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- PDB-7p71: The PDZ domain of MAGI1_2 complexed with the PDZ-binding motif of... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7p71 | ||||||
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Title | The PDZ domain of MAGI1_2 complexed with the PDZ-binding motif of HPV35-E6 | ||||||
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![]() | PEPTIDE BINDING PROTEIN / PDZ / complex | ||||||
Function / homology | ![]() : / : / 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 / positive regulation of vacuole organization / positive regulation of low-density lipoprotein particle clearance / phospholipase A2 inhibitor activity / positive regulation of vesicle fusion ...: / : / 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 / 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 / positive regulation of plasma membrane repair / positive regulation of plasminogen activation / PCSK9-AnxA2 complex / positive regulation of cell-cell adhesion / myelin sheath adaxonal region / cadherin binding involved in cell-cell adhesion / Schmidt-Lanterman incisure / vesicle budding from membrane / cornified envelope / plasma membrane protein complex / osteoclast development / calcium-dependent phospholipid binding / negative regulation of receptor internalization / collagen fibril organization / Dissolution of Fibrin Clot / S100 protein binding / vesicle membrane / positive regulation of low-density lipoprotein receptor activity / epithelial cell apoptotic process / positive regulation of receptor recycling / phosphatidylserine binding / alpha-actinin binding / positive regulation of exocytosis / regulation of neurogenesis / basement membrane / Smooth Muscle Contraction / bicellular tight junction / fibrinolysis / phosphatidylinositol-4,5-bisphosphate binding / cytoskeletal protein binding / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / lipid droplet / cell-matrix adhesion / response to activity / cell projection / cell periphery / PDZ domain binding / adherens junction / lung development / mRNA transcription by RNA polymerase II / serine-type endopeptidase inhibitor activity / sarcolemma / nuclear matrix / RNA polymerase II transcription regulator complex / calcium-dependent protein binding / azurophil granule lumen / cell-cell junction / melanosome / cell junction / late endosome membrane / midbody / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / protein-containing complex assembly / protease binding / basolateral plasma membrane / angiogenesis / collagen-containing extracellular matrix / vesicle / host cell cytoplasm / early endosome / cell surface receptor signaling pathway / cell adhesion / endosome / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / lysosomal membrane / DNA-templated transcription / calcium ion binding / host cell nucleus / Neutrophil degranulation / regulation of DNA-templated transcription / nucleolus / cell surface / signal transduction / positive regulation of transcription by RNA polymerase II / DNA binding / RNA binding / extracellular space / extracellular exosome / extracellular region / nucleoplasm / ATP binding / identical protein binding / membrane / nucleus / metal ion binding / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Gogl, G. / Cousido-Siah, A. / Trave, G. | ||||||
![]() | ![]() Title: Quantitative fragmentomics allow affinity mapping of interactomes. Authors: Gogl, G. / Zambo, B. / Kostmann, C. / Cousido-Siah, A. / Morlet, B. / Durbesson, F. / Negroni, L. / Eberling, P. / Jane, P. / Nomine, Y. / Zeke, A. / Ostergaard, S. / Monsellier, E. / Vincentelli, R. / Trave, G. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 350.6 KB | Display | ![]() |
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PDB format | ![]() | 290.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7p70C ![]() 7p72C ![]() 7p73C ![]() 7p74C ![]() 5n7dS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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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
-Protein / Protein/peptide , 2 types, 4 molecules ABCD
#1: Protein | Mass: 48099.840 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: MAGI1, AIP3, BAIAP1, BAP1, TNRC19, ANXA2, ANX2, ANX2L4, CAL1H, LPC2D Production host: ![]() ![]() #2: Protein/peptide | Mass: 1536.621 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: N-terminal biotin-ttds label / Source: (synth.) ![]() |
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-Non-polymers , 4 types, 29 molecules ![](data/chem/img/CA.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/CIT.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/CIT.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-CA / #4: Chemical | ChemComp-GOL / #5: Chemical | ChemComp-CIT / | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.92 Å3/Da / Density % sol: 57.86 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 20-25% polyethylene glycol 3000, 100 mM sodium citrate buffered at pH 5.5 and 100 mM trisodium-citrate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jul 4, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→48 Å / Num. obs: 33417 / % possible obs: 94.4 % / Redundancy: 4.5 % / CC1/2: 1 / Rrim(I) all: 0.05 / Net I/σ(I): 19.06 |
Reflection shell | Resolution: 2.6→2.67 Å / Mean I/σ(I) obs: 1.69 / Num. unique obs: 2471 / CC1/2: 0.852 / Rrim(I) all: 1.11 / % possible all: 94.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5N7D Resolution: 2.6→47.64 Å / SU ML: 0.58 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 37.89 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 1 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 254.8 Å2 / Biso mean: 103.2257 Å2 / Biso min: 47.29 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.6→47.64 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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