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Yorodumi- PDB-7pc9: The PDZ domain of SYNJ2BP complexed with the PDZ-binding motif of... -
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-Basic information
Entry | Database: PDB / ID: 7pc9 | ||||||
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Title | The PDZ domain of SYNJ2BP complexed with the PDZ-binding motif of HTLV1-TAX1 | ||||||
Components |
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Keywords | PEPTIDE BINDING PROTEIN / PDZ / complex / crystallization chaperone | ||||||
Function / homology | Function and homology information symbiont-mediated perturbation of host exit from mitosis / symbiont-mediated perturbation of host cell cycle G0/G1 transition checkpoint / positive regulation of low-density lipoprotein particle receptor binding / positive regulation of receptor-mediated endocytosis involved in cholesterol transport / AnxA2-p11 complex / membrane raft assembly / negative regulation of sprouting angiogenesis / positive regulation of vacuole organization / positive regulation of low-density lipoprotein particle clearance / phospholipase A2 inhibitor activity ...symbiont-mediated perturbation of host exit from mitosis / symbiont-mediated perturbation of host cell cycle G0/G1 transition checkpoint / positive regulation of low-density lipoprotein particle receptor binding / positive regulation of receptor-mediated endocytosis involved in cholesterol transport / AnxA2-p11 complex / membrane raft assembly / negative regulation of sprouting angiogenesis / positive regulation of vacuole organization / positive regulation of low-density lipoprotein particle clearance / phospholipase A2 inhibitor activity / positive regulation of vesicle fusion / negative regulation of low-density lipoprotein particle receptor catabolic process / embryo development / regulation of Notch signaling pathway / positive regulation of plasma membrane repair / positive regulation of plasminogen activation / PCSK9-AnxA2 complex / myelin sheath adaxonal region / receptor localization to synapse / cadherin binding involved in cell-cell adhesion / Schmidt-Lanterman incisure / vesicle budding from membrane / cornified envelope / plasma membrane protein complex / calcium-dependent phospholipid binding / negative regulation of receptor internalization / establishment or maintenance of epithelial cell apical/basal polarity / collagen fibril organization / S100 protein binding / Dissolution of Fibrin Clot / virion binding / osteoclast development / positive regulation of low-density lipoprotein receptor activity / negative regulation of endothelial cell migration / epithelial cell apoptotic process / positive regulation of receptor recycling / phosphatidylserine binding / receptor clustering / positive regulation of exocytosis / negative regulation of endothelial cell proliferation / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / Rho protein signal transduction / regulation of endocytosis / basement membrane / regulation of neurogenesis / Smooth Muscle Contraction / protein targeting / fibrinolysis / phosphatidylinositol-4,5-bisphosphate binding / cytoskeletal protein binding / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / lipid droplet / negative regulation of angiogenesis / cell-matrix adhesion / response to activity / postsynaptic density membrane / adherens junction / lung development / calcium channel activity / mRNA transcription by RNA polymerase II / serine-type endopeptidase inhibitor activity / neuromuscular junction / negative regulation of ERK1 and ERK2 cascade / sarcolemma / nuclear matrix / cell-cell adhesion / SH3 domain binding / RNA polymerase II transcription regulator complex / calcium-dependent protein binding / azurophil granule lumen / melanosome / late endosome membrane / midbody / chemical synaptic transmission / basolateral plasma membrane / angiogenesis / collagen-containing extracellular matrix / protease binding / vesicle / mitochondrial outer membrane / host cell cytoplasm / early endosome / endosome / neuron projection / lysosomal membrane / calcium ion binding / host cell nucleus / Neutrophil degranulation / positive regulation of DNA-templated transcription / cell surface / positive regulation of transcription by RNA polymerase II / mitochondrion / DNA binding / extracellular space / RNA binding / extracellular exosome / extracellular region / membrane / identical protein binding / metal ion binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) HTLV-1 subtype A (virus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Cousido-Siah, A. / Trave, G. / Gogl, G. | ||||||
Funding support | 1items
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Citation | Journal: Acta Crystallogr D Struct Biol / Year: 2022 Title: A scalable strategy to solve structures of PDZ domains and their complexes. Authors: Cousido-Siah, A. / Carneiro, L. / Kostmann, C. / Ecsedi, P. / Nyitray, L. / Trave, G. / Gogl, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7pc9.cif.gz | 343.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7pc9.ent.gz | 278.9 KB | Display | PDB format |
PDBx/mmJSON format | 7pc9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pc/7pc9 ftp://data.pdbj.org/pub/pdb/validation_reports/pc/7pc9 | HTTPS FTP |
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-Related structure data
Related structure data | 7pc3C 7pc4C 7pc5C 7pc7C 7pc8C 7pcbC 7qqlC 7qqmC 7qqnC 2jikS 5n7dS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-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: 47040.141 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SYNJ2BP, OMP25, ANXA2, ANX2, ANX2L4, CAL1H, LPC2D / Production host: Escherichia coli (E. coli) / References: UniProt: P57105, UniProt: P07355 #2: Protein/peptide | | Mass: 1264.363 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: N-terminal biotin-ttds (trioxatridecan-succinamic acid) label Source: (synth.) HTLV-1 subtype A (virus) / References: UniProt: P03409 #3: Chemical | ChemComp-CA / #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.81 Å3/Da / Density % sol: 56.3 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.1 M HEPES pH 7.5, 10% w/v PEG 8000, 8% v/v Ethylene glycol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Mar 17, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→49.327 Å / Num. obs: 41356 / % possible obs: 99.3 % / Redundancy: 13.46 % / CC1/2: 0.995 / Rrim(I) all: 0.316 / Net I/σ(I): 8.93 |
Reflection shell | Resolution: 2.4→2.46 Å / Mean I/σ(I) obs: 1.22 / Num. unique obs: 2991 / CC1/2: 0.449 / Rrim(I) all: 2.43 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5N7D, 2JIK Resolution: 2.4→49.327 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 25.39 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 171.46 Å2 / Biso mean: 53.8979 Å2 / Biso min: 20.82 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.4→49.327 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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