+Open data
-Basic information
Entry | Database: PDB / ID: 8caf | |||||||||||||||
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Title | N8C_Fab3b in complex with NEDD8-CUL1(WHB) | |||||||||||||||
Components |
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Keywords | CELL CYCLE / NEDD8 / Cullin-RING ligase / ubiquitin / antibody | |||||||||||||||
Function / homology | Function and homology information Parkin-FBXW7-Cul1 ubiquitin ligase complex / cullin-RING ubiquitin ligase complex / regulation of proteolysis / Loss of Function of FBXW7 in Cancer and NOTCH1 Signaling / protein neddylation / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / SCF ubiquitin ligase complex / ubiquitin ligase complex scaffold activity / Prolactin receptor signaling / protein monoubiquitination ...Parkin-FBXW7-Cul1 ubiquitin ligase complex / cullin-RING ubiquitin ligase complex / regulation of proteolysis / Loss of Function of FBXW7 in Cancer and NOTCH1 Signaling / protein neddylation / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / SCF ubiquitin ligase complex / ubiquitin ligase complex scaffold activity / Prolactin receptor signaling / protein monoubiquitination / TGF-beta receptor signaling activates SMADs / protein K48-linked ubiquitination / anatomical structure morphogenesis / Nuclear events stimulated by ALK signaling in cancer / Regulation of BACH1 activity / MAP3K8 (TPL2)-dependent MAPK1/3 activation / intrinsic apoptotic signaling pathway / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / Dectin-1 mediated noncanonical NF-kB signaling / Degradation of GLI1 by the proteasome / Activation of NF-kappaB in B cells / Negative regulation of NOTCH4 signaling / animal organ morphogenesis / Iron uptake and transport / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / G1/S transition of mitotic cell cycle / Degradation of GLI2 by the proteasome / GLI3 is processed to GLI3R by the proteasome / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / protein modification process / modification-dependent protein catabolic process / Degradation of beta-catenin by the destruction complex / protein localization / NOTCH1 Intracellular Domain Regulates Transcription / protein tag activity / CLEC7A (Dectin-1) signaling / SCF(Skp2)-mediated degradation of p27/p21 / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / FCERI mediated NF-kB activation / Interleukin-1 signaling / Orc1 removal from chromatin / Regulation of RUNX2 expression and activity / UCH proteinases / Cyclin D associated events in G1 / Regulation of PLK1 Activity at G2/M Transition / protein-macromolecule adaptor activity / Antigen processing: Ubiquitination & Proteasome degradation / Circadian Clock / Cargo recognition for clathrin-mediated endocytosis / Downstream TCR signaling / Neddylation / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / positive regulation of canonical NF-kappaB signal transduction / cell population proliferation / protein ubiquitination / ubiquitin protein ligase binding / regulation of transcription by RNA polymerase II / proteolysis / extracellular exosome / nucleoplasm / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | |||||||||||||||
Biological species | Homo sapiens (human) | |||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.66 Å | |||||||||||||||
Authors | Duda, D.M. / Yanishevski, D. / Henneberg, L.T. / Schulman, B.A. | |||||||||||||||
Funding support | United States, European Union, Germany, 4items
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Citation | Journal: Nat.Chem.Biol. / Year: 2023 Title: Activity-based profiling of cullin-RING E3 networks by conformation-specific probes. Authors: Henneberg, L.T. / Singh, J. / Duda, D.M. / Baek, K. / Yanishevski, D. / Murray, P.J. / Mann, M. / Sidhu, S.S. / Schulman, B.A. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8caf.cif.gz | 277.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8caf.ent.gz | 181.4 KB | Display | PDB format |
PDBx/mmJSON format | 8caf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ca/8caf ftp://data.pdbj.org/pub/pdb/validation_reports/ca/8caf | HTTPS FTP |
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-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-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: Antibody | Mass: 22958.494 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli K-12 (bacteria) #2: Antibody | Mass: 23391.992 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli K-12 (bacteria) #3: Protein | Mass: 9341.104 Da / Num. of mol.: 2 / Fragment: UNP residues 677-776 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CUL1 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: Q13616 #4: Protein | Mass: 8573.978 Da / Num. of mol.: 2 / Fragment: UNP residues 1-76 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: NEDD8 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: Q15843 |
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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: 3.64 Å3/Da / Density % sol: 66.24 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 2.0-2.1M Ammonium Sulfate, 0.1M Citrate pH 6.0, 10mM TCEP |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.979 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 16, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.66→180 Å / Num. obs: 56730 / % possible obs: 98.6 % / Redundancy: 6.7 % / Biso Wilson estimate: 77.01 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.055 / Net I/σ(I): 23.8 |
Reflection shell | Resolution: 2.66→2.74 Å / Rmerge(I) obs: 1.165 / Num. unique obs: 4609 / CC1/2: 0.612 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.66→90.33 Å / SU ML: 0.461 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.4446 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: 70.51 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.66→90.33 Å
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Refine LS restraints |
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LS refinement shell |
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