[English] 日本語
Yorodumi- PDB-3dow: Complex structure of GABA type A receptor associated protein and ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3dow | ||||||
---|---|---|---|---|---|---|---|
Title | Complex structure of GABA type A receptor associated protein and its binding epitope on calreticulin | ||||||
Components |
| ||||||
Keywords | PROTEIN TRANSPORT / alpha-beta / beta-grasp fold / Cytoplasm / Cytoskeleton / Golgi apparatus / Membrane / Microtubule / Transport / Calcium / Chaperone / Endoplasmic reticulum / Extracellular matrix / Lectin / Metal-binding / Secreted / Zinc | ||||||
Function / homology | Function and homology information Calnexin/calreticulin cycle / cytolytic granule / positive regulation of dendritic cell chemotaxis / cortical granule / Assembly of Viral Components at the Budding Site / negative regulation of trophoblast cell migration / ATF6 (ATF6-alpha) activates chaperone genes / positive regulation of protein K48-linked ubiquitination / negative regulation of retinoic acid receptor signaling pathway / cellular response to electrical stimulus ...Calnexin/calreticulin cycle / cytolytic granule / positive regulation of dendritic cell chemotaxis / cortical granule / Assembly of Viral Components at the Budding Site / negative regulation of trophoblast cell migration / ATF6 (ATF6-alpha) activates chaperone genes / positive regulation of protein K48-linked ubiquitination / negative regulation of retinoic acid receptor signaling pathway / cellular response to electrical stimulus / endoplasmic reticulum quality control compartment / nuclear receptor-mediated glucocorticoid signaling pathway / regulation of meiotic nuclear division / complement component C1q complex binding / sequestering of calcium ion / response to glycoside / sarcoplasmic reticulum lumen / regulation of Rac protein signal transduction / protein folding in endoplasmic reticulum / nuclear export signal receptor activity / negative regulation of intracellular steroid hormone receptor signaling pathway / hormone binding / GABA receptor binding / cardiac muscle cell differentiation / molecular sequestering activity / cellular response to nitrogen starvation / phosphatidylethanolamine binding / TBC/RABGAPs / protein maturation by protein folding / microtubule associated complex / Scavenging by Class F Receptors / Scavenging by Class A Receptors / cortical actin cytoskeleton organization / nuclear androgen receptor binding / Macroautophagy / cellular response to lithium ion / response to testosterone / beta-tubulin binding / axoneme / autophagosome membrane / autophagosome maturation / protein localization to nucleus / autophagosome assembly / extrinsic apoptotic signaling pathway via death domain receptors / negative regulation of neuron differentiation / smooth endoplasmic reticulum / autophagosome / protein targeting / positive regulation of cell cycle / ERAD pathway / positive regulation of substrate adhesion-dependent cell spreading / protein folding chaperone / positive regulation of phagocytosis / sperm midpiece / endocytic vesicle lumen / protein export from nucleus / positive regulation of endothelial cell migration / endoplasmic reticulum-Golgi intermediate compartment membrane / acrosomal vesicle / lumenal side of endoplasmic reticulum membrane / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / peptide binding / peptide antigen assembly with MHC class I protein complex / MHC class I peptide loading complex / cellular response to virus / microtubule cytoskeleton organization / intracellular calcium ion homeostasis / positive regulation of non-canonical NF-kappaB signal transduction / phagocytic vesicle membrane / cellular senescence / unfolded protein binding / protein transport / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / actin cytoskeleton / integrin binding / protein folding / response to estradiol / nuclear envelope / ER-Phagosome pathway / protein-folding chaperone binding / cytoplasmic vesicle / carbohydrate binding / spermatogenesis / microtubule binding / chemical synaptic transmission / regulation of apoptotic process / collagen-containing extracellular matrix / microtubule / lysosome / protein stabilization / negative regulation of translation / ribosome / response to xenobiotic stimulus / iron ion binding / endoplasmic reticulum lumen / external side of plasma membrane / Golgi membrane / focal adhesion / negative regulation of DNA-templated transcription / mRNA binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Thielmann, Y. / Weiergraeber, O.H. / Willbold, D. | ||||||
Citation | Journal: Febs J. / Year: 2009 Title: Structural framework of the GABARAP-calreticulin interface - implications for substrate binding to endoplasmic reticulum chaperones. Authors: Thielmann, Y. / Weiergraber, O.H. / Mohrluder, J. / Willbold, D. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3dow.cif.gz | 40.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3dow.ent.gz | 26.9 KB | Display | PDB format |
PDBx/mmJSON format | 3dow.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3dow_validation.pdf.gz | 434.2 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 3dow_full_validation.pdf.gz | 435.6 KB | Display | |
Data in XML | 3dow_validation.xml.gz | 7.5 KB | Display | |
Data in CIF | 3dow_validation.cif.gz | 9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/do/3dow ftp://data.pdbj.org/pub/pdb/validation_reports/do/3dow | HTTPS FTP |
-Related structure data
Related structure data | 1kjtS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Details | The predicted biological unit contains one copy of the monomeric GABARAP-CRT peptide complex. |
-Components
#1: Protein | Mass: 14086.176 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Product contains an N-terminal cloning artifact (glycine-serine) preceding the sequence of native GABARAP. Source: (gene. exp.) Homo sapiens (human) / Gene: GABARAP, FLC3B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: O95166 |
---|---|
#2: Protein/peptide | Mass: 1331.407 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: Synthetic peptide containing amino acids 195-205 of mature calreticulin, CALR_HUMAN, UniProt entry P27797 References: UniProt: P27797 |
#3: Chemical | ChemComp-ZN / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.47 Å3/Da / Density % sol: 50.19 % |
---|---|
Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.1 M MES, 27% v/v PEG MME 550, 10 mM ZnSO4, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 14, 2007 / Details: Mirrors |
Radiation | Monochromator: diamond, germanium / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→39.62 Å / Num. all: 6892 / Num. obs: 6892 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 6.8 % / Biso Wilson estimate: 45 Å2 / Rmerge(I) obs: 0.052 / Rsym value: 0.052 / Net I/σ(I): 11.1 |
Reflection shell | Resolution: 2.3→2.42 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.399 / Mean I/σ(I) obs: 1.9 / Num. measured all: 6540 / Num. unique all: 985 / Rsym value: 0.399 / % possible all: 100 |
-Processing
Software |
| ||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1KJT Resolution: 2.3→34.31 Å / Occupancy max: 1 / Occupancy min: 1 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
| ||||||||||||||||||||||||||||
Displacement parameters | Biso max: 75.56 Å2 / Biso mean: 45.275 Å2 / Biso min: 27.3 Å2
| ||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→34.31 Å
| ||||||||||||||||||||||||||||
Refine LS restraints |
|