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Yorodumi- PDB-7wh3: Solution structure of human stomatin SPFH domain in a phosphate buffer -
+Open data
-Basic information
Entry | Database: PDB / ID: 7wh3 | ||||||
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Title | Solution structure of human stomatin SPFH domain in a phosphate buffer | ||||||
Components | Stomatin | ||||||
Keywords | STRUCTURAL PROTEIN / erythrocyte / membrane skeleton / actin binding / molecular scaffold / Band 7.2 protein / oligomer/multimer formation | ||||||
Function / homology | Function and homology information : / positive regulation of viral process / positive regulation by host of viral genome replication / RNA polymerase binding / azurophil granule membrane / RHOB GTPase cycle / RHOJ GTPase cycle / RHOC GTPase cycle / RHOQ GTPase cycle / plasma membrane => GO:0005886 ...: / positive regulation of viral process / positive regulation by host of viral genome replication / RNA polymerase binding / azurophil granule membrane / RHOB GTPase cycle / RHOJ GTPase cycle / RHOC GTPase cycle / RHOQ GTPase cycle / plasma membrane => GO:0005886 / tertiary granule membrane / RHOH GTPase cycle / CDC42 GTPase cycle / RHOA GTPase cycle / positive regulation of protein targeting to membrane / specific granule membrane / Stimuli-sensing channels / melanosome / vesicle / blood microparticle / cytoskeleton / membrane raft / Neutrophil degranulation / perinuclear region of cytoplasm / endoplasmic reticulum / protein homodimerization activity / mitochondrion / extracellular space / extracellular exosome / membrane / identical protein binding / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
Authors | Kataoka, K. / Tenno, T. / Goda, N. / Hibino, E. / Hiroaki, H. | ||||||
Funding support | Japan, 1items
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Citation | Journal: Curr Res Struct Biol / Year: 2022 Title: A cryptic phosphate-binding pocket on the SPFH domain of human stomatin that regulates a novel fibril-like self-assembly Authors: Kataoka, K. / Suzuki, S. / Tenno, T. / Goda, N. / Hibino, E. / Oshima, A. / Hiroaki, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7wh3.cif.gz | 685.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7wh3.ent.gz | 574.2 KB | Display | PDB format |
PDBx/mmJSON format | 7wh3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wh/7wh3 ftp://data.pdbj.org/pub/pdb/validation_reports/wh/7wh3 | HTTPS FTP |
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-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 12477.999 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: STOM / Plasmid: pGEX-hSTOM(SPFH) / Details (production host): GST fusion protein / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P27105 |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details |
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Sample |
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Sample conditions | Details: 50 mM phosphate buffer (pH 6.4), 100 mM NaCl / Ionic strength: 200 mM / Label: phosphate buffer / pH: 6.4 pH* / PH err: 0.1 / Pressure: 1 atm / Temperature: 298 K |
-NMR measurement
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: simulated annealing / Software ordinal: 1 / Details: CNS | ||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 100 / Conformers submitted total number: 20 |