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Yorodumi- PDB-6jky: Crystal structure of MvcA-UBE2N-Ub complex from Legionella pneumophila -
+Open data
-Basic information
Entry | Database: PDB / ID: 6jky | ||||||
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Title | Crystal structure of MvcA-UBE2N-Ub complex from Legionella pneumophila | ||||||
Components |
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Keywords | SIGNALING PROTEIN / Legionella pneumophila effect factor complex | ||||||
Function / homology | Function and homology information UBC13-MMS2 complex / ubiquitin conjugating enzyme complex / ubiquitin-protein transferase activator activity / positive regulation of protein K63-linked ubiquitination / DNA double-strand break processing / postreplication repair / positive regulation of intracellular signal transduction / positive regulation of double-strand break repair / E2 ubiquitin-conjugating enzyme / ubiquitin conjugating enzyme activity ...UBC13-MMS2 complex / ubiquitin conjugating enzyme complex / ubiquitin-protein transferase activator activity / positive regulation of protein K63-linked ubiquitination / DNA double-strand break processing / postreplication repair / positive regulation of intracellular signal transduction / positive regulation of double-strand break repair / E2 ubiquitin-conjugating enzyme / ubiquitin conjugating enzyme activity / protein K63-linked ubiquitination / regulation of DNA repair / ubiquitin ligase complex / antiviral innate immune response / negative regulation of TORC1 signaling / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / positive regulation of DNA repair / TICAM1, RIP1-mediated IKK complex recruitment / IKK complex recruitment mediated by RIP1 / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / PINK1-PRKN Mediated Mitophagy / ubiquitin binding / activated TAK1 mediates p38 MAPK activation / Nonhomologous End-Joining (NHEJ) / NOD1/2 Signaling Pathway / double-strand break repair via homologous recombination / TAK1-dependent IKK and NF-kappa-B activation / G2/M DNA damage checkpoint / CLEC7A (Dectin-1) signaling / ISG15 antiviral mechanism / FCERI mediated NF-kB activation / Formation of Incision Complex in GG-NER / Interleukin-1 signaling / Aggrephagy / ubiquitin-protein transferase activity / Antigen processing: Ubiquitination & Proteasome degradation / Downstream TCR signaling / E3 ubiquitin ligases ubiquitinate target proteins / positive regulation of NF-kappaB transcription factor activity / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / T cell receptor signaling pathway / Processing of DNA double-strand break ends / proteasome-mediated ubiquitin-dependent protein catabolic process / positive regulation of canonical NF-kappaB signal transduction / protein ubiquitination / ubiquitin protein ligase binding / SARS-CoV-2 activates/modulates innate and adaptive immune responses / protein-containing complex / RNA binding / extracellular exosome / nucleoplasm / ATP binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Legionella pneumophila subsp. pneumophila str. Philadelphia 1 (bacteria) Homo sapiens (human) Schistosoma margrebowiei (invertebrata) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.454 Å | ||||||
Authors | Ouyang, S.Y. / Guan, H. | ||||||
Citation | Journal: Embo J. / Year: 2020 Title: Legionella pneumophila regulates the activity of UBE2N by deamidase-mediated deubiquitination. Authors: Gan, N. / Guan, H. / Huang, Y. / Yu, T. / Fu, J. / Nakayasu, E.S. / Puvar, K. / Das, C. / Wang, D. / Ouyang, S. / Luo, Z.Q. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6jky.cif.gz | 489.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6jky.ent.gz | 404.7 KB | Display | PDB format |
PDBx/mmJSON format | 6jky.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6jky_validation.pdf.gz | 469.3 KB | Display | wwPDB validaton report |
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Full document | 6jky_full_validation.pdf.gz | 484.2 KB | Display | |
Data in XML | 6jky_validation.xml.gz | 42.9 KB | Display | |
Data in CIF | 6jky_validation.cif.gz | 58.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jk/6jky ftp://data.pdbj.org/pub/pdb/validation_reports/jk/6jky | HTTPS FTP |
-Related structure data
Related structure data | 6k11SC 1jatS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-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: 44041.871 Da / Num. of mol.: 2 / Mutation: C83A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Legionella pneumophila subsp. pneumophila str. Philadelphia 1 (bacteria) Strain: Philadelphia 1 / Gene: lpg2148 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5ZTL3 #2: Protein | Mass: 17099.668 Da / Num. of mol.: 2 / Mutation: K94A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: UBE2N / Production host: Escherichia coli (E. coli) References: UniProt: P61088, E2 ubiquitin-conjugating enzyme #3: Protein | Mass: 8824.103 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Schistosoma margrebowiei (invertebrata) Gene: SMRZ_LOCUS12712 / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): K-12 / References: UniProt: A0A3P7ZMV6 #4: Water | ChemComp-HOH / | |
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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: 2.65 Å3/Da / Density % sol: 53.52 % |
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Crystal grow | Temperature: 289.15 K / Method: vapor diffusion, sitting drop Details: 0.2 M Sodium thiocyanate, 20% w/v Polyethylene glycol 3,350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97894 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 16, 2018 |
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97894 Å / Relative weight: 1 |
Reflection | Resolution: 2.45→65.14 Å / Num. obs: 52753 / % possible obs: 96.5 % / Redundancy: 6.5 % / Biso Wilson estimate: 58.29 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.066 / Rrim(I) all: 0.071 / Net I/σ(I): 14.9 |
Reflection shell | Resolution: 2.45→2.54 Å / Rmerge(I) obs: 0.547 / Num. unique obs: 7924 / Rrim(I) all: 0.591 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6K11 and 1JAT Resolution: 2.454→65.135 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 30.74 / 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: 193.14 Å2 / Biso mean: 79.9412 Å2 / Biso min: 33.06 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.454→65.135 Å
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Refine LS restraints |
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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 / Origin x: -42.7003 Å / Origin y: -18.1782 Å / Origin z: -32.783 Å
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Refinement TLS group |
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