+Open data
-Basic information
Entry | Database: PDB / ID: 4jqw | ||||||
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Title | Crystal Structure of a Complex of NOD1 CARD and Ubiquitin | ||||||
Components |
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Keywords | APOPTOSIS/SIGNALLING PROTEIN / death domain-like fold / innate immunity / RIP2 / ATG16L / S-dimethylarsenic / APOPTOSIS-SIGNALLING PROTEIN complex | ||||||
Function / homology | Function and homology information positive regulation of dendritic cell antigen processing and presentation / detection of biotic stimulus / positive regulation of xenophagy / xenophagy / nucleotide-binding oligomerization domain containing 1 signaling pathway / positive regulation of stress-activated MAPK cascade / cellular response to muramyl dipeptide / CARD domain binding / peptidoglycan binding / positive regulation of macrophage cytokine production ...positive regulation of dendritic cell antigen processing and presentation / detection of biotic stimulus / positive regulation of xenophagy / xenophagy / nucleotide-binding oligomerization domain containing 1 signaling pathway / positive regulation of stress-activated MAPK cascade / cellular response to muramyl dipeptide / CARD domain binding / peptidoglycan binding / positive regulation of macrophage cytokine production / pattern recognition receptor signaling pathway / pattern recognition receptor activity / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process / cysteine-type endopeptidase activator activity involved in apoptotic process / detection of bacterium / stress-activated MAPK cascade / JNK cascade / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / phagocytic vesicle / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / Prevention of phagosomal-lysosomal fusion / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / Glycogen synthesis / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Membrane binding and targetting of GAG proteins / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / Endosomal Sorting Complex Required For Transport (ESCRT) / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Negative regulation of FLT3 / Constitutive Signaling by NOTCH1 HD Domain Mutants / Regulation of FZD by ubiquitination / TICAM1,TRAF6-dependent induction of TAK1 complex / TICAM1-dependent activation of IRF3/IRF7 / NOTCH2 Activation and Transmission of Signal to the Nucleus / APC/C:Cdc20 mediated degradation of Cyclin B / ERK1 and ERK2 cascade / p75NTR recruits signalling complexes / Downregulation of ERBB4 signaling / NOTCH3 Activation and Transmission of Signal to the Nucleus / APC-Cdc20 mediated degradation of Nek2A / TRAF6-mediated induction of TAK1 complex within TLR4 complex / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / PINK1-PRKN Mediated Mitophagy / Pexophagy / Regulation of innate immune responses to cytosolic DNA / InlA-mediated entry of Listeria monocytogenes into host cells / VLDLR internalisation and degradation / Regulation of pyruvate metabolism / Downregulation of ERBB2:ERBB3 signaling / NF-kB is activated and signals survival / Regulation of PTEN localization / NRIF signals cell death from the nucleus / response to endoplasmic reticulum stress / Regulation of BACH1 activity / Activated NOTCH1 Transmits Signal to the Nucleus / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Translesion synthesis by REV1 / MAP3K8 (TPL2)-dependent MAPK1/3 activation / Translesion synthesis by POLK / TICAM1, RIP1-mediated IKK complex recruitment / Downregulation of TGF-beta receptor signaling / EGFR downregulation / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / Josephin domain DUBs / Regulation of activated PAK-2p34 by proteasome mediated degradation / InlB-mediated entry of Listeria monocytogenes into host cell / IKK complex recruitment mediated by RIP1 / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / positive regulation of interleukin-1 beta production / TNFR1-induced NF-kappa-B signaling pathway / Autodegradation of Cdh1 by Cdh1:APC/C / ubiquitin binding / APC/C:Cdc20 mediated degradation of Securin / Asymmetric localization of PCP proteins / TCF dependent signaling in response to WNT / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / Ubiquitin-dependent degradation of Cyclin D / Regulation of NF-kappa B signaling / positive regulation of interleukin-8 production / AUF1 (hnRNP D0) binds and destabilizes mRNA / TNFR2 non-canonical NF-kB pathway / activated TAK1 mediates p38 MAPK activation / Vpu mediated degradation of CD4 / Assembly of the pre-replicative complex / Negative regulators of DDX58/IFIH1 signaling / Deactivation of the beta-catenin transactivating complex / Degradation of DVL / CDK-mediated phosphorylation and removal of Cdc6 Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | ||||||
Authors | Ver Heul, A.M. / Gakhar, L. / Piper, R.C. / Ramaswamy, S. | ||||||
Citation | Journal: Plos One / Year: 2014 Title: Crystal structure of a complex of NOD1 CARD and ubiquitin Authors: Ver Heul, A.M. / Gakhar, L. / Piper, R.C. / Ramaswamy, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4jqw.cif.gz | 47.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4jqw.ent.gz | 32.3 KB | Display | PDB format |
PDBx/mmJSON format | 4jqw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4jqw_validation.pdf.gz | 441.2 KB | Display | wwPDB validaton report |
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Full document | 4jqw_full_validation.pdf.gz | 441.5 KB | Display | |
Data in XML | 4jqw_validation.xml.gz | 8.1 KB | Display | |
Data in CIF | 4jqw_validation.cif.gz | 9.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jq/4jqw ftp://data.pdbj.org/pub/pdb/validation_reports/jq/4jqw | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 12041.616 Da / Num. of mol.: 1 / Fragment: CARD domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CARD4, NOD1 / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q9Y239 |
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#2: Protein | Mass: 8576.831 Da / Num. of mol.: 1 / Fragment: Ubiquitin Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: UBC / Plasmid: pRSUb / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P0CG48 |
#3: Chemical | ChemComp-PO4 / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2 Å3/Da / Density % sol: 38.63 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.6 Details: 100mM PCB, 25% PEG1500, pH 8.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å |
Detector | Type: NOIR-1 / Detector: CCD / Date: Apr 23, 2011 |
Radiation | Monochromator: Rosenbaum-Rock monochromator double crystal focusing Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→38.982 Å / Num. all: 4052 / Num. obs: 4048 / % possible obs: 99.88 % / Observed criterion σ(I): 5 / Redundancy: 13.35 % / Biso Wilson estimate: 86.06 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 28.4 |
Reflection shell | Resolution: 2.9→3 Å / Redundancy: 13.92 % / Rmerge(I) obs: 0.207 / Mean I/σ(I) obs: 11.4 / Num. unique all: 395 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entries 2NSN, 1UBQ Resolution: 2.9→38.982 Å / Occupancy max: 1 / Occupancy min: 0.5 / SU ML: 0.39 / σ(F): 1.36 / 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: 99.84 Å2 / Biso mean: 57.4385 Å2 / Biso min: 27.52 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.9→38.982 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 3 / % reflection obs: 100 %
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