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- PDB-7say: Fragment of streptococcal M87 protein fused to GCN4 adaptor in co... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7say | ||||||
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Title | Fragment of streptococcal M87 protein fused to GCN4 adaptor in complex with human cathelicidin | ||||||
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![]() | IMMUNE SYSTEM / complex / virulence factor / antimicrobial peptide | ||||||
Function / homology | ![]() cytolysis / killing by host of symbiont cells / protein localization to nuclear periphery / FCERI mediated MAPK activation / Activation of the AP-1 family of transcription factors / neutrophil activation / response to amino acid starvation / specific granule / mediator complex binding / negative regulation of ribosomal protein gene transcription by RNA polymerase II ...cytolysis / killing by host of symbiont cells / protein localization to nuclear periphery / FCERI mediated MAPK activation / Activation of the AP-1 family of transcription factors / neutrophil activation / response to amino acid starvation / specific granule / mediator complex binding / negative regulation of ribosomal protein gene transcription by RNA polymerase II / positive regulation of cellular response to amino acid starvation / cellular response to peptidoglycan / nitrogen catabolite activation of transcription from RNA polymerase II promoter / cellular response to interleukin-6 / Oxidative Stress Induced Senescence / Antimicrobial peptides / TFIID-class transcription factor complex binding / cellular response to interleukin-1 / positive regulation of RNA polymerase II transcription preinitiation complex assembly / positive regulation of transcription initiation by RNA polymerase II / amino acid biosynthetic process / cellular response to nutrient levels / cellular response to amino acid starvation / innate immune response in mucosa / cell projection / lipopolysaccharide binding / RNA polymerase II transcription regulator complex / specific granule lumen / positive regulation of angiogenesis / antimicrobial humoral immune response mediated by antimicrobial peptide / tertiary granule lumen / cellular response to tumor necrosis factor / antibacterial humoral response / DNA-binding transcription activator activity, RNA polymerase II-specific / transcription regulator complex / cellular response to lipopolysaccharide / sequence-specific DNA binding / defense response to Gram-negative bacterium / RNA polymerase II-specific DNA-binding transcription factor binding / amyloid fibril formation / DNA-binding transcription factor activity, RNA polymerase II-specific / defense response to Gram-positive bacterium / intracellular signal transduction / defense response to bacterium / positive regulation of protein phosphorylation / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / innate immune response / chromatin binding / positive regulation of cell population proliferation / Neutrophil degranulation / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular exosome / extracellular region / identical protein binding / nucleus Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kolesinski, P. / Ghosh, P. | ||||||
Funding support | ![]()
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![]() | ![]() Title: An M protein coiled coil unfurls and exposes its hydrophobic core to capture LL-37 Authors: Kolesinski, P. / Wang, K.C. / Hirose, Y. / Nizet, V. / Ghosh, P. / Stallings, C.L. / Dotsch, V. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 172.9 KB | Display | ![]() |
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PDB format | ![]() | 113.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7safC ![]() 1kqlS 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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Components
#1: Protein | Mass: 8542.565 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: Amino acids 35-38: partial PreScission protease site; amino acids 39-67: GCN4 adaptor - GCN4 from Saccharomyces cerevisiae (amino acids 250-278); amino acids 68-105: M87 protein fragment ...Details: Amino acids 35-38: partial PreScission protease site; amino acids 39-67: GCN4 adaptor - GCN4 from Saccharomyces cerevisiae (amino acids 250-278); amino acids 68-105: M87 protein fragment from Streptococcus pyogenes (amino acids 68-105) Source: (gene. exp.) ![]() ![]() ![]() Strain: ATCC 204508 / S288c / Gene: GCN4, AAS101, AAS3, ARG9, YEL009C, emm Production host: ![]() ![]() References: UniProt: P03069, UniProt: Q6TLP8 #2: Protein/peptide | Mass: 4504.351 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) ![]() #3: Chemical | ChemComp-EDO / #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: 2.32 Å3/Da / Density % sol: 46.93 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 10% (v/v) acetonitrile, 0.1 M MES-NaOH, pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 2, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→45.02 Å / Num. obs: 22092 / % possible obs: 94.52 % / Redundancy: 6.1 % / Biso Wilson estimate: 26.42 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.118 / Rpim(I) all: 0.05 / Rrim(I) all: 0.128 / Net I/σ(I): 8.5 |
Reflection shell | Resolution: 2.1→2.16 Å / Rmerge(I) obs: 0.667 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 1694 / CC1/2: 0.878 / Rpim(I) all: 0.302 / Rrim(I) all: 0.735 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1KQL Resolution: 2.1→45.02 Å / SU ML: 0.2193 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 31.5329 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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 mean: 47.33 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→45.02 Å
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Refine LS restraints |
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LS refinement shell |
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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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