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Yorodumi- PDB-5ulk: Crystal Structure of RNF165 in complex with a UbcH5b~Ub conjugate -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ulk | ||||||
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Title | Crystal Structure of RNF165 in complex with a UbcH5b~Ub conjugate | ||||||
Components |
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Keywords | TRANSFERASE / Open conformation / Backside / Isopeptide-linked | ||||||
Function / homology | Function and homology information forelimb morphogenesis / muscle structure development / (E3-independent) E2 ubiquitin-conjugating enzyme / innervation / positive regulation of BMP signaling pathway / motor neuron axon guidance / hypothalamus gonadotrophin-releasing hormone neuron development / female meiosis I / positive regulation of protein monoubiquitination / mitochondrion transport along microtubule ...forelimb morphogenesis / muscle structure development / (E3-independent) E2 ubiquitin-conjugating enzyme / innervation / positive regulation of BMP signaling pathway / motor neuron axon guidance / hypothalamus gonadotrophin-releasing hormone neuron development / female meiosis I / positive regulation of protein monoubiquitination / mitochondrion transport along microtubule / fat pad development / E2 ubiquitin-conjugating enzyme / female gonad development / seminiferous tubule development / male meiosis I / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / ubiquitin conjugating enzyme activity / protein autoubiquitination / protein K48-linked ubiquitination / energy homeostasis / regulation of neuron apoptotic process / regulation of proteasomal protein catabolic process / ubiquitin ligase complex / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / 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 / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Membrane binding and targetting of GAG proteins / 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 / NOTCH2 Activation and Transmission of Signal to the Nucleus / TICAM1-dependent activation of IRF3/IRF7 / APC/C:Cdc20 mediated degradation of Cyclin B / p75NTR recruits signalling complexes / Downregulation of ERBB4 signaling / APC-Cdc20 mediated degradation of Nek2A / PINK1-PRKN Mediated Mitophagy / TRAF6-mediated induction of TAK1 complex within TLR4 complex / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / Pexophagy / Regulation of innate immune responses to cytosolic DNA / InlA-mediated entry of Listeria monocytogenes into host cells / VLDLR internalisation and degradation / Downregulation of ERBB2:ERBB3 signaling / NF-kB is activated and signals survival / NRIF signals cell death from the nucleus / Regulation of PTEN localization / Activated NOTCH1 Transmits Signal to the Nucleus / Regulation of BACH1 activity / Translesion synthesis by REV1 / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Translesion synthesis by POLK / MAP3K8 (TPL2)-dependent MAPK1/3 activation / TICAM1, RIP1-mediated IKK complex recruitment / Downregulation of TGF-beta receptor signaling / 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 / neuron projection morphogenesis / 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) / regulation of mitochondrial membrane potential / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Autodegradation of Cdh1 by Cdh1:APC/C / TNFR1-induced NF-kappa-B signaling pathway / APC/C:Cdc20 mediated degradation of Securin / positive regulation of protein ubiquitination / 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 / AUF1 (hnRNP D0) binds and destabilizes mRNA / TNFR2 non-canonical NF-kB pathway / activated TAK1 mediates p38 MAPK activation / Assembly of the pre-replicative complex / Vpu mediated degradation of CD4 / NOTCH3 Activation and Transmission of Signal to the Nucleus / Negative regulators of DDX58/IFIH1 signaling / Deactivation of the beta-catenin transactivating complex / Degradation of DVL / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Regulation of signaling by CBL Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.38 Å | ||||||
Authors | Middleton, A.J. / Day, C.L. / Wright, J.D. | ||||||
Citation | Journal: To be published Title: Discovery of new non-covalent ubiquitin binding sites on UbcH5 Authors: Middleton, A.J. / Wright, J.D. / Day, C.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ulk.cif.gz | 123.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ulk.ent.gz | 96.9 KB | Display | PDB format |
PDBx/mmJSON format | 5ulk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5ulk_validation.pdf.gz | 446.4 KB | Display | wwPDB validaton report |
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Full document | 5ulk_full_validation.pdf.gz | 448.6 KB | Display | |
Data in XML | 5ulk_validation.xml.gz | 11.6 KB | Display | |
Data in CIF | 5ulk_validation.cif.gz | 14.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ul/5ulk ftp://data.pdbj.org/pub/pdb/validation_reports/ul/5ulk | 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
#1: Protein | Mass: 17144.525 Da / Num. of mol.: 1 / Mutation: C21S, C85K, C107S, C111S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: UBE2D2, PUBC1, UBC4, UBC5B, UBCH4, UBCH5B / Cell line (production host): BL21 / Production host: Escherichia coli (E. coli) References: UniProt: P62837, E2 ubiquitin-conjugating enzyme, (E3-independent) E2 ubiquitin-conjugating enzyme |
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#2: Protein | Mass: 8576.831 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: UBB / Cell line (production host): BL21 / Production host: Escherichia coli (E. coli) / References: UniProt: P0CG47 |
#3: Protein | Mass: 10300.740 Da / Num. of mol.: 1 / Fragment: residues 292-340 / Mutation: M313A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RNF165 / Cell line (production host): BL21 / Production host: Escherichia coli (E. coli) References: UniProt: Q6ZSG1, RING-type E3 ubiquitin transferase |
#4: Chemical |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.15 Å3/Da / Density % sol: 42.76 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / Details: 200 mM ammonium nitrate, 20% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.979 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 11, 2014 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.381→60.779 Å / Num. all: 12481 / Num. obs: 12481 / % possible obs: 97.5 % / Redundancy: 6.9 % / Rpim(I) all: 0.028 / Rrim(I) all: 0.074 / Rsym value: 0.068 / Net I/av σ(I): 7.1 / Net I/σ(I): 13.3 / Num. measured all: 85553 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.38→60.78 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.941 / SU B: 39.609 / SU ML: 0.368 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.416 / ESU R Free: 0.279 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 137.93 Å2 / Biso mean: 83.06 Å2 / Biso min: 30 Å2
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Refinement step | Cycle: final / Resolution: 2.38→60.78 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.381→2.443 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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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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