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Yorodumi- PDB-2kpf: Spatial structure of the dimeric transmembrane domain of glycopho... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2kpf | ||||||
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Title | Spatial structure of the dimeric transmembrane domain of glycophorin A in bicelles soluton | ||||||
Components | Glycophorin-A | ||||||
Keywords | MEMBRANE PROTEIN / Glycophorin A / transmembrane dimer / micelles / bicelles / Blood group antigen / Cell membrane / Glycoprotein / Host-virus interaction / Membrane / Sialic acid / Transmembrane | ||||||
Function / homology | Function and homology information ankyrin-1 complex / Cell surface interactions at the vascular wall / virus receptor activity / nucleoplasm / membrane / identical protein binding / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / torsion angle dynamics | ||||||
Model details | fewest violations, model 1 | ||||||
Authors | Mineev, K.S. / Bocharov, E.V. / Goncharuk, M.V. / Arseniev, A.S. / Volynsky, P.E. / Efremov, R.G. | ||||||
Citation | Journal: Acta Naturae / Year: 2011 Title: Dimeric structure of the transmembrane domain of glycophorin a in lipidic and detergent environments. Authors: Mineev, K.S. / Bocharov, E.V. / Volynsky, P.E. / Goncharuk, M.V. / Tkach, E.N. / Ermolyuk, Y.S. / Schulga, A.A. / Chupin, V.V. / Maslennikov, I.V. / Efremov, R.G. / Arseniev, A.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2kpf.cif.gz | 486.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2kpf.ent.gz | 409.5 KB | Display | PDB format |
PDBx/mmJSON format | 2kpf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kp/2kpf ftp://data.pdbj.org/pub/pdb/validation_reports/kp/2kpf | HTTPS FTP |
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-Related structure data
Related structure data | 2kpeC C: citing same article (ref.) |
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Similar structure data | |
Other databases |
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-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein/peptide | Mass: 4240.090 Da / Num. of mol.: 2 / Fragment: transmembrane domain (UNP residues 80-117) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GYPA, GPA / Production host: Escherichia coli (E. coli) / References: UniProt: P02724 |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details | Contents: 1mM unlabeled Glycophorin A, 1mM 13-C/15-N labeled Glycophorin A, 16mM DMPC d-54, 64 mM DHPC d-22, 95% H2O/5% D2O Solvent system: 95% H2O/5% D2O | ||||||||||||||||
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Sample |
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Sample conditions | Ionic strength: 0 / pH: 5.5 / Pressure: ambient / Temperature: 313 K |
-NMR measurement
NMR spectrometer | Type: Varian Unity / Manufacturer: Varian / Model: UNITY / Field strength: 600 MHz |
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-Processing
NMR software |
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Refinement | Method: torsion angle dynamics / Software ordinal: 1 / Details: CYANA | ||||||||||||
NMR representative | Selection criteria: fewest violations | ||||||||||||
NMR ensemble | Conformer selection criteria: target function / Conformers calculated total number: 200 / Conformers submitted total number: 20 |