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- PDB-7qcr: MLLT4/Afadin PDZ domain in complex with the C-terminal peptide fr... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7qcr | |||||||||
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Title | MLLT4/Afadin PDZ domain in complex with the C-terminal peptide from protein E of SARS-CoV-2 | |||||||||
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![]() | CELL ADHESION / MLLT4-Afadin PDZ domain in complex with the C-terminal peptide from protein E of SARS-CoV-2 | |||||||||
Function / homology | ![]() disruption of cellular anatomical structure in another organism / viral budding from Golgi membrane / establishment of protein localization to plasma membrane / positive regulation of cell-cell adhesion mediated by cadherin / Tight junction interactions / SARS-CoV-2 targets PDZ proteins in cell-cell junction / pore complex assembly / establishment of endothelial intestinal barrier / cytoplasmic capsid assembly / positive regulation of cell-cell adhesion ...disruption of cellular anatomical structure in another organism / viral budding from Golgi membrane / establishment of protein localization to plasma membrane / positive regulation of cell-cell adhesion mediated by cadherin / Tight junction interactions / SARS-CoV-2 targets PDZ proteins in cell-cell junction / pore complex assembly / establishment of endothelial intestinal barrier / cytoplasmic capsid assembly / positive regulation of cell-cell adhesion / Regulation of gap junction activity / cell-cell adhesion mediated by cadherin / bicellular tight junction assembly / cell-cell contact zone / Adherens junctions interactions / tight junction / pore complex / host cell Golgi membrane / endoplasmic reticulum-Golgi intermediate compartment / Maturation of protein E / cell adhesion molecule binding / negative regulation of cell migration / adherens junction / small GTPase binding / regulation of protein localization / actin filament binding / cell-cell junction / cell junction / cell-cell signaling / monoatomic ion channel activity / Translation of Structural Proteins / Virion Assembly and Release / Induction of Cell-Cell Fusion / structural constituent of virion / Attachment and Entry / cell adhesion / nuclear speck / cadherin binding / positive regulation of gene expression / apoptotic process / SARS-CoV-2 activates/modulates innate and adaptive immune responses / virion membrane / signal transduction / nucleoplasm / identical protein binding / membrane / plasma membrane / cytosol Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Zhu, Y. / Alvarez, F. / Haouz, A. / Mechaly, A. / Caillet-Saguy, C. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Interactions of Severe Acute Respiratory Syndrome Coronavirus 2 Protein E With Cell Junctions and Polarity PSD-95/Dlg/ZO-1-Containing Proteins. Authors: Zhu, Y. / Alvarez, F. / Wolff, N. / Mechaly, A. / Brule, S. / Neitthoffer, B. / Etienne-Manneville, S. / Haouz, A. / Boeda, B. / Caillet-Saguy, C. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 82.3 KB | Display | ![]() |
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PDB format | ![]() | 61.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7qcsC ![]() 7qctC ![]() 3axaS 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: givenMatrix: (0.99015638853, -0.118219000272, 0.0749305960776), (-0.119214906114, -0.992828180042, 0.00894489094523), (0.0733357512682, -0.0177896848906, -0.9971486322)Vector: -1. ...NCS oper: (Code: given Matrix: (0.99015638853, -0.118219000272, 0.0749305960776), Vector: |
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Components
#1: Protein | Mass: 10063.574 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein/peptide | Mass: 1327.508 Da / Num. of mol.: 2 / Source method: obtained synthetically Source: (synth.) ![]() ![]() References: UniProt: P0DTC4 #3: Chemical | ChemComp-SO4 / | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.43 Å3/Da / Density % sol: 49.39 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, hanging drop / Details: 1 M Na3 Citrate, 0.1 M TRIS at pH 7, 0.2 M NaCl |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 7, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97857 Å / Relative weight: 1 |
Reflection | Resolution: 2.28→37.81 Å / Num. obs: 8373 / % possible obs: 98.9 % / Redundancy: 6.8 % / Biso Wilson estimate: 44.58 Å2 / CC1/2: 0.988 / Rmerge(I) obs: 0.2185 / Net I/σ(I): 6.59 |
Reflection shell | Resolution: 2.281→2.362 Å / Rmerge(I) obs: 1.454 / Num. unique obs: 746 / CC1/2: 0.506 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3AXA Resolution: 2.28→37.81 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.881 / SU R Cruickshank DPI: 0.362 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.377 / SU Rfree Blow DPI: 0.236 / SU Rfree Cruickshank DPI: 0.237
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Displacement parameters | Biso mean: 51.33 Å2
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Refine analyze | Luzzati coordinate error obs: 0.4 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.28→37.81 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.28→2.33 Å
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Refinement TLS params. | Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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