle orientation checkpoint signaling / : / pseudohyphal growth / ascospore formation / potassium ion transmembrane transporter activity / potassium ion export across plasma membrane / regulation of glycogen metabolic process / sodium:proton antiporter activity / sodium ion export across plasma membrane / intracellular potassium ion homeostasis / aggresome assembly / response to osmotic stress / negative regulation of ubiquitin protein ligase activity / DNA replication origin binding / sodium ion transmembrane transport / phosphoserine residue binding / enzyme activator activity / DNA damage checkpoint signaling / cytoplasmic stress granule / RNA polymerase II-specific DNA-binding transcription factor binding / Ras protein signal transduction / membrane => GO:0016020 / membrane raft / negative regulation of apoptotic process / negative regulation of transcription by RNA polymerase II / endoplasmic reticulum / signal transduction / nucleus / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Smidova, A. / Obsil, T. / Obsilova, V. | ||||||
Funding support | ![]()
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![]() | ![]() Title: The activity of Saccharomyces cerevisiae Na+, K+/H+antiporter Nha1 is negatively regulated by 14-3-3 protein binding at serine 481. Authors: Smidova, A. / Stankova, K. / Petrvalska, O. / Lazar, J. / Sychrova, H. / Obsil, T. / Zimmermannova, O. / Obsilova, V. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 177 KB | Display | ![]() |
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PDB format | ![]() | 139.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 465 KB | Display | ![]() |
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Full document | ![]() | 468.7 KB | Display | |
Data in XML | ![]() | 29.5 KB | Display | |
Data in CIF | ![]() | 41 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5n6nS S: Starting model for refinement |
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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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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 26750.881 Da / Num. of mol.: 4 / Mutation: M237Stop Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC 204508 / S288c / Gene: BMH1, YER177W / Production host: ![]() ![]() #2: Protein/peptide | Mass: 1116.212 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC 204508 / S288c / Gene: NHA1, YLR138W, L3149, L9606.4 / Production host: ![]() ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal grow | Temperature: 293.15 K / Method: vapor diffusion / pH: 7 / Details: KBr, PEG 2K MME |
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-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Nov 29, 2018 / Details: SAGITALLY BENDED SI111 CRYSTAL |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 2.917→41.141 Å / Num. obs: 16913 / % possible obs: 92.83 % / Redundancy: 2.98 % / Biso Wilson estimate: 43.77 Å2 / CC1/2: 0.986 / Rrim(I) all: 0.167 / Net I/σ(I): 7.23 |
Reflection shell | Resolution: 2.917→3.022 Å / Redundancy: 4.81 % / Mean I/σ(I) obs: 2.15 / Num. unique obs: 1720 / CC1/2: 0.723 / Rrim(I) all: 0.617 / % possible all: 94.51 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5N6N Resolution: 2.917→41.141 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 29.04
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.917→41.141 Å
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Refine LS restraints |
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LS refinement shell |
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